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bioRxiv2014

Particle size distribution and optimal capture of aqueous macrobial eDNA

O_LIDetecting aquatic macroorganisms with environmental DNA (eDNA) is a new survey method with broad applicability. However, the origin, state, and fate of aqueous macrobial eDNA - which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified, and assayed - are poorly understood.\nC_LIO_LIThe size of aquatic particles provides clues about their origin, state, and fate. We used sequential filtration size fractionation to measure, for the first time, the particle size distribution (PSD) of macrobial eDNA, specifically Common Carp (hereafter referred to as Carp) eDNA. We compared it to the PSDs of total eDNA (from all organisms) and suspended particle matter (SPM). We quantified Carp mitochondrial eDNA using a custom qPCR assay, total eDNA with fluorometry, and SPM with gravimetric analysis.\nC_LIO_LIIn a lake and a pond, we found Carp eDNA in particles from >180 to <0.2 m, but it was most abundant from 1-10 m. Total eDNA was most abundant below 0.2 m and SPM was most abundant above 100 m. SPM was [≤]0.1% total eDNA, and total eDNA was [≤]0.0004% Carp eDNA. 0.2 m filtration maximized Carp eDNA capture (85%{+/-}6%) while minimizing total (i.e., non-target) eDNA capture (48%{+/-}3%), but filter clogging limited this pore size to a volume <250 mL. To mitigate this limitation we estimated a continuous PSD model for Carp eDNA and derived an equation for calculating isoclines of pore size and water volume that yield equivalent amounts of Carp eDNA.\nC_LIO_LIOur results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling plays an important role in its fate. For optimal eDNA capture, we recommend 0.2 m filtration or a combination of larger pore size and water volume that exceeds the 0.2 m isocline. In situ filtration of large volumes could maximize detection probability when surveying large habitats for rare organisms. Our method for eDNA particle size analysis enables future research to compare the PSDs of eDNA from other organisms and environments, and to easily apply them for ecological monitoring.\nC_LI

Ecology↗

bioRxiv2014

On a solution of the biodiversity paradox and a competitive coexistence principle

The biodiversity paradox is the central problem in theoretical ecology. The paradox consists in the contradiction between the competitive exclusion principle and the observed biodiversity. This contradiction is the key subject of the long-standing and continuing biodiversity debates. The paradox impedes our insights into biodiversity conservation. Previously we proved that due to a soliton-like behaviour of population waves complete competitors can indefinitely coexist in one closed homogeneous habitat on one and the same limiting resource under constant conditions of environment, without any trade-offs and cooperations. As this fact violates the known formulations of the competitive exclusion principle we have reformulated the principle. Here we explain why this reformulation of the principle results in a solution of the biodiversity paradox. In addition, we generalize the competitive exclusion principle. Reasoning by contradiction, we formulate a generalized principle of competitive coexistence. These principles expand theoretical basis for biodiversity conservation and sustainable development.

Ecology↗

bioRxiv2014

Building realistic assemblages with a Joint Species Distribution Model

O_LISpecies distribution models (SDMs) can be used to predict how individual species--and whole assemblages of species--will respond to a changing environment. Until now, these models have either assumed (1) that species occurrence probabilities are uncorrelated, or (2) that species respond linearly to preselected environmental variables. These two assumptions currently prevent ecologists from modeling assemblages with realistic co-occurrence and species richness properties.\nC_LIO_LIThis 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 recently proposed Joint SDMs, mistnet can also learn nonlinear functions relating species occurrence probabilities to environmental predictors.\nC_LIO_LIMistnet 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 nearly 50,000 times more likely under the mistnet model than under independent combinations of single-species models.\nC_LIO_LIApart from improved accuracy, mistnet shows two other important benefits for ecological research and management. First: by analyzing co-occurrence data, mistnet can identify unmeasured--and perhaps unanticipated--environmental variables that drive species turnover. For example, mistnet 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 incomplete data sets 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.\nC_LI

Ecology↗

bioRxiv2014

Some plants dont play games: An ideal free distribution explains the root production of plants that do not engage in a tragedy of the commons game.

This is the pre-peer-reviewed version of the following article: G.G. McNickle and J.S. Brown. (2014) An ideal free distribution explains the root production of plants that do not engage in a tragedy of the commons game. Journal of Ecology. DOI: 10.1111/1365-2745.12259, which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12259/abstract\n\nO_LIGame theoretic models that seek to predict the most competitive strategy plants use for competition in soil are clear; they generally predict that over-proliferation of roots is the only evolutionarily stable strategy. However, empirical studies are equally clear that not all plants employ this strategy of over-proliferation of roots. Here, our goal was to develop and test an alternative non-game theoretic model that can be used to develop alternative hypotheses for plants that do not appear to play games.\nC_LIO_LIThe model is similar to previous models, but does not use a game theoretic optimization criterion. Instead, plants use only nutrient availability to select a root allocation strategy, ignoring neighbours. To test the model we compare root allocation and seed yield of plants grown either alone or with neighbours.\nC_LIO_LIThe model predicted plants that do not sense neighbours (or ignore neighbours) should allocate roots relative to resource availability following an ideal free distribution. This means that if a soil volume of quality R contains x roots, then a soil volume of quality R/n will contain x/n roots. The experimental data were consistent with this prediction. That is, plants grown with 1.2g of slow release fertilizer resources produced 0.043 g of roots, while plants grown with neighbours, or plants grown with half as much fertilizer produced half as much root mass (0.026g, and 0.24g respectively). Seed yield followed a similar pattern.\nC_LIO_LIThis model presents an alternative predictive framework for those plant species that do not seem to play a tragedy of the commons game for belowground competition.\nC_LIO_LISynthesis: It remains unclear why some plants do not engage in belowground games for competition. Models suggest over-proliferation is an unbeatable evolutionary stable strategy, yet plants that do not play the game apparently coexist with plants that do. We suggest that a greater understanding of trade-offs among traits that are important for other biotic interactions (above-ground competition, enemy defence, mutualisms) will lead to a greater understanding of why some species over-proliferate roots when in competition but other species do not.\nC_LI

Ecology↗

bioRxiv2014

Burrow architectural types of the Atlantic ghost crab, Ocypode quadrata (Fabricius, 1787) (Brachyura: Ocypodidae), in Brazil

A broad range of aspects from paleontology to physiology of the ghost crabs Ocypode quadrata have been studied worldwide. These crabs have been used as ecological indicators of the levels of anthropogenic impacts on sandy beaches. Our aim is to report the variety of burrow architecture types constructed by ghost crabs Ocypode quadrata on beaches of Maceio, Brazil. We found 20 types of burrows that differ in shape (number of axes, number of openings, orientation of blind end, number of branches). The slash-shaped burrows (type C) were the most frequent shape, followed by types K (spiral) and E (Y-shaped). Type C also showed the largest opening diameter and length ranges. Burrow types F, J, P, S and T were the least frequent. The G-test for goodness of fit to a time-independent uniform frequency distribution (G = 417.61; d.f. = 18; p < 0.005) reject the hypothesis that burrow types are constructed randomly (uniform distribution). The dominance of type C burrows and other simple-type burrows over more elaborate types indicates preference for simplicity.

Ecology↗

bioRxiv2014

A solution to the biodiversity paradox by logical deterministic cellular automata

The paradox of biological diversity is the key problem of theoretical ecology. The paradox consists in the contradiction between the competitive exclusion principle and the observed biodiversity. This principle was formulated incorrectly because of limitations of the traditional black-box models of interspecific competition. The principle is very important as the basis for understanding evolutionary processes. Our white-box multiscale models are based on logical deterministic individual-based cellular automata. This approach allows to provide an automatic deductive inference on the basis of a system of axioms and to get a direct holistic insight into the studied system. It is one of the most promising methods of artificial intelligence. Here on simplest models we show a mechanism of competitive coexistence which violates the known formulations of the competitive exclusion principle. We reformulate and generalize the competitive exclusion principle and explain why our formulations provide a solution of the biodiversity paradox. In addition, we propose a principle of competitive coexistence.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC=\"FIGDIR/small/006817_ufig1.gif\" ALT=\"Figure 1000\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@17f69c5org.highwire.dtl.DTLVardef@1f91196org.highwire.dtl.DTLVardef@f1ce70org.highwire.dtl.DTLVardef@12829e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

Ecology↗

bioRxiv2014

Quantifying and understanding reproductive allocation schedules in plants: a lifetime of decisions

O_LIA plant's reproductive allocation (RA) schedule describes the fraction of surplus energy allocated to reproduction as it increases in size. RA schedules distinguish between energy allocated to different tissue types and thus links to a key physiological trade-off in an organism's functioning and life history. While theorists have adopted RA schedules as an elegant connection between life history and energy allocation, little is known about RA schedules in real vegetation.\nC_LIO_LIHere we review what is known about RA schedules for woody plants using studies either directly quantifying RA, or which collected data from which the shape of an RA schedule can be inferred.\nC_LIO_LIWe find that RA schedules vary considerably across species: some species abruptly shift all resources from growth to reproduction (the \"big-bang\" strategy); most others gradually shift resources into reproduction, but under a variety of graded schedules (\"partial bang\", \"asymptotic\", \"gradual\", and \"declining\"). Available data suggest the maximum fraction of energy allocated to production ranges from 0.1 to 1 and that shorter-lived species have higher initial RA and increase their RA more quickly than do longer-lived species.\nC_LIO_LI Synthesis Available data suggests a wide variety of RA schedules exist among plant species. The collection of more data on RA, and not only on easy-to-measure proxies such as maximum height, would enable a tighter integration between theory and observation in plant ecology.\nC_LI

Ecology↗

bioRxiv2015

DYNAMICS OF AN EXPANDING BLACK RHINOCEROS (Diceros bicornis minor) POPULATION

Population dynamics is a central component of demography and critical for meta-population management, especially of endangered species. We employed complete individual life records to construct census data for a reintroduced black rhinoceros population over 22 years from its founding and investigated that populations dynamics to inform black rhinoceros meta-population management practice and, more generally, megaherbivore ecology. Akaikes information criterion applied to scalar models of population growth based on the generalized logistic unambiguously selected an exponential growth model (r = 0.102 {+/-} 0.017), indicating a highly successful reintroduction, but yielding no evidence of density dependence. This result is consistent with, but does not confirm, the threshold model of density dependence that has influenced black rhinoceros meta-population management. Our analysis did support previous work contending that the generalized logistic is unreliable when fit to data that do not sample the entire range of possible population sizes. A stage-based matrix model of the exponential population dynamics exhibited mild transient behaviour. We found no evidence of environmental stochasticity, consistent with our previous studies of this population that found no influence of rainfall on demographic parameters. Process noise derived from demographic stochasticity, principally reflected in annual sex-specific recruitment numbers that differed from deterministic predictions of the matrix model. Demographically driven process noise should be assumed to be a component of megaherbivore population dynamics, as these populations are typically relatively small, and should be considered in managed removals and introductions. We suggest that an extended period of exponential growth is common for megaherbivore populations growing from small size and that an increase in age at first reproduction with increasing population size, manifest in the study population, may provide a warning of density feedback prior to detectable slowing of population growth rate for megaherbivores.

Ecology↗

bioRxiv2015

Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management

Animal migrations provide important ecological functions and can allow for increased biodiversity through habitat and niche diversification. However, aquatic migrations in general, and those of the worlds largest fish in particular, are imperiled worldwide and are often poorly understood. Several species of large Amazonian catfish carry out some of the longest freshwater fish migrations in the world, travelling from the Amazon River estuary to the Andes foothills. These species are important apex predators in the main stem rivers of the Amazon Basin and make up the regions largest fishery. They are also the only species to utilize the entire Amazon Basin to complete their life cycle. Studies indicate both that the fisheries may be declining due to overfishing, and that the proposed and completed dams in their upstream range threaten spawning migrations. Despite this, surprisingly little is known about the details of these species migrations, or their life history. Otolith microchemistry has been an effective method for quantifying and reconstructing fish migrations worldwide across multiple spatial scales and may provide a powerful tool to understand the movements of Amazonian migratory catfish. Our objective was to describe the migratory behaviors of the three most populous and commercially important migratory catfish species, Dourada (Brachyplatystoma rousseauxii), Piramutaba (Brachyplatystoma vaillantii), and Piraiba (Brachyplatystoma filamentosum). We collected fish from the mouth of the Amazon River and the Central Amazon and used strontium isotope signatures (87Sr/86Sr) recorded in their otoliths to determine the location of early rearing and subsequent. Fish location was determined through discriminant function classification, using water chemistry data from the literature as a training set. Where water chemistry data was unavailable, we successfully in predicted 87Sr/86Sr isotope values using a regression-based approach that related the geology of the upstream watershed to the Sr isotope ratio. Our results provide the first reported otolith microchemical reconstruction of Brachyplatystoma migratory movements in the Amazon Basin. Our results indicate that juveniles exhibit diverse rearing strategies, rearing in both upstream and estuary environments. This contrasts with the prevailing understanding that juveniles rear in the estuary before migrating upstream; however it is supported by some fisheries data that has indicated the presence of alternate spawning and rearing life-histories. The presence of alternate juvenile rearing strategies may have important implications for conservation and management of the fisheries in the region.

Ecology↗

bioRxiv2015

Environmental DNA reveals that rivers are conveyer belts of biodiversity information

DNA sampled from the environment (eDNA) is becoming a game changer for uncovering biodiversity patterns. By combining a conceptual model and empirical data, we test whether eDNA transported in river networks can be used as an integrative way to assess eukaryotic biodiversity for broad spatial scales and across the land-water interface. Using an eDNA metabarcode approach we detected 296 families of eukaryotes, spanning 19 phyla across the catchment of a river. We show for a subset of these families that eDNA samples overcome spatial autocorrelation biases associated with classical community assessments by integrating biodiversity information over space. Additionally, we demonstrate that many terrestrial species can be detected; thus revealing that eDNA in river-water also incorporates biodiversity information across terrestrial and aquatic biomes. Environmental DNA transported in river networks offers a novel and spatially integrated way to assess total biodiversity for whole landscapes and will transform biodiversity data acquisition in ecology.\n\n\"Eventually, all things merge into one, 32 and a river runs through it.\" -- Norman Maclean

Ecology↗

bioRxiv2015

Re-examining the relationship between virus and microbial cell abundances in the global oceans

Marine viruses are critical drivers of ocean biogeochemistry and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 108 per ml. Over many years, a consensus has emerged that virus abundances are typically 10-fold higher than prokaryote abundances. The use of a fixed-ratio suggests that the relationship between virus and prokaryote abundances is both predictable and linear. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5671 prokaryote and virus abundance estimates from 25 distinct marine surveys to characterize the relationship between virus and prokaryote abundances. We find that the median virus-to-prokaryote ratio (VPR) is 10:1 and 16:1 in the near-and sub-surface oceans, respectively. Nonetheless, we observe substantial variation in the VPR and find either no or limited explanatory power using fixed-ratio models. Instead, virus abundances are better described as nonlinear, power-law functions of prokaryote abundances - particularly when considering relationships within distinct marine surveys. Estimated power-laws have scaling exponents that are typically less than 1, signifying that the VPR decreases with prokaryote density, rather than remaining fixed. The emergence of power-law scaling presents a challenge for mechanistic models seeking to understand the ecological causes and consequences of marine virus-microbe interactions. Such power-law scaling also implies that efforts to average viral effects on microbial mortality and biogeochemical cycles using \"representative\" abundances or abundance-ratios need to be refined if they are to be utilized to make quantitative predictions at regional or global ocean scales.

Ecology↗

bioRxiv2015

Phylogenetic community structure metrics and null models: a review with new methods and software

Competitive exclusion and habitat filtering are believed to have an important influence on the assembly of ecological communities, but ecologists and evolutionary biologists have not reached a consensus on how to quantify patterns that would reveal the action of these processes. No fewer than 22 phylogenetic community structure metrics and nine null models can be combined, providing 198 approaches to test for such patterns. Choosing statistically appropriate approaches is currently a daunting task. First, given random community assembly, we assessed similarities among metrics and among null models in their behavior across communities varying in species richness. Second, we developed spatially explicit, individual-based simulations where communities were assembled either at random, by competitive exclusion or by habitat filtering. Third, we quantified the performance (type I and II error rates) of all 198 approaches against each of the three assembly processes. Many metrics and null models are functionally equivalent, more than halving the number of unique approaches. Moreover, an even smaller subset of metric and null model combinations is suitable for testing community assembly patterns. Metrics like mean pairwise phylogenetic distance and phylogenetic diversity were better able to detect simulated community assembly patterns than metrics like phylogenetic abundance evenness. A null model that simulates regional dispersal pressure on the community of interest outperformed all others. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance. The package is programmed in parallel to readily accommodate integration of new row-wise matrix calculations (metrics) and matrix-wise randomizations (null models) to generate expectations and quantify error rates of proposed methods.

Ecology↗

bioRxiv2015

Recent Greater Sage Grouse (Centrocercus urophasianus) Population Dynamics in Wyoming Are Primarily Driven by Climate, not Oil and Gas Development

BackgroundSpatial scale is important when studying ecological processes. The Greater sage-grouse (Centrocercus urophasianus) is a large sexually dimorphic tetraonid that is endemic to the sagebrush biome of western North America. The impacts of oil and gas development at individual leks has been well-documented. However, no previous studies have quantified the population-level response.\n\nMethodsHierarchical models were used to estimate the effects of the areal disturbance due to well pads as well as climatic variation on individual lek counts and Greater sage-grouse populations (management units) over 32 years. The lek counts were analyzed using General Linear Mixed Models while the management units were analyzed using Gompertz Population Dynamic Models. The models were fitted using frequentist and Bayesian methods. An information-theoretic approach was used to identify the most important spatial scale and time lags. The relative importance of oil and gas and climate at the local and population-level scales was assessed using information-theoretic (Akaikes weights) and estimation (effect size) statistics.\n\nResultsAt the local scale, oil and gas was an important negative predictor of the lek count. At the population scale, there was only weak support for oil and gas as a predictor of density changes but the estimated impacts on the long-term carrying capacity were consistent with summation of the local impacts. Regional climatic variation, as indexed by the Pacific Decadal Oscillation, was an important positive predictor of density changes at both the local and population-level (particularly in the most recent part of the time series).\n\nConclusionsAdditional studies to reduce the uncertainty in the range of possible effects of oil and gas at the population scale are required. Wildlife agencies need to account for the effects of regional climatic variation when managing sage-grouse populations.

Ecology↗

bioRxiv2015

Aquatic insects of a lowland rainforest in Papua New Guinea: assemblage structure in relation to habitat type

Papua New Guinea is one of the most valuable tropical regions but ecological research of its freshwater invertebrates has been lacking. The goal of this paper is to evaluate the species richness, diversity and structure of aquatic insect assemblages in different habitats in the Wanang River catchment in a well-preserved lowland rainforest. Assemblage structure was studied on two spatial scales - in different habitats (river, streams and stagnant pools) and in three mesohabitats in the river (slow and fast sections and submerged wood). The results show that headwater streams had the highest morphospecies diversity, while the river had the highest insect abundance. Slow and fast sections of the river differed both in terms of insect abundance and diversity. Furthermore, a number of unique wood-associated species was found on submerged wood. The most notable feature of the assemblage structure was scarcity of shredders and dominance of predators. However, predatory beetles, bugs and dragonfly larvae exhibited contrasting habitat preferences. This study shows that Papua New Guinean lowland rainforests host diverse and distinctly structured freshwater insect assemblages.

Ecology↗

bioRxiv2015

Within and among-population variation in vital rates and population dynamics in a variable environment

Understanding the causes of within-and among-population differences in vital rates, life histories, and population dynamics is a central topic in ecology. To understand how within-and among-population variation emerges, we need long-term studies that include episodic events and contrasting environmental conditions, data to characterize individual and shared variation, and statistical models that can tease apart population-, shared-, and individual contribution to the observed variation.\n\nWe used long-term tag-recapture data and novel statistical and modeling techniques to investigate and estimate within-and among-population differences in vital rates, life histories and population dynamics of marble trout Salmo marmoratus, a endemic freshwater salmonid with a narrow range. Only ten populations of pure marble trout persist in headwaters of Alpine rivers in western Slovenia. Marble trout populations are also threatened by floods and landslides, which have caused the extinction of two populations in recent years. We estimated and determined causes of variation in growth, survival, and recruitment both within and among populations, and evaluated trade-offs between them. Specifically, we estimated the responses of these traits to variation in water temperature, density, sex, early life conditions, and the occurrence of extreme climatic events (e.g., flash floods and debris flows).\n\nWe found that the effects of population density on traits were mostly limited to the early stages of life and that individual growth trajectories were established early in life. We found no clear effects of water temperature on survival and recruitment. Population density varied over time, with flash floods and debris flows causing massive mortalities and threatening population persistence. Apart from flood events, variation in population density within streams was largely determined by variation in recruitment, with survival of older fish being relatively constant over time within populations, but substantially different among populations. Marble trout show a fast-to-slow continuum of life histories, with slow growth associated with higher survival at the population level, possibly determined by food conditions and age at maturity.\n\nOur work provides unprecedented insight into the causes of variation in vital rates, life histories, and population dynamics in an endemic species that is teetering on the edge of extinction.

Ecology↗

bioRxiv2015

The Abundance of Large Piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland

BackgroundFerox Trout are large, long-lived piscivorous Brown Trout (Salmo trutta). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However, despite their recreational and theoretical importance, little is known about the typical abundance of Ferox Trout.\n\nMethodsTo rectify this situation a 16 year angling-based mark-recapture study was conducted on Loch Rannoch, which at 19 km2 is one of the largest lakes in the United Kingdom.\n\nResultsA hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual differences in catchability are negligible the population of Ferox Trout in Loch Rannoch in 2009 was approximately 71 fish. The results also suggest that a single, often unaccompanied, highly-experienced angler was able to catch roughly 8% of the available fish on an annual basis.\n\nDiscussionIt is recommended that anglers adopt a precautionary approach and release all trout with a fork length [≥] 400 mm caught by trolling in Loch Rannoch. There is an urgent need to assess the status of Ferox Trout in other lakes.

Ecology↗

bioRxiv2015

Species sorting along a subsidy gradient alters community stability

The movement of resources between terrestrial and aquatic habitats has strong effects on ecological processes in recipient ecosystems. Allochthonous inputs modify the quality and quantity of the available resource pool in ways that may alter the composition and stability of recipient communities. Inputs of terrestrial dissolved organic carbon (tDOC) into aquatic ecosystems represent a large influx of resources that has the potential to affect local communities, especially microorganisms. To evaluate the effects terrestrial inputs on aquatic microbial community composition and stability, we manipulated the supply rate of tDOC to a set of experimental ponds. Along the tDOC supply gradient, we measured changes in diversity and taxon-specific changes in abundance and activity. We then determined community stability by perturbing each pond using a pulse of inorganic nutrients and measuring changes in composition and activity (i.e., responsiveness) along the gradient. Terrestrial DOC supply significantly altered the composition of the active microbial community. The composition of the active bacterial community changed via decreases in richness and evenness as well as taxon-specific changes in abundance and activity indicating species sorting along the gradient. Likewise, the responsiveness of the active bacterial community decreased along the gradient, which led to a more stable active community. We did not, however, observe these changes in diversity and stability in the total community (i.e., active and inactive organisms), which suggests that tDOC supply modifies microbial community stability through functional not structural changes. Together, these results show that altered aquatic terrestrial linkages can have profound effects on the activity and stability of the base of the food web and thus can alter ecosystem functioning.

Ecology↗

bioRxiv2015

Trait evolution in adaptive radiations: modelling and measuring interspecific competition on phylogenies

The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that includes interspecific competition amongst species. Competition is modelled as a tendency of sympatric species to evolve towards distinct niches, producing trait overdispersion and high phylogenetic signal. The model predicts elevated trait variance across species and a slowdown in evolutionary rate both across the clade and within each branch. The model also predicts a reduction in correlation between otherwise correlated traits. We used an Approximate Bayesian Computation (ABC) approach to estimate model parameters. We tested the power of the model to detect deviations from Brownian trait evolution using simulations, finding reasonable power to detect competition in sufficiently large (20+ species) trees. We applied the model to examine the evolution of bill morphology of Darwins finches, and found evidence that competition affects the evolution of bill length.

Ecology↗