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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.

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.

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.

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.

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