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bioRxiv2016

Measurement uncertainty matters: ecological management using POMDPs

Over the past 30 years, researchers have used various approximations to address the impact of measurement uncertainty on optimal management policy.This literature has consistently suggested the counter-intuitive proposition that increasing harvest levels in the presence of measurement error is often optimal. Here, we use state-of-the art algorithms for Partially Observed Markov Decision Processes (POMDPs) to provide the first complete solution to this classic problem, and demonstrate that contrary to previous work, the resulting policy is usually more conservative than without measurement error. We demonstrate that management which underestimates the measurement error results in both low economic returns and high frequency of stock collapses, while overestimating the role of measurement error can still result in nearly-optimal economic performance while avoiding stock collapse.

Ecology↗

bioRxiv2017

Using Mobile Phones As Acoustic Sensors For High-Throughput Surveillance Of Mosquito Ecology

The direct monitoring of mosquito populations in field settings is a crucial input for shaping appropriate and timely control measures for mosquito-borne diseases. Here, we demonstrate that commercially available mobile phones are a powerful tool for acoustically mapping mosquito species distributions worldwide. We show that even low-cost mobile phones with very basic functionality are capable of sensitively acquiring acoustic data on species-specific mosquito wingbeat sounds, while simultaneously recording the time and location of the human-mosquito encounter. We survey a wide range of medically important mosquito species, to quantitatively demonstrate how acoustic recordings supported by spatio-temporal metadata enable rapid, non-invasive species identification. As proof-of-concept, we carry out field demonstrations where minimally-trained users map local mosquitoes using their personal phones. Thus, we establish a new paradigm for mosquito surveillance that takes advantage of the existing global mobile network infrastructure, to enable continuous and large-scale data acquisition in resource-constrained areas.

ecology↗

bioRxiv2017

BipartGraph: An interactive application to plotbipartite ecological networks

Interactions between two different guilds of entities are pervasive in biology. They may happen at molecular level, like in a diseasome, or amongst individuals linked by biotic relationships, such as mutualism or parasitism. These sets of interactions are complex bipartite networks. Visualization is a powerful tool to explore and analyse them but the most common plots, the bipartite graph and the interaction matrix, become rather confusing when working with real biological networks. We have developed two new types of visualization that exploit the structural properties of these networks to improve readability. A technique called k-core decomposition identifies groups of nodes that share connectivity properties. With the results of this analysis it is possible to build a plot based on information reduction (Polar Plot) and another which takes the groups as elementary blocks for spatial distribution (Ziggurat plot). We describe the applications of both plots and the software to create them.

ecology↗

bioRxiv2017

The geometry of the distance-decay of similarity in ecological communities

Understanding beta-diversity has strong implications for evaluating the extent of biodiversity and formulating effective conservation policy. Here, we show that the distance-decay relationship, an important measure of beta-diversity, follows a universal form which we call the piecewise quadratic model. To derive the piecewise quadratic model, we develop a new conceptual framework which is based on geometric probability and several key insights about the roles of study design (e.g., plot dimensions and spatial distributions). We fit the piecewise quadratic model to six empirical distance-decay relationships, spanning a range of taxa and spatial scales, including surveys of tropical vegetation, mammals, and amphibians. We find that the model predicts the functional form of the relationships extremely well, with coefficients of determination in excess of 0.95. Moreover, the model predicts a phase transition at distance scales where sample plots are overlapping, which we confirm empirically. Our framework and model provide a fundamental, quantitative link between distance-decay relationships and the shapes of ranges of taxa.

ecology↗

bioRxiv2017

Coral reef carbonate budgets and ecological drivers in the naturally high temperature and high alkalinity environment of the Red Sea

The coral structural framework is crucial for maintaining reef ecosystem function and services. In the central Red Sea, a naturally high alkalinity is beneficial to reef growth, but rising water temperatures impair the calcification capacity of reef-building organisms. However, it is currently unknown how beneficial and detrimental factors affect the balance between calcification and erosion, and thereby the overall growth of the reef framework. To provide insight into present-day carbonate budgets and reef growth dynamics in the central Red Sea, we measured in situ net-accretion and net-erosion rates (Gnet) by deployment of limestone blocks and estimated census-based carbonate budgets (Gbudget) in four reef sites along a cross-shelf gradient (25 km). We assessed abiotic variables (i.e., temperature, inorganic nutrients, and carbonate system variables) and biotic drivers (i.e., calcifier and bioeroder abundances). On average, total alkalinity AT (2346 - 2431 mol kg-1), aragonite saturation state (4.5 - 5.2 {Omega}a), and pCO2 (283 -315 atm) were close to estimates of pre-industrial global ocean surface waters. Despite these calcification-favorable carbonate system conditions, Gnet and Gbudget encompassed positive (offshore) and negative net-production (midshore-lagoon and exposed nearshore site) estimates. Notably, Gbudget maxima were lower compared to reef growth from pristine Indian Ocean sites. Yet, a comparison with historical data from the northern Red Sea suggests that overall reef growth in the Red Sea has likely remained similar since 1995. When assessing sites across the shelf gradient, AT correlated well with reef growth rates ({rho} = 0.89), while temperature was a weaker, negative correlate ({rho} = -0.71). Further, AT explained about 65 % of Gbudget in a best fitting distance-based linear model. Interestingly, parrotfish abundances added up to 82% of explained variation, further substantiating recent studies highlighting the importance of parrotfish to reef ecosystem function. Our study provides a baseline that will be particularly useful in assessing future trajectories of reef growth capacities in the Red Sea under continuous ocean warming and acidification.

ecology↗

bioRxiv2018

From the cage to the wild: Introductions of Psittaciformes to Puerto Rico with emphasis on the invasive ecology of the white-winged parakeet

In this study, we assessed invasions of Psittaciformes in Puerto Rico. We reviewed the literature, public databases, citizen science records, and performed in situ population surveys across the island to determine the historical and current status and distribution of psittacine species. We used count data from Ebird to determine population trends. For species whose populations were increasing, we modelled their potential distribution using niche modeling techniques. Focusing on the white-winged parakeet (Brotogeris versicolurus), which was considered the most successful psittacine species by the year 2000, we evaluated the population size, calculated growth rates and estimated the breeding proportion in two populations by performing roost counts for four consecutive years. We found a total of 46 Psittaciformes present in Puerto Rico, of which 26% are only present as pets, at least 29 species have been reported in the wild, and of those, there is evidence that at least 12 species are breeding. Our results indicate that most introduced species which have been detected as established still persist, although mostly in localized areas and small populations. Clear evidence of invasiveness was found for B. versicolurus and Myiopsitta monachus, which have greatly expanded their range. Moreover, Psittacara erythrogenys and Eupsittacula canicularis also showed population increase. The niche models predicted suitable areas for the four species, and also indicate the potential for range expansion. Population estimates of the white-winged parakeet during the study period showed a steady increase, and exhibited exponential growth, with geometric mean population growth rates of 1.25 per year. Currently growth rate of the white-winged parakeet does not appear to be limited by any predator, resources or nest availability, and we expect them to continue increasing and expanding their range. We discuss the factors leading to invasion success, assess the potential impacts, and we discuss possible management strategies and research prospects.

ecology↗

bioRxiv2018

The ecology of the Drosophila-yeast mutualism in wineries

The fruit fly, Drosophila melanogaster, is preferentially found on fermenting fruits. The yeasts that dominate the microbial communities of these substrates are the primary food source for developing D. melanogaster larvae, and adult flies manifest a strong olfactory system-mediated attraction for the volatile compounds produced by these yeasts during fermentation. Although most work on this interaction has focused on the standard laboratory yeast Saccharomyces cerevisiae, a wide variety of other yeasts naturally ferment fallen fruit. Here we address the open question of whether D. melanogaster preferentially associates with distinct yeasts in different, closely-related environments. We characterized the spatial and temporal dynamics of Drosophila-associated fungi in Northern California wineries that use organic grapes and natural fermentation using high-throughput, short-amplicon sequencing. We found that there is nonrandom structure in the fungal communities that are vectored by flies both between and within vineyards. Within wineries, the fungal communities associated with flies in cellars, fermentation tanks, and pomace piles are distinguished by varying abundances of a small number of yeast species. To investigate the origins of this structure, we assayed Drosophila attraction to, oviposition on, larval development in, and longevity when consuming the yeasts that distinguish vineyard microhabitats from each other. We found that wild fly lines did not respond differentially to the yeast species that distinguish winery habitats in habitat specific manner. Instead, this subset of yeast shares traits that make them attractive to and ensure their close association with Drosophila.

ecology↗

bioRxiv2018

Mathematical and ecological traits of above and below ground biomass production of beech (Fagus silvatica L.) trees growing in pure even-aged stands in north-east France

Tree biomass and biomass increment equations were specially developed in 1996-1997 to study the ecophysiological functioning of an experimental European beech stand, aged about 30 year-old, in the Hesse forest (NE France). In order to extend such a study to beech stands of different age classes, it was necessary to build biomass and biomass increment equations that could be used for any age; we call them generalized biomass equations.\n\nTo build such generalized equations, trees were sampled in different forest plots covering the whole age range. Moreover, in each plot, several trees were chosen to represent the different crown classes (from dominant to suppressed). Sampled trees were felled down and the root system excavated for a sub-sample of trees, for biomass analysis by separating the main compartments of the above and belowground tree parts. When it was not possible to measure the total biomass of a given tree compartment (large trees), wood samples were taken in the concerned compartment. Moreover, equations were built to estimate the biomass of the missing parts of the root system and branch compartments that were likely to have suffered losses during root excavation and tree felling, respectively. Multivariate linear and non-linear models including possible random effects were tested to represent the biomass and biomass increment variations of each tree compartment and of their aggregation in the above and belowground parts of the tree.\n\nCompatible biomass and biomass increment equations for the different tree compartments and their combination in above and belowground tree parts were developed and fitted, allowing the analysis of the variations of the biomass distribution and allocation with tree age. Stem growth efficiency was also calculated and appeared dependent on tree age and tree social status.\n\nThe biomass and biomass increment equations established for beech in this study allow the estimation of the biomass and carbon stocks and fluxes (NPP) for the even-aged beech stands of the Hesse forest, whatever the age of the stand; they could also be used to analyze the effects of different silvicultural treatments on the biomass and carbon stocks and fluxes of beech stands, using the available stand growth and yield models developed for beech in France.

ecology↗

bioRxiv2018

Akaike information criteria and predictive geographical accuracy are not related in ecological niche modeling

AimEcological niche modeling (ENM) is an approach used to estimate species presence given its environmental preferences. Model complexity in ENMs has increasingly gained relevance in the last years. In particular, in Maxent algorithm is captured using the Akaike Information Criteria (AIC) based on the number of parameters and likelihoods of continuous raw outputs. However, it is not clear whether best-selected models using AIC are the models with the highest classification rate of correct presences and absences. Here, we test for a link between model complexity and accuracy of geographical predictions of Maxent models.\n\nInnovationWe created a set of virtual species and generate true geographical predictions for each one. We build a set of Maxent models using presence data from each virtual species with different regularization and features schemes. We compared AICc values for each model with the scores of standard validation metrics (e.g., Kappa, TSS) and with the number of pixels correctly predicted as presences, absences or both.\n\nMain ConclusionsWe found that binary predictions (i.e., presence-absence maps) selected as best models for AIC tend to predict incorrectly sites as presences and absences using independent datasets. We suggest that information criteria as AIC should be avoided when users are interested in binary predictions. Future applications that capture model complexity in ENM applications should be evaluated using standard validation metrics.

ecology↗

bioRxiv2018

Ecology, Not Distance, Explains Community Composition in Parasites of Sky-Island Audubon’s Warblers

O_LIHaemosporidian parasites of birds are ubiquitous in terrestrial ecosystems, but their coevolutionary dynamics remain poorly understood. If species turnover in parasites occurs at a finer scale than species turnover in hosts, widespread hosts would encounter diverse parasites and potentially diversify as a result. Previous studies have shown that some wide-ranging hosts encounter varied haemosporidian communities throughout their range, and vice-versa. However, it remains difficult to test spatial patterns of diversity in this complex multi-host multi-parasite system because it remains inadequately surveyed.\nC_LIO_LIWe sought to understand how and why a community of avian haemosporidian parasites varies in abundance and composition across an array of eight sky islands in southwestern North America. We tested whether bird community composition, aspects of the environment, or geographic distance explain parasite species turnover in a widespread, generalist host.\nC_LIO_LIWe sampled 178 Audubons Warblers (Setophaga auduboni) along elevational transects in eight mountain ranges and screened them for haemosporidian mtDNA. We tested predictors of infection using generalized linear models (GLMs) and we tested predictors of bird- and parasite-community dissimilarity using generalized dissimilarity modeling (GDM).\nC_LIO_LIPredictors of infection differed by genus: Parahaemoproteus was predicted by elevation and climate, Leucocytozoon varied idiosyncratically among mountain ranges, and Plasmodium was unpredictable, but rare. Parasite species turnover was nearly three-fold higher than bird species turnover and was predicted by elevation, climate, and bird community composition, but not by geographic distance.\nC_LIO_LIHaemosporidian communities vary strikingly at spatial scales of hundreds of kilometers, across which the bird community varies only subtly. The finer spatial scale of turnover among parasites species implies that their ranges tend to be smaller than those of their hosts. Avian host species should encounter different parasite species in different parts of their ranges, resulting in spatially varying selection on host immune systems. Furthermore, the fact that parasite turnover was predicted by bird turnover implies that different species within a host community affect each others parasites, potentially facilitating indirect antagonistic effects.\nC_LI

ecology↗

bioRxiv2018

Towards a pragmatic use of statistics in ecology

Although null hypothesis testing (NHT) is the primary method for analyzing data in many natural sciences, it has been increasingly criticized. Recently, a new method based on information theory (IT) has become popular and is held by many to be superior for many reasons, not least because is enables researchers to properly assess the strength of the evidence that data provide for competing hypotheses. Many studies have compared IT and NHT in the context of model selection and stepwise regression, but a systematic comparison of the most simple but realistic uses of statistics by ecologists is still lacking. We used computer simulations to compare how both methods perform in four basic test designs (t-test, ANOVA, correlation tests, and multiple linear regression). Performance was measured by the proportion of simulated samples for which each method provided the correct conclusion (power), the proportion of detected effects with a wrong sign (S-error), and the mean ratio of the estimated effect to the true effect (M-error). We also checked if the p-value from significance tests correlated to a measure of strength of evidence, the Akaike weight. In most cases both methods performed equally well. The concordance is explained by the monotonic relationship between p-values and evidence weights in simple designs, which agree with analytic results. Our results show that researchers can agree on the conclusions drawn from a data set even when they are using different statistical approaches. By focusing on the practical consequences of inferences, such a pragmatic view of statistics can promote insightful dialogue among researchers on how to find a common ground from different pieces of evidence. A less dogmatic view of statistical inference can also help to broaden the debate about the role of statistics in science to the entire path that leads from a research hypothesis to a statistical hypothesis.

ecology↗

bioRxiv2018

Non-heritable variation in individual fitness adds stability to neutral theories in ecology and evolution

Neutral theories in ecology1 and evolution2 contend that high diversity of natural communities and high rates of molecular evolution conform to models where individuals have equal fitness and mutations have no effects. Demographic stochasticity makes community and population compositions inherently unstable under these models, with overall levels of diversity being maintained by random processes. This is in contrast with niche and adaptive theories which emphasize differences between species or genotypes as the key to their coexistence3. Here we show that non-heritable variation in individual fitness within species or genotypes can stabilize coexistence without evoking niche differentiation. We construct two classes of mathematical models based on experimental evidence: (1) bacterial growth with variation in cell longevity4,5; and (2) microbial transmission in a host population with variation in host susceptibility6-11. We find stable coexistence of 2 bacterial species in the first model under a single oscillating resource, and 3 or more in the second with independent distributions of host susceptibility to the various microbial species. We discuss the implications of these findings for the interpretation of common measures of relative fitness and for the maintenance of biodiversity.

ecology↗

bioRxiv2018

Comparison of ecological, biological and anthropogenic causes of vehicle-wildlife collisions among three large herbivore species

Wildlife-vehicle collisions are of increasing concern with regards to the continuous and accelerating anthropogenic development. Preventing and mitigating collisions with wildlife will require a better understanding of the environmental and biological drivers of collision risks. Because species of large mammals differ in terms of food requirements, habitat selection and movement behaviours we tested at the management unit level if the density of collisions with red deer, roe deer and wild boar differed in terms of spatial distribution and explanatory factors. From 20,275 documented collisions in France between years 1990 and 2006, we found marked differences in the most influential environmental factors accounting for the density of collisions among the three species. The effect of road density was higher for the red deer than for the two other species and did not level off at our spatial-scale of observation. As expected, the annual hunting harvest - interpreted as a proxy of population abundance - was positively associated with the density of collisions for all species, being the strongest for red deer. While the collision density decreased with the proportion of forest in a management unit for wild boar, it increased with the fragmentation of forests for red deer that commute among forest patches between day and night. To reduce the number of wildlife- vehicle collisions, our results suggest to generalise road fencing and/or a control of abundance of large herbivore populations. Mitigation measures should target units where the collision risk is the highest for the most problematic species.

ecology↗

bioRxiv2018

Ecological niche modelling of the wattled crane (Bugeranus carunculatus) suggest range expansion and contraction during the Pleistocene

This paper attempts to understand the potential effects of historical climate changes on the distribution of the wattled crane (Bugeranus carunculatus). The potential distribution in past and present climatic scenarios is investigated through ensemble distribution modelling of 232 independent and sparsely distributed occurrence records. Potential effects of climate change were evaluated by means on niche overlap and niche gains and losses across time scales. Massive range expansion was observed from the Last Interglacial (LIG) era to the Last Glacial Maximum (LGM), with loss of suitability in most areas of western Africa and an increase in suitability across southern and eastern Africa. From the LGM, climate suitability tended to establish in southern and eastern Africa with slight disjunction in the mid-Holocene, a trend that was maintained through current distribution. Results indicate the presence of southern and northern refugia, with massive range expansion in central populations. These results support the idea that the current disjunct distribution of the wattled crane is driven by climate oscillations during the Pleistocene that generated range expansion and retraction of the species and also support the hypothesis that the current occurrence of the species is driven by other factors such as food and habitat availability.

ecology↗

bioRxiv2018

Generalized sample verification models to estimate ecological state variables with detection-nondetection data while accounting for imperfect detection and false positive errors.

Spatially-indexed repeated detection-nondetection data is widely collected by ecologists interested in estimating parameters associated with species distribution, relative abundance, phenology, and more while accounting for imperfect detection. Recent model development has focused on accounting for false positive error as well, given growing recognition that misclassification is common across many sampling protocols. To date, however, the development of model-based solutions to false positive error has been largely restricted to occupancy models. We describe a general form of the observation confirmation protocol originally described for occupancy estimation that permits investigators to flexibly and intuitively extend several models for detection-nondetection data to account for false positive error. Simulation results demonstrate that estimators for relative abundance and arrival time exhibit relative bias greater than 20% under realistic levels of false positive prevalence (e.g., 5% of detections are false positive). Bias increases as true and false positives occur in more distinct places or times, but can also be sensitive to the values of the state variables of interest, sampling design, and sampling efficiency. Results from an empirical study focusing on patterns of gray fox relative abundance across Wisconsin, USA suggest that false positive error can also distort estimated spatial patterns often used to guide decision-making. The extended estimators described within typically improve performance at any level of confirmation, and when false positive error occurs at random and constitutes less than 10% of all detections, the estimators are essentially unbiased when more than 50 observations can be confirmed as true or false positives. The generalized form of the observation-confirmation protocol is a flexible model-based solution to false positive error useful for researchers collecting data with sampling devices like trail or smartphone cameras, acoustic recorders, or other techniques where classifications can be reviewed post-hoc.

ecology↗

bioRxiv2018

Spatial ecology of Paraguay’s last remaining Atlantic forest jaguars (Panthera onca): implications for their long-term survival

Using GPS telemetry we quantified space use and movements of jaguar (Panthera onca) in remnant populations in the Paraguayan Atlantic forest within a comparative context with populations in the Argentine and Brazilian Atlantic forest. Mean estimated home range size was 160 km2; estimated to be nearly equal to jaguars in the Morro do Diabo State Park in Brazil but jaguars in other populations in Argentina and Brazil had a 73% (Iguazu/Iguacu national park complex) and 96% (Ivinhema State Park) probability of having larger home ranges. We found no relationship between home range size or movements and human population or the Human Footprint Index, while 75% of locations from all individuals were in protected areas. Our data and analysis highlight the dependence of Atlantic forest jaguars on protected areas, an avoidance of the landscape matrix and an extreme isolation of the remaining Paraguayan Atlantic forest jaguars.

ecology↗

bioRxiv2014

Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome

Average genome size (AGS) is an important, yet often overlooked property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate AGS from short-read metagenomics data and applied our tool to over 1,300 human microbiome samples. We found that AGS differs significantly within and between body sites and tracks with major functional and taxonomic differences. For example, in the gut, AGS ranges from 2.5 to 5.8 megabases and is positively correlated with the abundance of Bacteroides and polysaccharide metabolism. Furthermore, we found that AGS variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.

Bioinformatics↗

bioRxiv2015

Intragenomic homogeneity on Liberibacter 16S rDNA confirms phylogeny and explains ecological strategy

Three of the five currently recognized \"Candidatus Liberibacter\" spp., \"Ca. L. asiaticus\" (Las), \"Ca. L. americanus\" (Lam) and \"Ca. L. solanacearum\", and the newly erected genus Liberibacter species, L. crescens (Lcr), have had their genomes sequenced. In all four cases there are three homogeneous copies of the 16S rRNA gene, one present as the reverse complement of the other two. 16S intragenic homogeneity is common within the -Proteobacteria. The presence of three 16S rRNA copies indicates an advantage for a rapid response of population increase to favourable growth conditions. The metabolic cost of carrying multiple copies is avoided during periods of low cellular activity as this situation occurs at low temperatures, for example overwintering in deciduous plants or in a dormant insect host.\n\nA large insertion in the 16S rDNA sequence of three species compared to the other three species indicates a dichotomy in the Liberibacter genus and provides a phylogenetic signal of closeness to the proximal node within the Rhizobiaceae. In spite of similar symptoms in Citrus crops associated with Lam and Las infections, these species belong on either side of this dichotomy, thus confirming Lam as phylogenetically closer to the proximal node than Las.

Microbiology↗