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Boettiger C.,Center for Population Biology | Hastings A.,University of California at Davis
Journal of the Royal Society Interface | Year: 2012

Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite widespread appreciation of the difficulties and uncertainty involved in such forecasts, proposed methods hardly ever characterize their expected error rates. Without the benefits of replicates, controls or hindsight, applications of these approaches must quantify how reliable different indicators are in avoiding false alarms, and how sensitive they are to missing subtle warning signs. We propose a model-based approach to quantify this trade-off between reliability and sensitivity and allow comparisons between different indicators. We show these error rates can be quite severe for common indicators even under favourable assumptions, and also illustrate how a model-based indicator can improve this performance. We demonstrate how the performance of an early warning indicator varies in different datasets, and suggest that uncertainty quantification become a more central part of early warning predictions. © 2012 The Royal Society.

Eckert A.J.,University of California at Davis | Eckert A.J.,Center for Population Biology | Liechty J.D.,University of California at Davis | Tearse B.R.,University of California at Davis | And 2 more authors.
Molecular Ecology Resources | Year: 2010

Patterns of DNA sequence polymorphisms can be used to understand the processes of demography and adaptation within natural populations. High-throughput generation of DNA sequence data has historically been the bottleneck with respect to data processing and experimental inference. Advances in marker technologies have largely solved this problem. Currently, the limiting step is computational, with most molecular population genetic software allowing a gene-by-gene analysis through a graphical user interface. An easy-to-use analysis program that allows both high-throughput processing of multiple sequence alignments along with the flexibility to simulate data under complex demographic scenarios is currently lacking. We introduce a new program, named DnaSAM, which allows high-throughput estimation of DNA sequence diversity and neutrality statistics from experimental data along with the ability to test those statistics via Monte Carlo coalescent simulations. These simulations are conducted using the ms program, which is able to incorporate several genetic parameters (e.g. recombination) and demographic scenarios (e.g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file. © 2009 Blackwell Publishing Ltd.

White E.R.,University of Victoria | White E.R.,Center for Population Biology | Myers M.C.,University of Northern Iowa | Flemming J.M.,Dalhousie University | Baum J.K.,University of Victoria
Conservation Biology | Year: 2015

Fishing pressure has increased the extinction risk of many elasmobranch (shark and ray) species. Although many countries have established no-take marine reserves, a paucity of monitoring data means it is still unclear if reserves are effectively protecting these species. We examined data collected by a small group of divers over the past 21 years at one of the world's oldest marine protected areas (MPAs), Cocos Island National Park, Costa Rica. We used mixed effects models to determine trends in relative abundance, or probability of occurrence, of 12 monitored elasmobranch species while accounting for variation among observers and from abiotic factors. Eight of 12 species declined significantly over the past 2 decades. We documented decreases in relative abundance for 6 species, including the iconic scalloped hammerhead shark (Sphyrna lewini) (-45%), whitetip reef shark (Triaenodon obesus) (-77%), mobula ray (Mobula spp.) (-78%), and manta ray (Manta birostris) (-89%), and decreases in the probability of occurrence for 2 other species. Several of these species have small home ranges and should be better protected by an MPA, which underscores the notion that declines of marine megafauna will continue unabated in MPAs unless there is adequate enforcement effort to control fishing. In addition, probability of occurrence at Cocos Island of tiger (Galeocerdo cuvier), Galapagos (Carcharhinus galapagensis), blacktip (Carcharhinus limbatus), and whale (Rhincodon typus) sharks increased significantly. The effectiveness of MPAs cannot be evaluated by examining single species because population responses can vary depending on life history traits and vulnerability to fishing pressure. © 2015 Society for Conservation Biology.

Hawlena D.,Yale University | Hawlena D.,Hebrew University of Jerusalem | Hughes K.M.,Yale University | Hughes K.M.,University of California at Davis | And 2 more authors.
Functional Ecology | Year: 2011

1.Animals can mitigate the consequences of conflicting food-web constraints (e.g. resource availability vs. predation risk) through plasticity in the expression of functional traits. Because functional trait expression in turn determines a species' impact on ecosystem functions, e.g. its trophic function, there is a growing need to develop a predictive theory that links trait plasticity to ecosystem functioning. But there is currently an incomplete empirical foundation on which to develop such theory. 2.To address this issue, we explored the link between plasticity in a suite of traits (e.g. head morphology, gut size, bite size) that determine the trophic function of a generalist grasshopper herbivore facing predation risk. We reared grasshoppers in the field under two single-forage environments where the plant resources had different physical and nutritional properties and in intermediate mixed-forage environments with or without risk of spider predation. 3.We found that in the single-forage environments, grasshoppers became more efficient at ingesting the resource they were reared on. 4.In mixed-resource environments, grasshoppers developed a phenotype that was not intermediate to the phenotypes in the two single-forage environments, regardless of predation risk. 5.We propose that the suite of phenotypic changes observed in our study represent two alternative feeding strategies that vary with the possibility of using behavioural resource selection in different environmental contexts. 6.Our results suggest that plasticity in trophic function may not emerge from a direct link between the primary traits that determine consumer consumption efficiency given the physical properties of its resources (as is customarily presumed) but rather indirectly from secondary traits that may remain latent until such time that they are drawn into play when the species faces a particular challenge. This means that fully understanding how functional traits influence a species' role in an ecosystem requires consideration of a broader suite of traits than simply those assumed to constrain resource ingestion. © 2011 The Authors. Functional Ecology © 2011 British Ecological Society.

Berg J.J.,Graduate Group in Population Biology | Berg J.J.,Center for Population Biology | Berg J.J.,University of California at Davis | Coop G.,Center for Population Biology | Coop G.,University of California at Davis
Genetics | Year: 2015

The use of genetic polymorphism data to understand the dynamics of adaptation and identify the loci that are involved has become a major pursuit of modern evolutionary genetics. In addition to the classical “hard sweep” hitchhiking model, recent research has drawn attention to the fact that the dynamics of adaptation can play out in a variety of different ways and that the specific signatures left behind in population genetic data may depend somewhat strongly on these dynamics. One particular model for which a large number of empirical examples are already known is that in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation. Here, we pursue an analytical investigation of this model, bolstered and extended via simulation study. We use coalescent theory to develop an analytical approximation for the effect of a sweep from standing variation on the genealogy at the locus of the selected allele and sites tightly linked to it. We show that the distribution of haplotypes that the selected allele is present on at the time of the environmental change can be approximated by considering recombinant haplotypes as alleles in the infinite-alleles model. We show that this approximation can be leveraged to make accurate predictions regarding patterns of genetic polymorphism following such a sweep. We then use simulations to highlight which sources of haplotypic information are likely to be most useful in distinguishing this model from neutrality, as well as from other sweep models, such as the classic hard sweep and multiple-mutation soft sweeps. We find that in general, adaptation from a unique standing variant will likely be difficult to detect on the basis of genetic polymorphism data from a single population time point alone, and when it can be detected, it will be difficult to distinguish from other varieties of selective sweeps. Samples from multiple populations and/or time points have the potential to ease this difficulty. © 2015 by the Genetics Society of America.

Hortal J.,Center for Population Biology | Hortal J.,CSIC - National Museum of Natural Sciences | Hortal J.,Federal University of Goais | Diniz-Filho J.A.F.,Federal University of Goais | And 7 more authors.
Ecology Letters | Year: 2011

Current climate and Pleistocene climatic changes are both known to be associated with geographical patterns of diversity. We assess their associations with the European Scarabaeinae dung beetles, a group with high dispersal ability and well-known adaptations to warm environments. By assessing spatial stationarity in climate variability since the last glacial maximum (LGM), we find that current scarab richness is related to the location of their limits of thermal tolerance during the LGM. These limits mark a strong change in their current species richness-environment relationships. Furthermore, northern scarab assemblages are nested and composed of a phylogenetically clustered subset of large-range sized generalist species, whereas southern ones are diverse and variable in composition. Our results show that species responses to current climate are limited by the evolution of assemblages that occupied relatively climatically stable areas during the Pleistocene, and by post-glacial dispersal in those that were strongly affected by glaciations. © 2011 Blackwell Publishing Ltd/CNRS.

Bezemer T.M.,Netherlands Institute of Ecology | Bezemer T.M.,Center for Population Biology | Jones T.H.,Center for Population Biology | Jones T.H.,University of Cardiff
Ecological Research | Year: 2012

We studied short- and long-term growth responses of Poa annua L. (Gramineae) at ambient and elevated (ambient +200 μmol mol -1) atmospheric CO 2. In experiment 1 we compared plant growth during the early, vegetative and final, reproductive growth phases. Plant growth in elevated CO 2 was significantly enhanced during the early phase, but this was reversed in the reproductive phase. Seed mass and percentage germination were significantly reduced in elevated CO 2. Experiment 2 tested for the impact of transgenerational and nutrient effects on the response of Poa annua to elevated CO 2. Plants were grown at ambient and elevated CO 2 for one or two consecutive generations at three soil nutrient levels. Leaf photosynthesis was significantly higher at elevated CO 2, but was also affected by both soil nutrient status and plant generation. Plants grown at elevated CO 2 and under conditions of low nutrient availability showed photosynthetic acclimation after 12 weeks of growth but not after 6 weeks. First-generation growth remained unaffected by elevated CO 2, while second-generation plants produced significantly more tillers and flowers when grown in elevated CO 2 compared to ambient conditions. This effect was strongest at low nutrient availability. Average above- and belowground biomass after 12 weeks of growth was enhanced in elevated CO 2 during both generations, but more so during plant generation 2. This study demonstrates the importance of temporal/maternal effects in plant responses to elevated CO 2. © 2012 The Author(s).

Boakes E.H.,Center for Population Biology | Mace G.M.,Center for Population Biology | McGowan P.J.K.,Northumbria University | Fuller R.A.,University of Queensland
Proceedings of the Royal Society B: Biological Sciences | Year: 2010

Habitat clearance remains the major cause of biodiversity loss, with consequences for ecosystem services and for people. In response to this, many global conservation schemes direct funds to regions with high rates of recent habitat destruction, though some also emphasize the conservation of remaining large tracts of intact habitat. If the pattern of habitat clearance is highly contagious, the latter approach will help prevent destructive processes gaining a foothold in areas of contiguous intact habitat. Here, we test the strength of spatial contagion in the pattern of habitat clearance. Using a global dataset of land-cover change at 50 × 50 km resolution, we discover that intact habitat areas in grid cells are refractory to clearance only when all neighbouring cells are also intact. The likelihood of loss increases dramatically as soon as habitat is cleared in just one neighbouring cell, and remains high thereafter. This effect is consistent for forests and grassland, across biogeographic realms and over centuries, constituting a coherent global pattern. Our results show that landscapes become vulnerable to wholesale clearance as soon as threatening processes begin to penetrate, so actions to prevent any incursions into large, intact blocks of natural habitat are key to their long-term persistence. © 2009 The Royal Society.

Milcu A.,Center for Population Biology | Manning P.,Center for Population Biology | Manning P.,Northumbria University
Oikos | Year: 2011

There is increasing evidence that litter decomposition is faster beneath the plant species it was derived from, an effect called home-field advantage (HFA). Adaptation of soil biota to decompose the litter that they encounter most often has been proposed as the main mechanism to explain HFA. However, there is little direct evidence supporting this assumption and the contribution of different decomposer groups to the HFA is unknown. Furthermore, the large observed variation in the strength of the HFA may be linked to litter quality, with increasing HFA for more recalcitrant substrates. To test the relationship between HFA, litter quality and soil fauna, we performed a field litter bag experiment, with different mesh sizes and reciprocal litter transplants, across a successional gradient varying in litter quality inputs and soil fauna composition. The results show that the HFA was stronger in sites dominated by more recalcitrant litter inputs and provide evidence that a range of soil fauna size classes contribute to this effect. Our findings help explain the lack of HFA in ecosystems with simple litters and in studies where experimental artefacts (e.g. fine mesh sizes) affect the contribution from certain classes of soil fauna. © 2011 The Authors. Oikos © 2011 Nordic Society Oikos.

Harris D.J.,Center for Population Biology
Methods in Ecology and Evolution | Year: 2015

Species distribution models (SDMs) represent important analytical and predictive tools for ecologists. Until now, these models have either assumed (i) that species' occurrence probabilities are uncorrelated or (ii) that species respond linearly to preselected environmental variables. These two assumptions currently prevent ecologists from modelling assemblages with realistic co-occurrence and species richness properties. This paper introduces a stochastic feedforward neural network, called 'mistnet', which makes neither assumption. Thus, unlike most SDMs, mistnet can account for non-independent co-occurrence patterns driven by unobserved environmental heterogeneity. And unlike several recently proposed joint SDMs, the model can also learn nonlinear functions relating species' occurrence probabilities to environmental predictors. Mistnet makes more accurate predictions about the North American bird communities found along Breeding Bird Survey transects than several alternative methods tested. In particular, typical assemblages held out of sample for validation were each tens of thousands of times more likely under the mistnet model than under independent combinations of single-species predictions. Apart from improved accuracy, mistnet shows two other important benefits for ecological research and management. First: by analysing co-occurrence data, mistnet can identify unmeasured - and perhaps unanticipated - environmental variables that drive species turnover. For example, the model identified a strong grassland/forest gradient, even though only temperature and precipitation were given as model inputs. Second: mistnet is able to take advantage of outside information to guide its predictions towards more realistic assemblages. For example, mistnet automatically adjusts its expectations to include more forest-associated species in response to a stray observation of a forest-dwelling warbler. © 2015 British Ecological Society.

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