Publications
60 results found
Vila JCC, Jones ML, Patel M, et 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.
Alzate A, Janzen T, Bonte D, et 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
<jats:title>Abstract</jats:title><jats:sec><jats:title>Aim</jats:title><jats:p>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 relationship between dispersal and range size remains scarce. Here, we unveil the role of dispersal on the range size distribution of reef‐associated fishes using empirical data and a novel spatially explicit model.</jats:p></jats:sec><jats:sec><jats:title>Location</jats:title><jats:p>Tropical Eastern Pacific.</jats:p></jats:sec><jats:sec><jats:title>Major taxa studied</jats:title><jats:p>Reef‐associated fishes.</jats:p></jats:sec><jats:sec><jats:title>Time period</jats:title><jats:p>Underlying records are from the 20th and 21st centuries.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We estimated range size distributions for all reef‐associated fishes separated into six guilds, each with different dispersal abilities. We used a one‐dimensional spatially explicit neutral model, which simulates the distribution of species along a linear and contiguous coastline, to explore the effect of dispersal, speciation and sampling on the distribution of range sizes. Our model incorporates biologically important long‐distance dispersal events with a fat‐tailed dispersal kernel and also adopts a more realistic gradual “protracted” speciation process than originally used in neutral theory. We fitted the model to the empirical data using an approximate Bayesian computation approach, with a sequential Monte Carlo algorithm.</jats:p></jats:sec>
Alzate A, Janzen T, Bonte D, et 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
Banks-Leite C, Fletcher R, Didham R, et 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.
Chisholm RA, Lim F, Yeoh YS, et 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.
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.
Rosindell J, Harmon LJ, Etienne RS, 2015, Unifying ecology and macroevolution with individual-based theory, Ecology Letters, Vol: 18, Pages: 472-482, ISSN: 1461-023X
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 organisms. Here, we develop a new parsimonious individual‐based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology.
Nunes LA, Turvey ST, Rosindell J, 2015, The price of conserving avian phylogenetic diversity: a global prioritization approach, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 370, ISSN: 0962-8436
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- Citations: 18
Warren BH, Simberloff D, Ricklefs RE, et al., 2015, Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson, ECOLOGY LETTERS, Vol: 18, Pages: 200-217, ISSN: 1461-023X
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- Citations: 293
Rosindell J, Cornell SJ, 2013, Universal scaling of species-abundance distributions across multiple scales, OIKOS, Vol: 122, Pages: 1101-1111, ISSN: 0030-1299
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- Citations: 26
Rosindell J, Harmon LJ, 2013, A unified model of species immigration, extinction and abundance on islands, JOURNAL OF BIOGEOGRAPHY, Vol: 40, Pages: 1107-1118, ISSN: 0305-0270
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- Citations: 35
Rosindell J, Harmon LJ, 2012, OneZoom: A Fractal Explorer for the Tree of Life, PLOS BIOLOGY, Vol: 10, ISSN: 1544-9173
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- Citations: 48
Wennekes PL, Rosindell J, Etienne RS, 2012, The Neutral-Niche Debate: A Philosophical Perspective, ACTA BIOTHEORETICA, Vol: 60, Pages: 257-271, ISSN: 0001-5342
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- Citations: 55
Etienne RS, Rosindell J, 2012, Comment on "Global Correlations in Tropical Tree Species Richness and Abundance Reject Neutrality", SCIENCE, Vol: 336, ISSN: 0036-8075
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- Citations: 2
Etienne RS, de Visser SN, Janzen T, et al., 2012, Can clade age alone explain the relationship between body size and diversity?, INTERFACE FOCUS, Vol: 2, Pages: 170-179, ISSN: 2042-8898
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- Citations: 17
Rosindell J, Hubbell SP, He F, et al., 2012, The case for ecological neutral theory, TRENDS IN ECOLOGY & EVOLUTION, Vol: 27, Pages: 203-208, ISSN: 0169-5347
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- Citations: 202
Desjardins-Proulx P, Rosindell JL, Poisot T, et al., 2012, A simple model to study phylogeographies and speciation patterns in space
In this working paper, we present a simple theoretical framework based onnetwork theory to study how speciation, the process by which new speciesappear, shapes spatial patterns of diversity. We show that this framework canbe expanded to account for different types of networks and interactions, andincorporates different modes of speciation.
Etienne RS, Rosindell J, 2012, Prolonging the Past Counteracts the Pull of the Present: Protracted Speciation Can Explain Observed Slowdowns in Diversification, SYSTEMATIC BIOLOGY, Vol: 61, Pages: 204-213, ISSN: 1063-5157
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- Citations: 131
Rosindell J, Jansen PA, Etienne RS, 2012, Age structure in neutral theory resolves inconsistencies related to reproductive-size threshold, Journal of Plant Ecology, Vol: 5, Pages: 64-71
AimsNeutral 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 defining a reproductive-size threshold, which for trees is usually set arbitrarily to a diameter at breast height (DBH) of 100 mm. The inevitable exclusion of some reproductive adults and inclusion of some saplings cause a non-random sampling bias in neutral model fits. Here, we investigate this problem and resolve it by introducing simple age structure into a neutral model.MethodsWe compared the performance and sensitivity of DBH threshold of three variants of a spatially explicit neutral model: the traditional model, a model incorporating random sampling and a model with two distinct age classes—reproductive adults and saplings. In the age-structured model, saplings are offspring from adults that disperse according to a Gaussian dispersal kernel around the adults. The only extra parameter is the ratio of adults to saplings, which is not a free parameter but directly measurable. We used species–area relation- ships (SARs) to explore the predicted effect of saplings on the species richness at different scales in our model. We then evaluated the three model variations to find the parameters required to maintain the ob- served level of species richness in the 50-ha plot on Barro Colorado Island (BCI). We repeated our analysis filtering the data at differentINTRODUCTIONNeutral theory refers to a collection of neutral models each as- suming ecological equivalence between individuals (Bellminimum tree-size thresholds in order to find the effect this threshold has on our results. Lastly, we used empirical species–individual rela- tionships (SIRs) to test the pre-existing hypothesis that environmental filtering i
McInnes L, Baker WJ, Barraclough TG, et al., 2011, Integrating ecology into macroevolutionary research, BIOLOGY LETTERS, Vol: 7, Pages: 644-646, ISSN: 1744-9561
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- Citations: 10
Rosindell J, Hubbell SP, Etienne RS, 2011, The <i>Unified Neutral Theory of Biodiversity and Biogeography</i> at Age Ten, TRENDS IN ECOLOGY & EVOLUTION, Vol: 26, Pages: 340-348, ISSN: 0169-5347
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- Citations: 422
Rosindell J, Phillimore AB, 2011, A unified model of island biogeography sheds light on the zone of radiation, ECOLOGY LETTERS, Vol: 14, Pages: 552-560, ISSN: 1461-023X
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- Citations: 156
Etienne RS, Rosindell J, 2011, The Spatial Limitations of Current Neutral Models of Biodiversity, PLOS ONE, Vol: 6, ISSN: 1932-6203
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- Citations: 30
Keil P, Herben T, Rosindell J, et al., 2010, Predictions of Taylor's power law, density dependence and pink noise from a neutrally modeled time series, JOURNAL OF THEORETICAL BIOLOGY, Vol: 265, Pages: 78-86, ISSN: 0022-5193
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- Citations: 16
Kurka P, Sizling AL, Rosindell J, 2010, Analytical evidence for scale-invariance in the shape of species abundance distributions, MATHEMATICAL BIOSCIENCES, Vol: 223, Pages: 151-159, ISSN: 0025-5564
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- Citations: 16
Rosindell J, Cornell SJ, Hubbell SP, et al., 2010, Protracted speciation revitalizes the neutral theory of biodiversity, Ecology Letters, Pages: 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 singletons and consequently makes unrealistic predictions about species lifetimes, speciation rates and number of rare species. Here, we resolve these anomalies – without compromising any of the original model’s existing achievements and retaining computational and analytical tractability – by modelling speciation as a gradual, protracted, process rather than an instantaneous event. Our model also makes new predictions about the diversity of ÔincipientÕ species and rare species in the metacommunity. We show that it is both necessary and straightforward to incorporate protracted speciation in future studies of neutral models, and argue that non- neutral models should also model speciation as a gradual process rather than an instantaneous one.
Leigh EG, Rosindell J, Etienne RS, 2010, Unified neutral theory of biodiversity and biogeography, Scholarpedia, Vol: 5
Rosindell J, Cornell SJ, 2009, Species-area curves, neutral models, and long-distance dispersal, ECOLOGY, Vol: 90, Pages: 1743-1750, ISSN: 0012-9658
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- Citations: 76
Rosindell J, Wong Y, Etienne RS, 2008, A coalescence approach to spatial neutral ecology, Ecological Informatics, Vol: 3, Pages: 259-271
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 for modelling spatially explicit neutral processes in ecology using coalescence. Furthermore, we present several novel extensions to these methods including procedures for dealing with system boundaries which enable improved investigation of the effects of dispersal. We also present a semi-analytical algorithm that calculates the expected species richness in a sample, for any speciation rate. By eliminating the effect of stochasticity in the speciation process, we reduce the variance in estimates of species richness. Our benchmarks show that the combination of existing coalescence theory and our extensions produces higher quality results in vastly shorter time scales than previously possible: years of simulation time are reduced to minutes. As an example application, we find parameters for a spatially explicit neutral model to approximate the species richness of a tropical forest dataset.
Rosindell J, Cornell SJ, 2007, Species-area relationships from a spatially explicit neutral model in an infinite landscape, ECOLOGY LETTERS, Vol: 10, Pages: 586-595, ISSN: 1461-023X
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- Citations: 122
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