James Rosindell

James Rosindell
Imperial College London | Imperial · Division of Cell and Molecular Biology

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70
Publications
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2,686
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Publications

Publications (70)
Preprint
A bstract Phylogenetic metrics are essential tools in ecology, evolution and conservation, and Phylogenetic Diversity (PD) is one of the most prominent measures of biodiversity. PD is based on the idea that biological features accumulate along the branches of phylogenetic trees, and that these features are of biological importance. We argue that PD...
Preprint
Full-text available
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...
Preprint
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 div...
Article
Full-text available
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 me...
Article
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. Our approach is to automate data processing, synthesise dat...
Preprint
Ecological and economic systems both comprise of autonomous adaptive agents. It is thus possible that similar mechanisms determine the organization of both these complex systems. Indeed several economic theories have already been successfully applied in an ecological context. Here we show that 'efficient market theory' in economics, where future ea...
Article
Full-text available
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 f...
Article
Full-text available
Some lineages radiate spectacularly when colonizing a region, but others do not. Large radiations are often attributed to species’ adaptation into niches, or to other drivers, such as biogeography including dispersal ability and spatial structure of the landscape. Here we aim to disentangle the factors determining radiation size, by modeling simpli...
Preprint
The structure of communities is influenced by many processes, both ecological and evolutionary, but these processes are hard to distinguish from available data. The aim of this work is to distinguish the ecological footprint of selection from that of neutral processes that are invariant to species identity. To do this, we build on existing theory t...
Chapter
Full-text available
The species–area relationship (SAR) describes a range of related phenomena that are fundamental to the study of biogeography, macroecology and community ecology. While the subject of ongoing debate for a century, surprisingly, no previous book has focused specifically on the SAR. This volume addresses this shortfall by providing a synthesis of the...
Chapter
The species–area relationship (SAR) describes a range of related phenomena that are fundamental to the study of biogeography, macroecology and community ecology. While the subject of ongoing debate for a century, surprisingly, no previous book has focused specifically on the SAR. This volume addresses this shortfall by providing a synthesis of the...
Preprint
Full-text available
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 Diversity's Post-2020 Global Biodiversity Framework (GBF) presents us with the opportunity to preserve Nature's Contributions to People (NCPs) for current and future generations through conse...
Preprint
Full-text available
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. Our approach is to automate data processing, synthesise dat...
Article
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 fo...
Article
Full-text available
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 prioritis...
Article
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. Her...
Preprint
Full-text available
Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Reconciling the relative importance of these processes is hindered by current theory, which tends to focus on a single spatial, temporal or taxonomic scale. We introduce a mechanistic model of community assembly, rooted in classic island biogeog...
Article
Full-text available
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 dynami...
Article
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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 publi...
Article
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 dis...
Article
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-th...
Article
Full-text available
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 using airborne imaging spectroscopy to estimate canopy β‐diversity for an extensive region of a Bornean rainforest and challenge these data with models...
Preprint
Full-text available
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...
Article
Full-text available
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 recognized as important. To shed light on the factors affecting the...
Preprint
Full-text available
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-th...
Article
Full-text available
Aim The great variation in range sizes among species has fascinated ecologists for decades. Reef‐associated fish species live in highly spatially structured habitats and adopt a wide range of dispersal strategies. We consequently expect species with greater dispersal ability to occupy larger ranges. However, empirical evidence for such a positive r...
Chapter
The usual approach to organising human knowledge in any field is to invent an intuitive, often hierarchical system of classification. Perhaps uniquely to natural history, humans did not so much invent such a system as discover one: the tree of life. This now iconic object has utility, not only in biodiversity research but also in conservation and s...
Preprint
Full-text available
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...
Article
Full-text available
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 habi...
Article
Full-text available
The historic richness ofmost 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 rate...
Article
Full-text available
A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage-based models, whereas ecology often focuses on individual organis...
Article
The combination of rapid biodiversity loss and limited funds available for conservation represents a major global concern. While there are many approaches for conservation prioritization, few are framed as financial optimization problems. We use recently published avian data to conduct a global analysis of the financial resources required to conser...
Article
Full-text available
The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, ‘An equilibrium theory of insular zoogeography’, was a recent milestone for this theme. Since 1963, island systems have provided new insights into the fo...
Conference Paper
Background/Question/Methods Understanding the mechanisms that maintain biodiversity is a core issue in ecology. Classic ecological theory asserts that stable coexistence requires ecological differences among species whilst neutral theory assumes that individual organisms are ecologically equivalent and explains species coexistence and composition...
Article
The scale-dependent species abundance distribution (SAD) is fundamental in ecology, but few spatially explicit models of this pattern have thus far been studied. Here we show spatially explicit neutral model predictions for SADs over a wide range of spatial scales, which appear to match empirical patterns qualitatively. We find that the assumption...
Article
MacArthur and Wilson's theory of island biogeography was revolutionary, and also inspired the more recent unified neutral theory of biodiversity and biogeography. The unified neutral theory has the potential to make predictions about island biogeography that are not well studied. Here we aim to unify the two theories by using an ecological neutral...
Data
Full-text available
Technical details of the algorithms used in OneZoom. (PDF)
Data
A self-contained version of the OneZoom software as a single html file. This file contains an embedded mammal tree using data from [8] and incorporates IUCN red list metadata and common names [13]. For further information we refer readers to the website www.onezoom.org, launched on the day of publication. Phylogeneticists are encouraged to download...
Data
A self-contained version of the OneZoom software as a single html file (as Software S1). This file contains an embedded 408,135-tip phylogeny of small-subunit RNAs using data from SILVA [9] and is zipped to allow easy download. (ZIP)
Article
Full-text available
An intuitively simple zooming interface offers a visually appealing way to explore very large phylogenetic trees with metadata.
Article
Ricklefs and Renner (Reports, 27 January 2012, p. 464) showed correlations of species richness and individual abundance within families across continents and claimed that neutral theory predicts no such correlation. However, they did not substantiate this claim quantitatively with a neutral model. Here, we show that neutral theory can be consistent...
Article
Full-text available
One of the most striking patterns observed among animals is that smaller-bodied taxa are generally much more diverse than larger-bodied taxa. This observation seems to be explained by the mere fact that smaller-bodied taxa tend to have an older evolutionary origin and have therefore had more time to diversify. A few studies, based on the prevailing...
Article
Ecological neutral theory has elicited strong opinions in recent years. Here, we review these opinions and strip away some unfortunate problems with semantics to reveal three major underlying questions. Only one of these relates to neutral theory and the importance of ecological drift, whereas the others involve the link between pattern and process...
Article
Full-text available
Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species' differences and the neutral theory of biodiversity that claims that much of the diversit...
Article
Full-text available
Aims Neutral theory consists of a suite of models that assume ecological equivalence among individual organisms. They have been most commonly applied to tropical forest tree communities either as null models or as approximations. Neutral models typically only include reproductive adults; therefore, fitting to empirical tree community data requires...
Article
Full-text available
Phylogenetic trees show a remarkable slowdown in the increase of number of lineages towards the present, a phenomenon which cannot be explained by the standard birth–death model of diversification with constant speciation and extinction rates. The birth–death model instead predicts a constant or accelerating increase in the number of lineages, whic...
Article
A decade has now passed since Hubbell published The Unified Neutral Theory of Biodiversity and Biogeography. Neutral theory highlights the importance of dispersal limitation, speciation and ecological drift in the natural world and provides quantitative null models for assessing the role of adaptation and natural selection. Significant advances hav...
Article
Ecology letters (2011) 14: 552–560 Islands acquire species through immigration and speciation. Models of island biogeography should capture both processes; however quantitative island biogeography theory has either neglected speciation or treated it unrealistically. We introduce a model where the dominance of immigration on small and near islands g...
Article
Full-text available
On 9 March, over 150 biologists gathered in London for the Centre for Ecology and Evolution spring symposium, 'Integrating Ecology into Macroevolutionary Research'. The event brought together researchers from London-based institutions alongside others from across the UK, Europe and North America for a day of talks. The meeting highlighted methodolo...
Article
Full-text available
The unified neutral theory of biodiversity and biogeography is increasingly accepted as an informative null model of community composition and dynamics. It has successfully produced macro-ecological patterns such as species-area relationships and species abundance distributions. However, the models employed make many unrealistic auxiliary assumptio...
Conference Paper
Background/Question/Methods Results/Conclusions We present a generalization of Hubbell's Unified Neutral Theory of Biodiversity and Biogeography. The original neutral model has demonstrated its ability to reproduce many widespread ecological patterns such as locally sampled species abundance distributions and species area curves, but it has mostl...
Article
There has recently been increasing interest in neutral models of biodiversity and their ability to reproduce the patterns observed in nature, such as species abundance distributions. Here we investigate the ability of a neutral model to predict phenomena observed in single-population time series, a study complementary to most existing work that con...
Article
Ecology Letters (2010) 13: 716–727 Understanding the maintenance and origin of biodiversity is a formidable task, yet many ubiquitous ecological patterns are predicted by a surprisingly simple and widely studied neutral model that ignores functional differences between species. However, this model assumes that new species arise instantaneously as s...
Article
Ecological neutral theory, like its population genetics counterpart, has been most useful as a null hypothesis. For example, neutral theory predicts that if a single adult, or a group of \(n\) adults, has descendants \(t\) generations later, with probability nearly \(\exp\left({-k}\right)\) they will have \(>kt\) descendants then if \(n \ll t\) (Le...
Article
The distribution of species abundances within an ecological community provides a window into ecological processes and has important applications in conservation biology as an indicator of disturbance. Previous work indicates that species abundance distributions might be independent of the scales at which they are measured which has implications for...
Article
We simulate species-area curves (SACs) using a spatially explicit neutral model. These display three distinct phases with the central phase being well approximated by a "power law" where species richness (S) is related to area (A) by S = cA(z). If seeds are normally distributed in space about their parent, the power law phase of the SAC is unrealis...
Article
Neutral models in ecology have attracted much attention in recent literature. They can provide considerable insight into the roles of non-species-specific factors (e.g. stochasticity, dispersal, speciation) on community dynamics but often require intensive simulations, particularly in spatial settings. Here, we clearly explain existing techniques f...
Article
We use recently developed technical methods to study species-area relationships from a spatially explicit extension of Hubbell's neutral model on an infinite landscape. Our model includes variable dispersal distances and exhibits qualitatively different behaviour from the cases of nearest-neighbour dispersal and finite periodic landscapes that have...

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