SEARCH · Search bioRxiv

Results for “ecology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 793 records · Page 44Linked to original sources

bioRxiv2017

Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat

In the first longitudinal study of bat microbiomes, we find that unlike the pattern described in humans and other mammals, the prominent dynamics in Egyptian fruit bats fur microbiomes are those of change over time at the level of the colony as a whole. Thus, on average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats fur, but differs from the more individualized pattern found in the bats gut microbiome.

ecology↗

bioRxiv2017

The compound topology of a continent-wide host-parasite network explained by an integrative hypothesis of specialization.

Is there a prevalent pattern among interaction networks: nestedness or modularity? Must consumers always trade-off generalism for average performance in resource exploitation? These two questions have been addressed in various systems, with contradictory results. A recent integrative hypothesis combines both questions within a common theoretical framework, proposing that ecological specialization is structured by different prevailing processes in smaller and larger network units. This should produce both a compound interaction network, formed by internally nested modules, and a scale-dependence on the relationship between consumer performance and generalism. Here, we confirm both predictions in a large dataset on host-parasite interactions. We show that modules indeed constrain nestedness at the whole network level, and that the relationship between parasite generalism and performance on their hosts changed from negative at large to positive at small scales. Our results shed light on both debates, and provide some clues to their integration and solution.

ecology↗

bioRxiv2018

Defining the seafloor microbiome of the Gulf of Mexico and its response to oil perturbation

The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in >700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Further, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after two years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.

ecology↗

bioRxiv2017

Quantifying long-term predictability in microbial plankton dynamics

Determining predictability in community turnover is a key ecological question. In the microbial world, seasonality has been reported for communities inhabiting temperate zones, but not much is known on seasonality for individual species. Specifically, we have a vague understanding on the amount of species displaying predictability during temporal community turnover as well as on their dynamics. Here we developed a Recurrence Index to quantify predictability in microbial species. Applying our index to 18S rDNA metabarcoding data from one of the longest temporal observatories of marine plankton we determined that 13% of the picoeukaryotic and 19% of the nanoeukaryotic species, accounting for about 40% of the community abundance in both fractions, feature predictable dynamics when sampled monthly during 10 years. Thus, most of the species analysed had unpredictable temporal abundance patterns. Altogether, we show that species with both predictable and unpredictable temporal dynamics can occur within the same seasonal microbial community.

ecology↗

bioRxiv2017

Diversification, sympatry, and the emergence of mega-diverse tropical assemblages

Geographic gradients in species richness, including latitudinal gradients, can arise from geographic variation in any of three mechanisms: the geologic age of habitats, net rates of evolutionary diversification, or rates of sympatry among diversifying lineages. Here we show that variation in rates of sympatry is a dominant force structuring geographic richness gradients in birds. Species-rich sites contain disproportionately high numbers of recently diverged sympatric species but contain lineages with slower-than-average diversification rates. The positive sympatry-diversity relationship consistently overwhelms the negative diversification-diversity relationship, particularly among high-diversity sites (>250 species). These patterns repeat across biomes and continents with striking regularity, and remain consistent across multiple timescales, including the recent evolutionary past. Biogeographic and evolutionary patterns in birds are consistent with a role for ecological conditions in promoting species coexistence, which allows sister species to co-occur and potentially lowers extinction rates.

ecology↗

bioRxiv2018

Modeling sound attenuation in heterogeneous environments for improved bioacoustic sampling of wildlife populations

Acoustic sampling methods are becoming increasingly important in biological monitoring. Sound attenuation is one of the most important dynamics affecting the utility of bioacoustic data as it directly affects the probability of detection of individuals from bioacoustic arrays and especially the localization of acoustic signals necessary in telemetry studies. Therefore, models of sound attenuation are necessary to make efficient use of bioacoustic data in ecological monitoring and assessment applications. Models of attenuation in widespread use are based on Euclidean distance between source and sensor, which is justified under spherical attenuation of sound waves in homogeneous environments. In some applications there are efforts to evaluate the detection range of sensors in response to local environmental characteristics at the sensor or at sentinel source locations with known environmental characteristics. However, attenuation is a function of the total environment between source and sensor, not just their locations. In this paper I develop a model of signal attenuation based on a non-Euclidean cost-weighted distance metric which contains resistance parameters that relate to environmental heterogeneity in the vicinity of an array. Importantly, these parameters can be estimated by maximum likelihood using experimental data from an array of fixed sources, thus allowing investigators who use bioacoustic methods to devise explicit models of sound attenuation in situ. In addition, drawing on analogy with classes of models known as spatial capture-recapture, I show that parameters of the non-Euclidean model of attenuation can be estimated when source locations are unknown. Thus, the models can be applied to real field studies which require localization of signals in heterogeneous environments.

ecology↗

bioRxiv2017

Competitive release from native range does not predict invasive success of a globally dominant exotic ant species

A major goal of invasion biology is to understand under what conditions exotic species thrive in the introduced range. High competitive abilities are thought to be an important characteristic of exotic species. Most invasion studies focus on the competitive ability of exotic species in the introduced range and attribute their ecological success to competitive release, but fewer studies have compared the relative competitive differences within the native range. These comparative studies are important in order to determine if competitive abilities of exotic species are strong predictors of invasion success. The little fire ant Wasmmnia auropunctata is a highly invasive species that has spread from its original range (Central and South America) to becoming a globally distributed exotic species in recent decades. It is generally accepted that island ecosystems offer weak biotic resistance to exotic species as compared to their native range. Here, we examined this empirically by comparing the relative competitive difference of W. auropunctata and locally dominant ants, between its native range of Mexico and introduced range of Puerto Rico. Resource competition was assessed between W. auropunctata and native ants under field conditions and in the laboratory. Furthermore, we compared resource competition at different temporal intervals ranging from short-term (< 2 hours) to long-term (14-days) dynamics. Our results are in contrast to common invasion predictions on island communities because we show that native species were resistant to W. auropunctata in its introduced range of Puerto Rico. We observed that the ground-foraging ant Solenopsis invicta competitive displaced W. auropunctata in Puerto Rico during short-term experiments. Meanwhile, the native arboreal ant Linepithema iniquum withstood competitive pressure from W. auropunctata. In the native range of Mexico, W. auropunctata was superior against Solenopsis Picea and Pheidole protensa species, but was outcompeted by dominant ants Solenopsis geminata and Pheidole synanthropica. This study challenges the relative importance of competitive ability in predicting invasion success. This is one of the few detailed comparative studies that examines exotic species performance between native and introduced habitats.

ecology↗

bioRxiv2017

Mesophotic Coral Ecosystems Inside and Outside a Caribbean Marine Protected Area

Recent widespread shallow coral reef loss has led to calls for more holistic approaches to coral reef management, requiring inclusion of all ecosystems interacting with coral reefs in management plans. Yet almost all current reef management is biased towards shallow reefs, and overlooks that many reef species can also be found on mesophotic coral ecosystems (MCEs; reefs 30 -150 m). This study presents the first detailed quantitative characterisation of MCEs off Cozumel, in the Mexican Caribbean and provides insights into their general state. We investigate whether MCEs within the marine park have similar ecological communities to mesophotic reefs outside protection, despite widely recognised shallow reef impacts outside the protected area. Results show some taxon specific differences in MCE benthic communities between sites within the protected area and areas outside; although overall communities are similar. Regardless of protection and location, and in contrast to shallow reefs, all observed Cozumel MCEs were continuous reefs dominated by calcareous macroalgae, sponges, octocorals, and black corals. Hard corals were present on MCEs, but at low abundance. We found that 42.5 % of fish species recorded on Cozumel could be found on both shallow reefs and MCEs, including many commercially-important fish species. This suggest that MCEs may play a role in supporting fish populations. However, regardless of protection status and depth we found that large-body fishes (>500 mm) were nearly absent at all studied sites. MCEs should be incorporated into the existing shallow-reef focused management plan in Cozumel, with well informed and implemented fisheries and harvesting regulations.

ecology↗

bioRxiv2018

Coexistence theory and the frequency dependence of priority effects

Priority effects encompass a broad suite of ecological phenomena. Several studies have suggested reframing priority effects around the stabilizing and equalizing concepts of coexistence theory. We show that the only compatible priority effects are those characterized by positive frequency dependence.

ecology↗

bioRxiv2018

Is phylogenetic diversity a surrogate for functional diversity across clades and space?

In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have advocated for a \"phylogenetic gambit\": maximizing phylogenetic diversity (PD) should indirectly capture FD. For the first time, we empirically test this gambit using data from >15,000 vertebrate species and ecologically-relevant traits. Maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain hides the fact that in over 1/3 of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky strategy.\n\nStatement of authorshipFM, MP, MC, SD, GVDR, RG, AOM, CT and WP conceived the design of the study. FM and GVDR conducted the analysis. FM, RG, MP and WP interpreted the results and wrote the first draft of the manuscript. All authors edited the final version.\n\nData accessibility statementMost of the data is publicly available (see methods). The Fish data is available upon request.\n\nCode accessibility statementR functions developed in this paper are available at https://github.com/FloMazel/FD_PD_Max

ecology↗

bioRxiv2018

MoB (Measurement of Biodiversity): a method to separate the scale-dependent effects of species abundance distribution, density, and aggregation on diversity change

O_LILittle consensus has emerged regarding how proximate and ultimate drivers such as productivity, disturbance, and temperature may affect species richness and other aspects of biodiversity. Part of the confusion is that most studies examine species richness at a single spatial scale and ignore how the underlying components of species richness can vary with spatial scale.\nC_LIO_LIWe provide an approach for the measurement of biodiversity (MoB) that decomposes changes in species rarefaction curves into proximate components attributed to: 1) the species abundance distribution, 2) density of individuals, and 3) the spatial arrangement of individuals. We decompose species richness by comparing spatial and nonspatial sample- and individual-based species rarefaction curves that differentially capture the influence of these components to estimate the relative importance of each in driving patterns of species richness change.\nC_LIO_LIWe tested the validity of our method on simulated data, and we demonstrate it on empirical data on plant species richness in invaded and uninvaded woodlands. We integrated these methods into a new R package (mobr).\nC_LIO_LIThe metrics that mobr provides will allow ecologists to move beyond comparisons of species richness in response to ecological drivers at a single spatial scale towards a dissection of the proximate components that determine species richness across scales.\nC_LI

ecology↗

bioRxiv2018

CityNet - Deep Learning Tools for Urban Ecoacoustic Assessment

O_LICities support unique and valuable ecological communities, but understanding urban wildlife is limited due to the difficulties of assessing biodiversity. Ecoacoustic surveying is a useful way of assessing habitats, where biotic sound measured from audio recordings is used as a proxy for biodiversity. However, existing algorithms for measuring biotic sound have been shown to be biased by non-biotic sounds in recordings, typical of urban environments.\nC_LIO_LIWe develop CityNet, a deep learning system using convolutional neural networks (CNNs), to measure audible biotic (CityBioNet) and anthropogenic (CityAnthroNet) acoustic activity in cities. The CNNs were trained on a large dataset of annotated audio recordings collected across Greater London, UK. Using a held-out test dataset, we compare the precision and recall of CityBioNet and CityAnthroNet separately to the best available alternative algorithms: four acoustic indices (AIs): Acoustic Complexity Index, Acoustic Diversity Index, Bioacoustic Index, and Normalised Difference Soundscape Index, and a state-of-the-art bird call detection CNN (bulbul). We also compare the effect of non-biotic sounds on the predictions of CityBioNet and bulbul. Finally we apply CityNet to describe acoustic patterns of the urban soundscape in two sites along an urbanisation gradient.\nC_LIO_LICityBioNet was the best performing algorithm for measuring biotic activity in terms of precision and recall, followed by bulbul, while the AIs performed worst. CityAnthroNet outperformed the Normalised Difference Soundscape Index, but by a smaller margin than CityBioNet achieved against the competing algorithms. The CityBioNet predictions were impacted by mechanical sounds, whereas air traffic and wind sounds influenced the bulbul predictions. Across an urbanisation gradient, we show that CityNet produced realistic daily patterns of biotic and anthropogenic acoustic activity from real-world urban audio data.\nC_LIO_LIUsing CityNet, it is possible to automatically measure biotic and anthropogenic acoustic activity in cities from audio recordings. If embedded within an autonomous sensing system, CityNet could produce environmental data for cites at large-scales and facilitate investigation of the impacts of anthropogenic activities on wildlife. The algorithms, code and pre-trained models are made freely available in combination with two expert-annotated urban audio datasets to facilitate automated environmental surveillance in cities.\nC_LI

ecology↗

bioRxiv2018

Genetic Diversity and Distributional Pattern of Ammonia Oxidizing Archaea Lineages in the Global Oceans

In the study, we used miTAG approach to analyse the distributional pattern of the ammonium oxidizing archaea (AOA) lineages in the global oceans using the metagenomics datasets of the Tara Oceans global expedition (2009-2013). Using ammonium monooxygenase alpha subunit gene as biomarker, the AOA communities were obviously segregated with water depth, except the upwelling regions. Besides, the AOA communities in the euphotic zones are more heterogeneous than in the mesopelagic zones (MPZs). Overall, water column A clade (WCA) distributes more evenly and widely in the euphotic zone and MPZs, while water column B clade (WCB) and SCM-like clade mainly distribute in MPZ and high latitude waters, respectively. At fine-scale genetic diversity, SCM1-like and 2 WCA subclades showed distinctive niche separation of distributional pattern. The AOA subclades were further divided into ecological significant taxonomic units (ESTUs), which were delineated from the distribution pattern of their corresponding subclades. For examples, ESTUs of WCA have different correlation with depth, nitrate to silicate ratio and salinity; SCM1-like-A was negatively correlated with irradiation; the other SCM-like ESTUs preferred low temperature and high nutrient conditions, etc. Our study provides new insight to the genetic diversity of AOA in global scale and its connections with environmental factors.

ecology↗

bioRxiv2018

Climatic effects on turnover of lowland forest bird communities across a precipitation gradient

One of the main goals of community ecology is to understand the influence of the abiotic environment on the abundance and distribution of species. It has been hypothesized that dry forests are harsher environments than wet forests, which leads to the prediction that environmental filtering should be a more important determinant of patterns of species abundance and composition than in wet forest, where biotic interactions or random assembly should be more important. We attempt to understand the influence of rainfall on the abundance and distribution of bird species along a steep precipitation gradient in an inter-Andean valley in Colombia. We gathered data on species distributions, abundance, morphological traits and phylogenetic relationships to determine the influence of rainfall on the taxonomic, functional and phylogenetic turnover of species along the Magdalena Valley. We demonstrate that there is a strong turnover of community composition at the limit of the dry forest. The taxonomic turnover is steeper than the phylogenetic turnover, suggesting that replacement of closely related species accounts for a disproportionate number of changes along the gradient. We found evidence for environmental filtering in dry forest as species tend to be more tolerant of higher temperature ranges, stronger rainfall seasonality and lower minimum rainfall. On the other hand, wet forest species tend to compete actively for nest space but not for the resources associated with the axes we measured. Our results suggest that rainfall is a strong determinant of community composition when comparing localities above and below the 2400 mm rainfall isocline.

ecology↗

bioRxiv2018

New mining concessions will severely decrease biodiversity and ecosystem services in Ecuador

Ecuador has the worlds highest biodiversity, despite being a tiny fraction of the worlds land area. The threat of extinction for much of this biodiversity has dramatically increased since April 2016, during which time the Ecuadorian government has opened approximately 2.9 million hectares of land for mining exploration, with many of the concessions in previously protected forests. Herein, we describe the system of protected lands in Ecuador, their mining laws, and outline the scale of threat by comparing the mammals, amphibians, reptiles, birds, and orchids from several now threatened protected areas, classed as \"Bosques Protectores\" (BPs), in the NW montane cloud forests. We examine two large (>5,000 ha) BPs, Los Cedros and El Chontal, and two medium BPs, Mashpi (1,178 ha) and Maquipucuna (2,474 ha). Since BP El Chontal is so poorly explored, we used several other small reserves (<500 hectares) in the Intag Valley to gain an idea of its biodiversity. Together, these BPs and reserves form a buffer and a southern corridor for the still-protected Cotacachi-Cayapas Ecological Reserve, which is otherwise now surrounded by mining concessions. We gathered published literature, \"gray literature\", information from reserve records and websites, and our previously unpublished observations to make comparative species tables for each reserve. Our results from these still incompletely known reserves reveal the astonishing losses that mining will incur: eight critically endangered species, including two primates (brown-headed spider monkey and white-fronted capuchin), 37 endangered species, 149 vulnerable and 85 near threatened and a large number of less threatened species Our data show that each of the reserves protects a unique subset of taxa in this land of highly localized endemics. Each of the reserves also generates sustainable income for the local people. The short-term national profits from mining will not compensate for the permanent biodiversity losses, and the long-term ecosystem service and economic losses at the local and regional level.

ecology↗

bioRxiv2018

Modeling Avian Full Annual Cycle Distribution and Population Trends with Citizen Science Data

Information on species distributions and abundances, and how these change over time are central to the study of the ecology and conservation of animal populations. This information is challenging to obtain at relevant scales across range-wide extents for two main reasons. First, local and regional processes that affect populations vary throughout the year and across species ranges, requiring fine-scale, year-round information across broad -- sometimes hemispheric -- spatial extents. Second, while citizen science projects can collect data at these scales, using these data requires appropriate analysis to address known sources of bias. Here we present an analytical framework to address these challenges and generate year-round, range-wide distributional information using citizen science data. To illustrate this approach, we apply the framework to Wood Thrush (Hylocichla mustelina), a long-distance Neotropical migrant and species of conservation concern, using data from the citizen science project eBird. We estimate occurrence and relative abundance with enough spatiotemporal resolution to support inference across a range of spatial scales throughout the annual cycle. Additionally, we generate intra-annual estimates of the range, intra-annual estimates of the associations between species and the local environment, and inter-annual trends in relative abundance. This is the first example of an analysis to capture intra- and inter-annual distributional dynamics across the entire range of a broadly distributed, highly mobile species.

ecology↗

bioRxiv2018

Alien leaf beetles of European Russia: native ranges, invasion history, biology and vectors of dispersal

Invasions of leaf beetles are of great ecological and economic significance, but poorly studied. The rate of these invasions in Europe is dramatically increasing. Some established species spread quickly occupying almost the whole continent within several decades. We present the first inventory of alien leaf beetles of European Russia. For each species the map of distribution is provided and the history of invasion in the world is discussed. Two species native to Mediterranean Region: Chrysolina americana (pest of Rosmarinus and Lavandula) and Leptomona erythrocephala feeding on Lotus corniculatus are recorded in European Russia for the first time. A polyphagous pest of floriculture Luperomorpha xanthodera native to China and Korea and pest of soybeans Medythia nigrobilineata native to East Asia were recorded in 2016. A pest of tobacco Epitrix hirtipennis native to North America was recorded in 2013. A pest of corn Diabrotica virgifera was intercepted at the border of Russia in 2011, but is not established. Three alien species were recorded in the 20th century: Zygogramma suturalis introduced from North America for control of Ambrosia, Phyllotreta reitteri native to Afghanistan and Tajikistan and feeding on Lepidium latifolium, and the Colorado potato beetle Leptinotarsa decemlineata. The Black Sea region is more prone to leaf beetle invasions than other regions of European Russia. Leaf beetles usually occur only on alien or cultivated plants. Some species feed on native plants in native communities. So it is difficult to distinguish species established before the 20th century from native ones.

ecology↗

bioRxiv2018

Evidence for subsoil specialization in arbuscular mycorrhizal fungi

Arbuscular mycorrhizal (AM) fungal communities are now known to vary with depth in arable land. Here we use two previously published high-throughput Illumina sequencing data sets, and compare a 52 year long chronosequence of recultivated agriculture fields after a topsoil and subsoil mixing event, with a set of undisturbed topsoil and subsoil samples from a similar field. We show that AM taxa identified as subsoil indicators are exclusively present in early stages of the chronosequence, whereas topsoil indicator taxa can be found across the chronosequence, and that similarities from the chronosequence fields to the subsoil communities decrease with time. Our results provide evidence on the ecological specialization of certain AM fungal taxa to deep soil layers.

ecology↗