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bioRxiv2015

Evolution arrests invasions of cooperative populations

Population expansions trigger many biomedical and ecological transitions, from tumor growth to invasions of non-native species. Although population spreading often selects for more invasive phenotypes, we show that this outcome is far from inevitable. In cooperative populations, mutations reducing dispersal have a competitive advantage. Such mutations then steadily accumulate at the expansion front bringing invasion to a halt. Our findings are a rare example of evolution driving the population into an unfavorable state and could lead to new strategies to combat unwelcome invaders. In addition, we obtain an exact analytical expression for the fitness advantage of mutants with different dispersal rates.\n\nPACS numbers: 87.23.Kg, 05.60.Cd, 64.60.-i, 87.23.Cc

Ecology↗

bioRxiv2015

A Multiscale Framework for Deconstructing the Ecosystem Physical Template of High-Altitudes Lakes

An ecosystem is generally sustained by a set of integrated physical elements forming a functional landscape unit - ecotope, which supplies nutrients, microclimate, and exchanges matter and energy with the wider environment. To better predict environmental change effects on ecosystems, particularly in critically sensitive regions such as high altitudes, it is imperative to recognise how their natural landscape heterogeneity works at different scales to shape habitats and sustain biotic communities prior to major changes.\n\nWe conducted a comprehensive survey of catchment physical, geological and ecological properties of 380 high altitude lakes and ponds in the axial Pyrenees at a variety of scales, in order to formulate and test an integrated model encompassing major flows and interactions that drive lake ecosystems.\n\nThree composite drivers encompassed most of the variability in lake catchment characteristics. In order of total percentage of variance explained they were: (i) hydrology/hydrodynamics-responsible for type and discharge of inlets/outlets, and for water body size; (ii) bedrock geomorphology, summarizing geology, slope and fractal order-all dictating vegetation cover of catchment slope and lake shore, and the presence of aquatic vegetation; and, (iii) topography, i.e. catchment formation type-driving lakes connectivity, and the presence of summer snow deposits. While driver (i) appeared to be local, (ii) and (iii) showed gradient changes along altitude and latitude. These three drivers differentiated several lake ecotopes based on their landscape similarities. The three-driver model was successfully tested on a riparian vegetation composition dataset, further illustrating the validity and fundamental nature of the concept.\n\nThe findings inform on the relative contribution of scale-dependent catchment physical elements to lake ecotope and ecosystem formation in high altitude lakes, which should be considered in any assessment of potentially major deleterious effects due to environmental/climate change.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC=\"FIGDIR/small/034405_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (85K):\norg.highwire.dtl.DTLVardef@4b92e5org.highwire.dtl.DTLVardef@198fca4org.highwire.dtl.DTLVardef@f2801dorg.highwire.dtl.DTLVardef@b8f588_HPS_FORMAT_FIGEXP M_FIG Lake Bassia at 2275m a.s.l. in the Pyrenees National Park, France, is one of the millions of remote high altitude lakes worldwide whose catchments are likely to experience severe effects due to climate change. Photo credit: Antonio Palanca-Soler.\n\nC_FIG

Ecology↗

bioRxiv2016

The genetic Allee effect: a unified framework for the genetics and demography of small populations

The Allee effect is a theoretical model predicting low growth rates and the possible extinction of small populations. Historically, studies of the Allee effect have focused on demography. As a result, underlying processes other than the direct effect of population density on fitness components are not generally taken into account. There has been heated debate about the potential of genetic processes to drive small populations to extinction, but recent studies have shown that such processes clearly impact small populations over short time scales, and some may generate Allee effects. However, as opposed to the ecological Allee effect, which is underpinned by cooperative interactions between individuals, genetically driven Allee effects require a change in genetic structure to link the decline in population size with a decrease in fitness components. We therefore define the genetic Allee effect as a two-step process whereby a decrease in population size leads to a change in population genetic structure, and in turn, to a decrease in individual fitness. We describe potential underlying mechanisms, and review the evidence for this original type of component Allee effect, using published examples from both plants and animals. The possibility of considering demogenetic feedback in light of genetic Allee effects clarifies the analysis and interpretation of demographic and genetic processes, and the interplay between them, in small populations.

Ecology↗

bioRxiv2016

Stochastic processes dominate community assembly in cichlid communities in Lake Tanganyika

The African Great Lakes are characterized by an extraordinary diversity of endemic cichlid fish species. The cause of this diversity is still largely unknown. Most studies have tried to solve this question by focusing on macro-evolutionary processes, such as speciation. However, the ecological processes determining local cichlid diversity have so far been understudied, even though knowledge on these might be crucial for understanding larger scale biodiversity patterns.\n\nUsing trait, environmental and abundance data of cichlid fishes along 36 transects, we have studied how differences in local environmental conditions influence cichlid community assembly in the littoral of Lake Tanganyika, Zambia. We investigated changes in average trait values and in trait-based community assembly processes along three key environmental gradients.\n\nSpecies diversity and local abundance decreased with increasing sand cover and diet-associated traits changed with depth. Analyses on within-community trait diversity patterns indicated that cichlid community assembly was mainly driven by stochastic processes, to a smaller extent by processes that limit the similarity among co-existing species and least by filtering processes that limit the range of species traits occurring in an environment. Despite, the low impact of habitat filtering processes, we find community dissimilarity to increase with increasing environmental difference.\n\nOur results suggest that local environmental conditions determine cichlid abundance, while the predominance of stochastic community assembly across all environments explains why the communities with the highest abundances contain most species.

Ecology↗

bioRxiv2016

Do persistent rare species experience stronger negative frequency dependence than common species?

Understanding why so many species are rare yet persistent remains a significant challenge for both theoretical and empirical ecologists. Yenni, Adler, and Ernest (2012) proposed that strong negative frequency dependence causes species to be rare while simultaneously buffering them against extinction. This hypothesis predicts that, on average, rare species should experience stronger negative frequency dependence than common species. However, it is unknown if ecological communities generally show this theoretical pattern, or if rarity is primarily determined by other processes that overwhelm the effects of strong negative frequency dependence. We discuss the implications of this mechanism for natural communities, and develop a method to test for a non-random relationship between negative frequency dependence and relative abundance, using species abundance data from 90 communities across a broad range of environments and taxonomic groups. To account for biases introduced by measurement error, we compared the observed correlation between species relative abundance and the strength of frequency dependence against expectations from a randomization procedure. In approximately half of the analyzed communities, rare species showed disproportionately strong negative frequency dependence compared to common species. Specifically, we found a pattern of increasingly strong negative frequency dependence with decreasing relative abundance. Our results suggest that strong negative frequency dependence is a signature of both rarity and persistence for many species in many communities.

Ecology↗

bioRxiv2016

The long-term sand crab study: phenology, geographic size variation, and a rare new colour morph in Lepidopa benedicti (Decapoda: Albuneidae)

Little is known about the basic ecology of albuneid sand crabs because they conceal themselves by digging in sand, and are typically found at low densities. I sampled sand crabs, Lepidopa benedicti were sampled at South Padre Island, Texas, regularly for more than five years. Density is high in the summer, and low in the winter. The sex ratio is slightly, but consistently, female skewed. Ovigerous females, carrying about one thousand eggs, are found in mid-summer, with most of the young of the year settling in autumn. The average size of individuals in the South Texas population is smaller than individuals in the Atlantic Ocean, but the population density appear to be higher in Texas. I also describe a new orange colour morph. The results are not consistent with an earlier suggestion that South Texas acts as a population sink for L. benedicti.

Ecology↗

bioRxiv2016

Effect of stand characteristics on tree species richness in and around a conservation area of Bangladesh

We investigated the effect of tree cover, forest patch and disturbances on tree species richness in a highly diverse conservation area of northeast Bangladesh. A systematic sampling protocol was adopted and 80 sub-plots from twenty five 1 ha plots were used for the vegetation survey. Linear regression analysis was performed to understand the effect of patch area, disturbances and tree cover on tree species richness. Ordination using Redundancy analysis (RDA) and Non-metric Multi Dimensional Scaling (NMDS) were also performed to explore the tree species compositional similarities along the stand characteristics gradient and locations of the sample plots. Our study revealed that, forest patch size has greater influence on species richness. Areas with medium level of disturbances have shown greater species richness. In constrained ordination the selected explanatory variables regulated the richness of common species. Our findings can be useful for better forest management and restoration of landscapes of conservation needs using ecologically important species.

Ecology↗

bioRxiv2016

Estimating dispersal kernels using genetic parentage data

Dispersal kernels are the standard method for describing and predicting the relationship between dispersal strength and distance. Statistically-fitted dispersal kernels allow observations of a limited number of dispersal events to be extrapolated across a wider landscape, and form the basis of a wide range of theories and methods in ecology, evolution and conservation. Genetic parentage data are an increasingly common source of dispersal information, particularly for species where dispersal is difficult to observe directly. It is now routinely applied to coral reef fish, whose larvae disperse over many kilometers and are too small to follow directly. However, it is not straightforward to estimate dispersal kernels from parentage data, and existing methods each have substantial limitations. Here we develop and proof a new statistical estimator for fitting dispersal kernels to parentage data, applying it to simulated and empirical datasets of reef fish parentage. The method incorporates a series of factors omitted in previous methods: the partial sampling of adults and juveniles on sampled reefs; the existence of unassigned dispersers from unsampled reefs; and post-settlement processes (e.g., density dependent mortality) that follow dispersal but precede parentage sampling. Power analyses indicate that the highest levels of sampling currently used for reef fishes is sufficient to fit accurate dispersal kernels. Sampling is best distributed equally between adults and juveniles, and over more than ten populations. Importantly, we show that accounting for unsampled or unassigned individuals - including adult individuals on partially-sampled and unsampled patches - is essential for a precise and unbiased estimate of dispersal.

Ecology↗

bioRxiv2016

Bias in community-weighted mean analysis relating species attributes to sample attributes: justification and remedy

One way to analyze the relationship between species attributes and sample attributes via the matrix of species composition is to calculate the community-weighted mean of species attributes (CWM) and relate it to sample attributes by correlation, regression or ANOVA. This weighted-mean approach is frequently used by vegetation ecologists to relate species attributes like plant functional traits or Ellenberg-like species indicator values to sample attributes like measured environmental variables, biotic properties, species richness or sample scores in ordination analysis.\n\nThe problem with the weighted-mean approach is that, in certain cases, it yields biased results in terms of both effect size and P-values, and this bias is contingent upon the beta diversity of the species composition data. The reason is that CWM values calculated from samples of communities sharing some species are not independent of each other. This influences the number of effective degrees of freedom, which is usually lower than the actual number of samples, and the difference further increases with decreasing beta diversity of the data set. The discrepancy between the number of effective degrees of freedom and the number of samples in analysis turns into biased effect sizes and an inflated Type I error rate in those cases where the significance of the relationship is tested by standard tests, a problem which is analogous to analysis of two spatially autocorrelated variables. Consequently, results of studies using rather homogeneous (although not necessarily small) compositional data sets may be overly optimistic, and effect sizes of studies based on data sets differing by their beta diversity are not directly comparable.\n\nHere, I introduce guidelines on how to decide in which situation the bias is actually a problem when interpreting results, recognizing that there are several types of species and sample attributes with different properties and that ecological hypotheses commonly tested by the weighted-mean approach fall into one of three broad categories. I also compare available analytical solutions accounting for the bias (modified permutation test and sequential permutation test using the fourth-corner statistic) and suggest rules for their use.\n\nAbbreviations

Ecology↗

bioRxiv2016

Elevated nonlinearity as indicator of transition to overexploitation in fish stocks

Ecosystems may experience abrupt changes such as species extinctions, reorganisations of trophic structure, or transitions from stable population dynamics to strongly irregular fluctuations. Although most of these changes have important ecological and at times economic implications, they remain notoriously difficult to detect in advance. Here, we use a Ricker-type model to simulate the transition of a hypothetical stable fisheries population either to irregular boom-bust dynamics or to overexploitation. Our aim is to infer the risk of extinction in these two scenarios by comparing changes in variance, autocorrelation, and nonlinearity between unexploited and exploited populations. We find that changes in these statistical metrics reflect the risk of extinction but depend on the type of dynamical transition. Variance and nonlinearity increase similarly in magnitude along both transitions. In contrast, autocorrelation depends strongly on the presence of underlying oscillating dynamics. We also compare our theoretical expectations to indicators measured in long-term datasets of fish stocks from the California Cooperative Oceanic Fisheries Investigation in the Eastern Pacific and from the Northeast Shelf in the Western Atlantic. Our results suggest that elevated variance and nonlinearity could be potentially used to rank exploited fish populations according to their risk of extinction.

Ecology↗

bioRxiv2016

Behavioural effects of temperature on ectothermic animals: unifying thermal physiology and behavioural plasticity

Temperature imposes significant constraints on ectothermic animals, and these organisms have evolved numerous adaptations to respond to these constraints. While the impacts of temperature on the physiology of ectotherms have been extensively studied, there are currently no frameworks available that outline the multiple and often simultaneous pathways by which temperature can affect behaviour. Drawing from the literature on insects, we propose a unified framework that should apply to all ectothermic animals, generalizing temperature's behavioural effects into (1) Kinetic effects, resulting from temperature's bottom-up constraining influence on metabolism and neurophysiology over a range of timescales (from short-to long-term), and (2) Integrated effects, where the top-down integration of thermal information intentionally initiates or modifies a behaviour (behavioural thermoregulation, thermal orientation, thermosensory behavioural adjustments). We discuss the difficulty in distinguishing adaptive behavioural changes due to temperature from behavioural changes that are the products of constraints, and propose two complementary approaches to help make this distinction and class behaviours according to our framework: (i) behavioural kinetic null modeling and (ii) behavioural ecology experiments using temperature-insensitive mutants. Our framework should help to guide future research on the complex relationship between temperature and behaviour in ectothermic animals.

Ecology↗

bioRxiv2016

pcadapt: an R package to perform genome scans for selection based on principal component analysis

The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers with respect to how they are related to population structure. Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data. By contrast to population-based approaches, the package handle admixed individuals and does not require grouping individuals into populations. Since its first release, pcadapt has evolved both in terms of statistical approach and software implementation. We present results obtained with robust Mahalanobis distance, which is a new statistic for genome scans available in the 2.0 and later versions of the package. When hierarchical population structure occurs, Mahalanobis distance is more powerful than the communality statistic that was implemented in the first version of the package. Using simulated data, we compare pcadapt to other software for genome scans (BayeScan, hapflk, OutFLANK, sNMF). We find that the proportion of false discoveries is around a nominal false discovery rate set at 10% with the exception of BayeScan that generates 40% of false discoveries. We also find that the power of BayeScan is severely impacted by the presence of admixed individuals whereas pcadapt is not impacted. Last, we find that pcadapt and hapflk are the most powerful software in scenarios of population divergence and range expansion. Because pcadapt handles next-generation sequencing data, it is a valuable tool for data analysis in molecular ecology.

Ecology↗

bioRxiv2016

Particularity of “Universal resilience patterns in complex networks”

In a recent Letter to Nature,Gao, Barzel and Barabasi 1 describe an elegant procedure to reduce the dimensionality of complex dynamical networks, which they claim reveals \"universal patterns of network resilience\", offering \"ways to prevent the collapse of ecological, biological or economic systems, and guiding the design of technological systems resilient to both internal failures and environmental changes\". However, Gao et al restrict their attention to systems for which all interactions between nodes are mutualistic. Since antagonism is ubiquitous in natural and social networks, we clarify why this stringent hypothesis is necessary and what happens when it is relaxed. By analyzing broad classes of competitive and predator-prey networks we provide novel insights into the underlying mechanisms at work in Gao et als theory, and novel predictions for dynamical systems that are not purely mutualistic.

Ecology↗

bioRxiv2016

Dark diversity illuminates the dim side of conservation and restoration

1 Dark diversity is a promising concept for prioritizing management efforts as it focuses on missing species, i.e., species present in the regional pool, but locally absent despite suitable environmental conditions. 2 We applied the concept to a massive national plant diversity database (236,923 records from 15,160 surveys involving 564 species) to provide the first geographically comprehensive assessment of dark diversity across a large area (43,000 km2), at a spatial scale (~75 m2) relevant for conservation and restoration planning and across multiple terrestrial habitats, thus maximising its practical application potential. The likelihood for a given plant species to belong to the dark diversity pool was computed and logistically regressed against its ecological preferences (nutrient availability, pH etc.), strategies (competitor, stress tolerance, ruderal), mycorrhizal dependence and infection percentage, seed mass and maximum dispersal distance. 3 Forty-six percent of the species were absent in >95 % of the suitable sites, whereas 7 % of the species were absent in less than 60 % of sites that were deemed suitable. 4 Species that were more likely to belong to the dark diversity tended to depend on mycorrhiza, were mostly adapted to low light and nutrient levels, had poor dispersal abilities, were ruderals and had a low stress tolerance. Synthesis and applications Our findings have important implications for the planning and management of natural ecosystems requiring detailed knowledge of what triggers the presence/absence of individual plant species in a seemingly suitable habitat. We conclude that practitioners may need to carefully consider mycorrhizal inoculations with a suitable assemblage of fungi for certain plant species to become established. Also assisted migration might be necessary to help poor dispersers although spatial and temporal processes are also important to have in mind. Finally, it is important to vary nutrient loads making room for plant species to colonise both nutrient-poor and nutrient-rich localities.

Ecology↗

bioRxiv2016

Retreat Site Selection in Vaejovis carolinianus Populations of Tennessees Upper Cumberland Region

Abstract:My study examined Tennessees only native scorpion species, Vaejovis carolinianus. Little is known about its ecology, so the objectives of my study were to determine if: (1) V. carolinianus selected cover objects based on surface area; (2) V. carolinianus preferred moister soils under the cover object; and (3) length of time in captivity altered the preferences. Scorpions were captured from two different locations: (1) a roadcut parallel to State Highway 96 near Edgar Evins State Park; (2) France Mountain in Overton County. In laboratory trials, scorpions were allowed to choose among three retreat sites and three soil moisture levels. Transects were established at both field locations to count and measure rocks that may serve as retreat sites. Surface area trials indicated that V. carolinianus selected large objects as retreat sites most often, but overall retreat site selection did not differ from that expected based on random choice weighted by cover object size. Soil moisture trial results varied, with no statistical significance in the results from the Highway 96 and 2013 France Mountain populations. The 2014 France Mountain population did show statistically significant differences. The surface area trials did not exhibit a time in captivity effect, but the soil moisture trials indicated a time in captivity effect between the 2013 and 2014 France Mountain populations. Based on test results, it appears V. carolinianus selected larger rocks as cover sites, perhaps due to chance or perhaps to escape sunlight and heat, for predator avoidance, or for higher soil moisture levels.

Ecology↗

bioRxiv2016

Aggregation tendencies of a female Vaejovis carolinianus population of France Mountain, Tennessee

France Mountain is located within Overton County which is part of the Upper Cumberland region of Middle Tennessee contains only one species of scorpion, also the only species native to the state, Vaejovis carolinianus. This species is poorly researched, and little is known about its life history and ecology. The objectives of this study were to determine if female V. carolinianus prefer to form aggregations under large cover objects or seek out retreat sites where they would be the sole occupant. Based on past research, we hypothesized that females would form aggregations under large cover objects instead of being the sole occupant. A total of 32 scorpions were captured during August and September 2014. During laboratory trials, three scorpions were placed in a plywood tray containing sand substrate and three equally-sized large ceramic tiles. The scorpions were left undisturbed for a 24-hour period, after which the tiles were lifted to check for aggregations. Each group of three scorpions was in the research tray for three consecutive days. Four rounds of aggregation trials were conducted, and t-tests as well as linear regression were used to analyze the data collected. The results of the t-test showed that female V. carolinianus, when given a choice of similarly-sized large cover objects, would select a retreat site where they were the sole occupant; therefore, our initial hypothesis was rejected. Linear regression found relative humidity affected aggregation occurrence, for the largest number of aggregations occurred when the relative humidity was between 67 and 73%.

Ecology↗

bioRxiv2016

DECONTEXTUALIZING BIG DATA FOR A BETTER PERCEPTION OF MACROECOLOGY

ABSTRACTFish species are charismatic subjects widely used for ecological assessment and modelling. We investigated the influence of electrofishing in an attempt to illuminate the extent to which datasets might be merged together. Three American Midwestern regions in Ohio were chosen as study area and the changes in the size-biomass spectra of more than 2000 fish assemblages were analysed. These communities behaved differently according to the sampling method in conjunction to the morphology of the investigated streams and rivers, as shown by decreasing predatory species and lowering of allometric slopes. There are here several lines of evidence indicating that the chosen sampling method, as determined by different habitats, acts as a pitfall and strongly influences the allometry of fish spectra. In the ongoing data-rich era, our results highlight that macroecological investigations, often performed by machine-learning systems without considering the different procedures adopted to collect original data, can easily produce artefactual allometric scalings.

Ecology↗

bioRxiv2016

Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory

Human-mediated selection can strongly influence the evolutionary response of natural organisms within ecological timescales. But what traits allow for, or even facilitate, adaptation to the strong selection humans impose on natural systems? Using a combination of lab and greenhouse studies of 32 natural populations of the common agricultural weed, Ipomoea purpurea, we show that herbicide resistant populations self-fertilize more than susceptible populations. We likewise show that anther-stigma distance, a floral trait associated with self-fertilization in this species, exhibits a non-linear relationship with resistance such that the most and least resistant populations exhibit lower anther-stigma separation compared to populations with moderate levels of resistance. Overall, our results extend the general finding that plant mating can be impacted by human-mediated agents of selection to that of the extreme selection of the agricultural system. This work highlights the influence of human-mediated selection on rapid responses of natural populations that can lead to unexpected long-term evolutionary consequences.\n\nStatement of authorshipAK collected seeds, performed experiments, analyzed data and wrote the paper; EF collected data; SMC collected data and contributed to the manuscript; RSB designed the study, performed the analyses, and wrote the paper. All authors discussed the results and commented on the manuscript.\n\nData accessibilityPrimary data used in these analyses will be made available in the public github repository https://github.com/rsbaucom/MatingSystem2015, which can be anonymously accessed. Upon acceptance, data will be made available through the Dryad public repository.

Ecology↗