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bioRxiv2018

Haemolymph removal by the parasite Varroa destructor can trigger the proliferation of the Deformed Wing Virus in mite infested bees (Apis mellifera), contributing to enhanced pathogen virulence

The association between the Deformed Wing Virus and the parasitic mite Varroa destructor has been identified as a major cause of worldwide honey bee colony losses. The mite acts as a vector of the viral pathogen and can trigger its replication in infected bees. However, the mechanistic details underlying this tripartite interaction are still poorly defined, and, in particular, the causes of viral proliferation in mite infested bees.\n\nHere we develop and test a novel hypothesis - grounded in ecological predator-prey theory - that mite feeding destabilizes viral immune control through the removal of both viral prey and immune predators, triggering uncontrolled viral replication. Consistent with this hypothesis, we show that experimental removal of increasing volumes of haemolymph from individual bees results in increasing viral densities. In contrast, we find no support for alternative proposed mechanisms of viral expansion via mite immune-suppression or within-host viral evolution.\n\nOverall, these results provide a new model for the mechanisms driving pathogen-parasite interactions in bees, which ultimately underpin honey bee health decline and colony losses.

ecology↗
bioRxiv2018

Caterpillars Count! A citizen science project for monitoring foliage arthropod abundance and phenology

Caterpillars Count! is a citizen science project that allows participants to collect data on the seasonal timing, or phenology, of foliage arthropods that are important food resources for forest birds. This project has the potential to address questions about the impacts of climate change on birds over biogeographic scales. Here, we provide a description of the projects two survey protocols, evaluate the impact of survey methodology on results, compare findings made by citizen scientist participants versus trained scientists, and identify the minimum levels of sampling frequency and intensity in order to accurately capture phenological dynamics. We find that beat sheet surveys and visual surveys yield similar relative and absolute density estimates of different arthropod groups, with beat sheet surveys recording a higher frequency of beetles and visual surveys recording a higher frequency of flies. Citizen scientists generated density estimates within 6% of estimates obtained by trained scientists regardless of survey method. However, patterns of phenology were more consistent between citizen scientists and trained scientists when using beat sheet surveys than visual surveys. By subsampling our survey data, we found that conducting 30 foliage surveys on a weekly basis led to 95% of peak caterpillar date estimates to fall within one week of the \"true\" peak. We demonstrate the utility of Caterpillars Count! for generating a valuable dataset for ecological research, and call for future studies to evaluate how training and resource materials impact data quality and participant learning gains.

ecology↗
bioRxiv2018

Using movement data to estimate contact rates in a simulated environmentally-transmitted disease system

Agent-based models have become important tools in ecology, particularly in the study of infectious disease dynamics. Simulations of near-continuous movement paths guided by empirical data offer new avenues of investigation into disease transmission. Here, we simulate the spatiotemporal transmission dynamics of anthrax, the acute disease caused by the bacterium Bacillus anthracis, a pathogen transmitted primarily via environmental reservoirs. We explore how calculations of the probabilities of contact between a host and infectious reservoirs are affected by the scale and method of analysis. At both the landscape and individual scales, empirical movement tracks offer previously unattainable estimates of impacts of movement decisions on contact rate metrics. However, the analytical method selected for the calculation of the probability of contact has notable impacts on the resulting estimates, with convex polygons virtually canceling out variation, and unions of local convex hulls (LoCoH methods) and space-time prisms reflecting reasonable variation, but differing in the magnitude of their estimates. The explicit consideration of behavioral states along movement pathways also impacts evaluations of exposure risk, though its effects differ across methods of analysis. Ultimately, simulations demonstrate that the incorporation of movement data into pathogen transmission analyses helps clarify the role of movement processes underlying the observed dynamics of infectious disease.

ecology↗
bioRxiv2018

Competition and immigration lead to clusters of similar species, not trait separation

Patterns of trait distribution among competing species can potentially reveal the processes that allow them to coexist. It has been recently proposed that competition may drive the spontaneous emergence of niches comprising clusters of similar species, in contrast with the dominant paradigm of greater-than-chance species differences. However, current clustering theory relies largely on heuristic rather than mechanistic models. Furthermore, studies of models incorporating demographic stochasticity and immigration, two key players in community assembly, did not observe clusters. Here we demonstrate clustering under partitioning of resources, partitioning of environmental gradients, and a competition-colonization tradeoff. We show that clusters are robust to demographic stochasticity, and can persist under immigration. While immigration may sustain clusters that are otherwise transient, too much dilutes the pattern. In order to detect and quantify clusters in nature, we introduce and validate metrics which have no free parameters nor require arbitrary trait binning, and weigh species by their abundances rather than relying on a presence-absence count. By generalizing beyond the circumstances where clusters have been observed, our study contributes to establishing them as an update to classical trait patterning theory.\n\nAuthor SummarySpecies traits determine how they compete with each other. As such, patterns in the distributions of traits in a community of competing species may reveal the processes responsible for coexistence. One central idea in theoretical ecology is that the strength of competition relates to similarity in species needs and strategies, and therefore if competition plays out at short timescales, coexisting species should be more different than expected by chance. However, recent theory suggests that competition may lead species to temporarily self-organize into groups with similar traits. Here we show that this clustering is a generic feature of competitive dynamics, which is robust to demographic stochasticity and can be indefinitely maintained by immigration. We show that clustering arises whether species coexist by partitioning resources, environmental preferences, or through tradeoffs in life-history strategies. We introduce and validate metrics that, given species traits and abundances, determine whether they are clustered, and if so, how many clusters occur. By showing the generality of self-organized species clusters and providing a tools for their detection, our study contributes to updating classical ideas about how competition shapes communities, and motivates searches for them in nature.

ecology↗
bioRxiv2018

Homogenization of species composition and species association networks are decoupled

Ecological communities are comprised of both species and the biotic relationships among them. Biotic homogenization in species composition (i.e. increased site-to-site similarity) is recognized a common consequence of global change, but less is known about how species relationships change over space and time. Does homogenization of species composition lead to homogenization of species relationships or are the dynamics of species relationships decoupled from changes in species composition? To answer this question, we used long-term resurvey data to analyze changes in plant species association patterns between the 1950s and 2000s at 266 sites distributed among three community types in Wisconsin, USA. We used species associations (quantified via local co-occurrence patterns) as a proxy for species relationships. Species pairs that co-occur more/less than expected by chance have positive/negative associations. Shifts in species associations consistently exceeded the shifts observed in species composition. Less disturbed forests of northern Wisconsin have converged somewhat in species composition but not much in species associations. In contrast, forests in central Wisconsin succeeding from pine barrens to closed-canopy forests have strongly homogenized in both species composition and species associations. More fragmented forests in southern Wisconsin also tended to converge in species composition and in the species negative associations, but their positive associations diverged over the last half century. We conclude that long-term shifts in species relationships may be decoupled from those of species composition despite being affected by similar environmental variables.

ecology↗
bioRxiv2018

Spatial Capture-Recapture for Categorically Marked Populations with An Application to Genetic Capture-Recapture

Recently introduced unmarked spatial capture-recapture (SCR), spatial mark-resight (SMR), and 2-flank spatial partial identity models (SPIM) extend the domain of SCR to populations or observation systems that do not always allow for individual identity to be determined with certainty. For example, some species do not have natural marks that can reliably produce individual identities from photographs, and some methods of observation produce partial identity samples as is the case with remote cameras that sometimes produce single flank photographs. These models share the feature that they probabilistically resolve the uncertainty in individual identity using the spatial location where samples were collected. Spatial location is informative of individual identity in spatially structured populations with home range sizes smaller than the extent of the trapping array because a latent identity sample is more likely to have been produced by an individual living near the trap where it was recorded than an individual living further away from the trap. Further, the level of information about individual identity that a spatial location contains is determined by two key ecological concepts, population density and home range size. The number of individuals that could have produced a latent or partial identity sample increases as density and home range size increase because more individual home ranges will overlap any given trap. We show this uncertainty can be quantified using a metric describing the expected magnitude of uncertainty in individual identity for any given population density and home range size, the Identity Diversity Index (IDI). We then show that the performance of latent and partial identity SCR models varies as a function of this index and produces imprecise and biased estimates in many high IDI scenarios when data are sparse. We then extend the unmarked SCR model to incorporate partially identifying covariates which reduce the level of uncertainty in individual identity, increasing the reliability and precision of density estimates, and allowing reliable density estimation in scenarios with higher IDI values and with more sparse data. We illustrate the performance of this \"categorical SPIM\" via simulations and by applying it to a black bear data set using microsatellite loci as categorical covariates, where we reproduce the full data set estimates with only slightly less precision using fewer loci than necessary for confident individual identification. The categorical SPIM offers an alternative to using probability of identity criteria for classifying genotypes as unique, shifting the \"shadow effect\", where more than one individual in the population has the same genotype, from a source of bias to a source of uncertainty. We discuss the difficulties that real world data sets pose for latent identity SCR methods, most importantly, individual heterogeneity in detection function parameters, and argue that the addition of partial identity information reduces these concerns. We then discuss how the categorical SPIM can be applied to other wildlife sampling scenarios such as remote camera surveys, where natural or researcher-applied partial marks can be observed in photographs. Finally, we discuss how the categorical SPIM can be added to SMR, 2-flank SPIM, or other future latent identity SCR models.

ecology↗
bioRxiv2018

Predicting The Effects Of Hemlock Woolly Adelgid On Microhabitat Structure And Small Mammal Communities

Hemlock woolly adelgid (HWA) invasion and preemptive logging practices alter the habitat structure of New England forests and may indirectly affect associated small mammal communities. Microhabitat structure was measured and small mammals were censused in eight large experimental plots to quantify and predict these effects. The Harvard Forest Long-Term Ecological Research experiment is a replicated two-block design that includes four 0.81-ha canopy treatments: 1) Hemlock Control, 2) Hardwood Control, 3) Girdled Treatment, in which hemlock trees were killed by girdling in 2005 and left standing to simulate HWA invasion, and 4) Logged Treatment, in which trees were removed to simulate preemptive logging management practices. Nine microhabitat characteristics were measured from plot photos revealing differences among microhabitat structure. Small mammals were censused with arrays of 49 Sherman traps per plot and population sizes of common species were estimated with mark-recapture analysis. Between 6 and 8 mammal species were recorded in all treatments and species composition varied slightly. Populations of two common rodents (Peromyscus spp.) were not affected by treatment, but the southern red-backed vole population was greatest in the Girdled treatment. Estimated species richness was greater in the Girdled treatment than the Hemlock control, but richness did not differ between Girdled and Logged treatments, which suggests preemptive logging is as detrimental to some small mammal species as HWA invasion. Overall, nine years post disturbance, there is little evidence of a major shift in small mammal community structure in response to woolly adelgid invasion, with only minor changes in relative abundance.

ecology↗
bioRxiv2018

Market Smells: Olfactory Detection and Identification in the Built Environment

ObjectivesWe know little about human olfactory ability in natural settings because current knowledge derives from lab-based studies using non-representative samples of convenience. The primary objective was to use a validated lab tool, the five-item odor identification test, to assess variation in olfactory ability in different environments. MethodsUsing the five-item test, we conducted two repeated measures experiments that assessed participant ability to correctly identify an odor source in different odor environments. We also examined consistency in odor labelling due to documented potential bias from idiosyncrasies in odor terms. ResultsWe found no variation in olfactory ability due to environment, but this may be due to methodological biases. First, subjective bias results from idiosyncratic differences in participant labelling and researcher coding of answer correctness. Second, better ability to learn odors may provide an advantage to women. Third, reducing positive female learning bias by analyzing consistency in response (regardless of correct odor source identification) fails to assess functional olfactory ability. Functional olfactory ability (naming correct odor source) is significantly better in females, especially in food-rich odor environments. ConclusionsEnvironment was not a significant factor in olfactory ability in this study but that result may be confounded by methodological biases. We not recommend odor identification as a field tool. Functional olfactory ability exhibits a sex-based pattern but consistency in recognizing the same odor does not. Food-rich odors may enhance olfactory ability in females. We discuss evolutionary and ecological implications of superior female functional olfactory ability relative to food foraging activity.

ecology↗
bioRxiv2018

The dynamic tumor ecosystem: how cell turnover and trade-offs affect cancer evolution

AO_SCPCAPBSTRACTC_SCPCAPTumors are not static masses of cells but rather dynamic ecosystems where cancer cells experience constant turnover and evolve fitness-enhancing phenotypes. Selection for different phenotypes may vary with 1) the tumor niche (edge or core), 2) cell turnover rates, 3) the nature of the tradeoff between traits (proliferation vs migration), and 4) whether deaths occur in response to demographic or environmental stochasticity. In an agent based, spatially-explicit model, we observe how two traits (proliferation rate and migration speed) evolve under different trade-off conditions with different turnover rates. Migration rate is favored over proliferation at the tumors edge and vice-versa for the interior. Increasing cell turnover rates only slightly slows the growth of the tumor, but accelerates the rate of evolution for both proliferation and migration. The absence of a tradeoff favors ever higher values for proliferation and migration. A convex tradeoff tends to favor proliferation over migration while often promoting the coexistence of a generalist and specialist phenotype. A concave tradeoff slows the rate of evolution, and favors migration at low death rates and proliferation at higher death rates. Mortality via demographic stochasticity favors proliferation at the expense of migration; and vice-versa for environmental stochasticity. All of these factors and their interactions contribute to the ecology of the tumor, tumor heterogeneity, trait evolution, and phenotypic variation. While diverse, these effects may be predictable and empirically accessible.

ecology↗
bioRxiv2018

Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage

Coral-dinoflagellate symbiosis is the key biological interaction enabling existence of modern-type coral reefs, but the mechanisms regulating initial host-symbiont attraction, recognition and symbiont proliferation thus far remain largely unclear. A common reef-building coral, Acropora millepora, displays conspicuous fluorescent polymorphism during all phases of its life cycle, due to the differential expression of fluorescent proteins (FPs) of the green fluorescent protein family. In this study, we examine whether fluorescent variation in young coral juveniles exposed to natural sediments is associated with the uptake of disparate Symbiodinium assemblages determined using ITS-2 deep sequencing. We found that Symbiodinium assemblages varied significantly when redness values varied, specifically in regards to abundances of clades A and C. Whether fluorescence was quantified as a categorical or continuous trait, clade A was found at higher abundances in redder juveniles. These preliminary results suggest juvenile fluorescence may be associated with Symbiodinium uptake, potentially acting as either as an attractant to ecologically specific types or as a mechanism to modulate the internal light environment to control Symbiodinium physiology within the host.

ecology↗
bioRxiv2018

Worldwide cross-ecosystem carbon subsidies and their contribution to ecosystem functioning

Ecosystems are widely inter-connected by spatial flows of resources1,2, yet primarily studied in a local context. Meta-ecosystem models suggest that cross-ecosystem subsidies can play an essential role in ecosystem functioning, notably by controlling local availability of resources for biological communities3-6. The general contribution of these resource connections to ecosystem functioning, however, remains unclear in natural systems, due to the heterogeneity and dispersion of data across the ecological literature. Here we provide the first quantitative synthesis on spatial flows of carbon connecting ecosystems worldwide. These cross-ecosystem subsidies range over eight orders of magnitude, between 10-3 and 105 gC m-2 yr-1, and are highly diverse in their provenance. We found that spatial carbon flows and local carbon fluxes are of the same order of magnitudes in freshwater and benthic ecosystems, suggesting an underlying dependency of these systems on resources provided by connected terrestrial and pelagic ecosystems respectively. By contrast, in terrestrial systems, cross-ecosystem subsidies were two to three orders of magnitude lower than local production (grasslands and forests), indicating a weaker quantitative influence on functioning. Those subsidies may still be qualitatively important, however, as some have high nutrient content7,8. We also find important gaps in carbon flow quantification, notably of cross-ecosystem subsidies driven by animal movements, which likely leads to general underestimations of the magnitude and direction of cross-ecosystem linkages9. Overall, we demonstrate strong ecosystem couplings, suggesting that ecosystems can be vulnerable to alterations of these flows and pointing to an urgent need to re-think ecosystem functioning in a spatial perspective.

ecology↗
bioRxiv2018

Does Borrelia burgdorferi sensu lato facilitate the colonisation of marginal habitats by Ixodes ricinus? A correlative study in the Swiss Alps

Parasites can alter host and vector phenotype and thereby affect ecological processes in natural populations. Laboratory studies have shown that Borrelia burgdorferi sensu lato, the causative agent of human Lyme borreliosis, induces physiological alterations in its main tick vector in Europe, Ixodes ricinus, which increase its survival under challenging conditions. We hypothesise that these phenotypic alterations may allow I. ricinus to colonise marginal habitats, thereby fuelling the ongoing range expansion of I. ricinus towards higher elevations and latitudes induced by climate change. To explore the potential for such an effect under natural conditions, we studied the prevalence of B. burgdorferi s.l. in questing I. ricinus and its variation with elevation in the Swiss Alps. We screened for B. burgdorferi s.l. infection in questing nymphs of I. ricinus (N = 411) from 15 sites between 528 and 1774 m.a.s.l to test if B. burgdorferi s.l. prevalence is higher at high elevations (i.e. in marginal habitats). We found that B. burgdorferi s.l. prevalence in I. ricinus nymphs decreased linearly with increasing elevation and that it was 12.6% lower in I. ricinus nymphs collected at high elevations compared to nymphs in the core range. Thus, we found no evidence that the B. burgdorferi s.l.-induced alterations of I. ricinus phenotype facilitate the colonisation of marginal habitats in the wild. These findings have implications for a better understanding of eco-evolutionary processes in natural host-parasite systems, as well as the assessment of Lyme borreliosis risk in regions where I. ricinus is newly emerging.

ecology↗
bioRxiv2018

How optimal foragers should respond to habitat changes? On the consequences of habitat conversion.

The Marginal Value Theorem (MVT) provides a framework to predict how habitat modifications related to the distribution of resources over patches should impact the realized fitness of individuals and their optimal rate of movement (or patch residence times) across the habitat. Most MVT theory has focused on the consequences of changing the shape of the gain functions in some patches, describing for instance patch enrichment. However an alternative form of habitat modification is habitat conversion, whereby patches are converted from one existing type to another (e.g. closed habitat to open habitat). In such a case the set of gain functions existing in the habitat does not change, only their relative frequencies does. This has received comparatively very little attention in the context of the MVT. Here we analyze mathematically the consequences of habitat conversion under the MVT. We study how realized fitness and the average rate of movement should respond to changes in the frequency distribution of patch-types, and how they should covary. We further compare the response of optimal and non-plastic foragers. We find that the initial pattern of patch-exploitation in a habitat, characterized by the regression slope of patch yields over residence times, can help predict the qualitative responses of fitness and movement rate following habitat conversion. We also find that for some habitat conversion patterns, optimal and non-plastic foragers exhibit qualitatively different responses, and that adaptive foragers can have opposite responses in the early and late phases following habitat conversion. We suggest taking into account behavioral responses may help better understand the ecological consequences of habitat conversion.

ecology↗
bioRxiv2018

Metabolic adjustment enhances food web stability

Understanding ecosystem stability is one of the greatest challenges of ecology. Over several decades, it has been shown that allometric scaling of biological rates and feeding interactions provide stability to complex food web models. Moreover, introducing adaptive responses of organisms to environmental changes (e.g. like adaptive foraging that enables organisms to adapt their diets depending on resources abundance) improved species per-sistence in food webs. Here, we introduce the concept of metabolic adjustment, i.e. the ability of species to slow down their metabolic rates when facing starvation and to increase it in time of plenty. We study the reactions of such a model to nutrient enrichment and the adjustment speed of metabolic rates. We found that increasing nutrient enrichment leads to a paradox of enrichment (increase in biomasses and oscillation amplitudes and ultimately extinction of species) but metabolic adjustment stabilises the system by dampening the oscillations. Metabolic adjustment also increases the average biomass of the top predator in a tri-trophic food chain. In complex food webs, metabolic adjustment has a stabilising effect as it promotes species survival by creating a large diversity of metabolic rates. However, this stabilising effect is mitigated in enriched ecosystems. Phenotypic plasticity of organisms must be considered in food web models to better understand the response of organisms to their environment. As metabolic rate is central in describing biological rates, we must pay attention to its variations to fully understand the population dynamics of natural communities.

ecology↗
bioRxiv2018

Microhabitat Heterogeneity Promotes Partition of Resources by Syntopic Peromyscus in a Midlatitude Temperate Forest

One of the basics and fundamentals problems in ecology is understand the factors that shape the spatial patterns in the distribution of the species and the coexistence of close relatives species. Among the most important factors governing the distributions and the coexistence of species are the spatiotemporal changes occurring in the microhabitat heterogeneity. Here, we assessed the heterogeneity of microhabitats and how they have an effect in the spatial segregation of two species of small mammals (i. e., Peromyscus difficilis and P. melanotis), which coexist in a temperate, mixed forest. We evaluated the microhabitat heterogeneity through multivariate statistics, using onto 23 habitat variables for vertical-horizontal habitat structure along pluvial seasons. To detect specific microdistribution changes and habitat preferences by two species of small mammals, we used second order spatial statistics and general linear models. According to their respective morphology and locomotive adaptations, the middle sized, midscansorial P. difficilis was resident all year long and preferred microhabitats with a high log ground cover, while the opportunistic, small sized, cursorial P. melanotis changed its occupancy area, depending on density of herbaceous and woody plants cover. Under the more benign microhabitat conditions of rainy season (denser plant coverage, milder temperature), both species showed closer microdistribution patterns; while these became repulsive at the less benign conditions of dry season (scarcer plant cover, colder temperature). Thus, we could confirm that seasonal changes of microhabitat heterogeneity promoted Peromyscus coexistence, through dispersion patterns reflecting partition of microhabitat resources.

ecology↗
bioRxiv2018

Assessing macrophyte seasonal dynamics using dense time series of medium resolution satellite data

Thanks to the improved spatial and temporal resolution of new generation Earth Observation missions, such as Landsat 8 and Sentinel-2, the potential of remote sensing techniques in mapping land surface phenology of terrestrial biomes can now be tested in inland water systems.\n\nWe assessed the capabilities of dense time series of medium resolution satellite data to deliver quantitative information about macrophyte phenology metrics, focusing on three temperate European shallow lakes with connected wetlands, located in Italy, France and Romania.\n\nLeaf area index (LAI) maps for floating and emergent macrophyte growth forms were derived from semi-empirical regression modelling based on the best performing spectral index, with an error level around 0.11 m2 m-2. Phenology metrics were computed from LAI time series using TIMESAT code and used to analyse macrophyte seasonal dynamics in terms of spatial patterns and species-dependent variability. Peculiar patterns of autochthonous and allochthonous species seasonality across the three study areas were related to the environmental characteristics of each area in terms of ecological and hydrological conditions.\n\nIn addition, the influence of satellite dataset characteristics - i.e. cloud cover thresholding, temporal resolution and missing acquisitions - on phenology timing metrics retrieval was assessed. Results have shown that with full resolution (5-day revisit) time series, cloud cover can bias phenology timing metrics by less than 2 days, and that reducing temporal resolution to 15 days (similar to Landsat revisit) still allows for mapping the start and peak of macrophyte growth with an error level around 2-3 days.

ecology↗
bioRxiv2018

Spatial extinction date estimation: a novel method for reconstructing spatiotemporal patterns of extinction and identifying potential zones of rediscovery

O_LIThe estimation of extinction dates from limited and incomplete sighting records is a key challenge in conservation (when experts are uncertain whether a species has gone extinct) and historical ecology (when the date and mechanism of extinction is controversial).\nC_LIO_LIWe introduce a spatially-explicit method of interpolating extinction date estimators, allowing users to estimate spatiotemporal surfaces of population persistence from georeferenced sighting data of variable quality.\nC_LIO_LIWe present the R package spatExtinct, which produces spatially-explicit extinction date surfaces from geolocated sightings, including options for custom randomization schemes to improve accuracy with limited datasets. We use simulations to illustrate the sensitivity of the method to parameterization, and apply the method to identify potential areas where Bachmans warbler (Vermivora bachmanii) might be rediscovered.\nC_LIO_LIOur method, and the spatExtinct package, has the potential to help describe and differentiate different drivers of extinction for historical datasets, and could be used to identify possible regions of population persistence for species with an uncertain extinction status, improving on non-spatial or imprecise methods that are currently in use.\nC_LI

ecology↗
bioRxiv2018

Inter-population variation in the Atlantic salmon microbiome reflects environmental and genetic diversity

Microbial communities have a crucial influence on host phenotype, and are of broad interest to ecological and evolutionary research. Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterised the skin and gut microbiome of seven populations of juvenile Atlantic salmon (Salmo salar) inhabiting a diverse range of environments, including hatchery-reared and wild populations. We found shared skin OTUs across all populations and core gut microbiota for all wild fish, but the diversity and structure of both skin and gut microbial communities were distinct between populations. There was a marked difference between the gut microbiome of wild and captive fish. Hatchery-reared fish had lower intestinal microbial diversity, lacked core microbiota found in wild fish, and showed altered community structure and function. Captive fish skin and gut microbiomes were also less variable within populations, reflecting more uniform artificial rearing conditions. Surrounding water influenced the microbiome of the gut and, especially, the skin, but could not explain the degree of variation observed between populations. For both the gut and the skin, we found that there was greater difference in microbial community structure between more genetically distinct fish populations, and also that population genetic diversity was positively correlated with microbiome diversity. However, dietary differences are likely to be the major factor contributing to the large differences found in the gut microbiome between wild and captive fish. Our results highlight the scope of inter-population variation in the microbiome, and offer insights into the contributing deterministic factors.

ecology↗