Measuring ecological niche overlap from occurrence and spatial environmental data

1. Aim - Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data.¦2. Location - Europe, North America, South America¦3. Methods - The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with predefined distributions and amounts of niche overlap to evaluate several ordination and species distribution modeling techniques for quantifying niche overlap. We illustrate the approach with data on two well-studied invasive species.¦4. Results - We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographic space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results.¦5. Main conclusions - The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate to study niche differences between species, subspecies or intraspecific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intraspecific lineage has changed over time.

Ecological niche overlap in sister species: how do oil-collecting bees Macropis europaea and M. fulvipes (Hymenoptera: Melittidae) avoid competition and hybridization?

Oil-collecting bees are found worldwide and always in association with particular oil-producing flowers. In the Western Palearctic, three oil-collecting bee species within the genus Macropis (Hymenoptera, Melittidae) interact in a tight pollination mutualism with species of the only European oil-producing plant genus Lysimachia L. (Myrsinaceae). Two of these oil-collecting bees (Macropis europaea and Macropis fulvipes) show overlapping geographic distributions, comparable morphologies, and similar ecological characteristics (e.g., habitat type, floral preferences). In view of these similarities, we presume that hybridization should occur between the two species unless potential variation among the species' ecological niches prevents it, simultaneously decreasing competition for resources. Using modern genetic analyses and ecological niche modeling on a large bee sampling throughout Europe, we discuss new perspectives on the ecology and evolutionary history of this mutualism.

Global ASCII grids with daylenth values during summer and winter solstice and ASCII grids representing habitat suitability of Fucus distichus and its niche overlap with temperate macroalgae under present-day and future (2100, 2200) conditions

Abstract has to be submitted by the author!

Trophic niche overlap of sprat and commercial small pelagic teleosts in the Gulf of Lions (NW Mediterranean Sea)

Increasing abundance of non-commercial sprats and decreasing biomass and landings of commercial anchovies and sardines justify the need to study the feeding ecology and trophic niche overlap of these planktivorous species in the Gulf of Lions. Their diet has been investigated on the basis of stomach content and stable isotope analyses in 2011 and 2012 according to different depths and regions in the study area. The main prey were Corycaeidae copepods, Clauso/Paracalanus, Euterpina acutifrons and Microsetella, for sprats and small copepods, such as Microsetella, Oncaea and Corycaeidae, for anchovies and sardines. This is the first time that the diet of sprats is described in the Gulf of Lions. Sprats fed on a larger size spectrum of prey and seem to be more generalist feeders compared to anchovies and sardines. Ontogenetic changes as well as spatial and temporal variations of the diet occurred in the three species. Stable isotope analysis revealed mobility of sardines and sprats among feeding areas while anchovies exhibited preferred feeding areas. Sprats showed a higher relative condition assessed by C/N ratios than sardines and anchovies. Our results showed an overlap of the trophic niches for the three species, indicating a potential trophic competition in the Gulf of Lions.

Niche conservatism in non-native birds in Europe: niche unfilling rather than niche expansion

Aim Niche conservatism, or the extent to which niches are conserved across space and time, is of special concern for the study of non-native species as it underlies predictions of invasion risk. Based on the occurrence of 28 non-native birds in Europe, we assess to what extent Grinnellian realized niches are conserved during invasion, formulate hypotheses to explain the variation in observed niche changes and test how well species distribution models can predict non-native bird occurrence in Europe. Location Europe. Methods To quantify niche changes, a recent method that applies kernel smoothers to densities of species occurrence in a gridded environmental space was used. This corrects for differences in the availability of environments between study areas and allows discrimination between 'niche expansion' into environments new to the species and 'niche unfilling', whereby the species only partially fills its niche in the invaded range. Predictions of non-native bird distribution in Europe were generated using several distribution modelling techniques. Results Niche overlap between native and non-native bird populations is low, but niche changes are smaller for species having a higher propagule pressure and that were introduced longer ago. Non-native birds in Europe occupy a subset of the environments they inhabit in their native ranges. Niche expansion into novel environments is rare for most species, allowing species distribution models to accurately predict invasion risk. Main conclusions Because of the recent nature of most bird introductions, species occupy only part of the suitable environments available in the invaded range. This signals that apart from purely ecological factors, patterns of niche conservatism may also be contingent on population-specific historical factors. These results also suggest that many claims of niche differences may be due to a partial filling of the native niche in the invaded range and thus do not represent true niche changes.

Residence time, expansion toward the equator in the invaded range and native range size matter to climatic niche shifts in non-native species

Aim Identifying climatic niche shifts and their drivers is important to accurately predict the risk of biological invasions. The niches of non-native plants and birds have recently been assessed in large-scale multi-species studies, but such large-scale tests are lacking for non-native reptiles and amphibians (herpetofauna). Furthermore, little is known about the factors contributing to niche shifts when they occur. Based on the occurrence of 71 reptile and amphibian species, we compared native and non-native realized niches in 101 invaded ranges at a worldwide scale and identified the factors that affect niche shifts. Location The world except the Antarctic. Methods We assessed climatic niche dynamics in a gridded environmental space allowing the quantification of niche overlap and expansion into climatic conditions not colonized by the species in their native range. We analyzed the factors affecting niche shifts using a model averaging approach based on generalized linear mixed-effects models. Results Approximately 57% of the invaded ranges (51% for amphibians and 61% for reptiles) showed niche shifts (≥10% expansion in the realized climatic niche). Island endemics, species introduced to Oceania and invaded ranges outside the native biogeographic realm showed a higher proportion of niche shifts. Niche shifts were more likely for species that had smaller native range sizes, were introduced earlier into a new range or invaded areas located at lower latitudes than the native range. Main conclusions The proportion of niche shifts for non-native herpetofauna was higher than those for Holarctic non-native plants and European non-native birds. The 'climate matching hypothesis' should be used with caution for species shifting their niche because it could underestimate the risk of their establishment.

Testing the competitive exclusion principle using various niche parameters in a native (Natrix maura) and an introduced (N. tessellata) colubrid

Despite the increase of animal and plant introductions worldwide and the strong augmentation of the reptile trade, few invasive snake populations have been studied. Dice snakes (Natrix tessellata) were introduced to the shores of Lake Geneva (Switzerland) in the early 1920s, and are now well established. This region of introduction was previously inhabited by Viperine snakes (N. maura). Ever since these two species have been under monitoring (which began in 1996) the Viperine snake population has shown drastic decline. We examine here the possibility of trophic competition by analysing diet composition, prey size and trophic niche overlap. Spatial distribution is also assessed in order to address the question of spatial competitive exclusion. We found very similar diets, and thus a high trophic niche overlap, indicating no partitioning of the trophic resource. No arguments in favour of spatial competitive exclusion were found. Our study suggests that trophic competition may occur between the two natricines and that it may give an explanation for the drastic decline of the Viperine snake in this area. Other pathways potentially playing a role in the exclusion of the Viperine snake are discussed.

Climate niche conservatism does not explain restricted distribution patterns in Tynanthus (Bignonieae, Bignoniaceae)

Studies on niche evolution allow us to establish how species niches have changed over time as well as to identify how long-term evolutionary processes have led to present-day species distributions. Here, we investigate the patterns of climatic niche evolution in Tynanthus (Bignonieae, Bignoniaceae), a genus comprising narrowly distributed species. We test the hypothesis that niche conservatism has played an important role in the diversification history of this group of Neotropical lianas. For that, we perform univariate and multivariate comparisons between species' climatic niches and associated environmental data with information on species' phylogenetic relationships. We encountered considerable divergence in niches among species, indicating that niche conservatism in climatic variables has does not seem to havenot played a key role in the diversification of the genus. Our results are used as a basis to discuss patterns of ecological niche evolution in the group and to suggest novel approaches for future analyses.

Niche occupancy and the relative role of micro-habitat and diet in resource partitioning among pond dwelling tadpoles.

We determined microhabitat and diet niche for tadpoles from two ponds in an agricultural landscape. Additionally, we verified the intraspecific variation in resource use, and if diet and microhabitat use were correlated. Tadpoles found in the two ponds differed in microhabitat use, because in the larger pond they explored deeper places far from the margin. There were three groups with high microhabitat niche overlap. In both ponds, plant cover was the best descriptor to explain interspecific variation in microhabitat use. Tadpoles of all species ingested mainly Bacillariophyceae and Trachellomonas however the diet differed intraspecifically in the species from the two ponds. Ten items in the temporary pond and 15 items in the permanent one were ingested by all species; however, the relative abundance of each item differed. Diet similarity was not correlated to similarity in microhabitat use. In this study, diet was as important as microhabitat use to explain resource partitioning.

A Stable Niche Assumption-Free Test of Ecological Divergence

Understanding the impact of geological events on diversification processes is central to evolutionary ecology. The recent amalgamation between ecological niche models (ENMs) and phylogenetic analyses has been used to estimate historical ranges of modern lineages by projecting current ecological niches of organisms onto paleoclimatic reconstructions. A critical assumption underlying this approach is that niches are stable over time. Using Notophthalmus viridescens (eastern newt), in which four ecologically diverged subspecies are recognized, we introduce an analytical framework free from the niche stability assumption to examine how refugial retreat and subsequent postglacial expansion have affected intraspecific ecological divergence. We found that the current subspecies designation was not congruent with the phylogenetic lineages. Thus, we examined ecological niche overlap between the refugial and modern populations, in both subspecies and lineage, by creating ENMs independently for modern and estimated last glacial maximum (LGM) newt populations, extracting bioclimate variables by randomly generated points, and conducting principal component analyses. Our analyses consistently showed that when tested as a hypothesis, rather than used as an assumption, the niches of N. viridescens lineages have been unstable since the LGM (both subspecies and lineages). There was greater ecological niche differentiation among the subspecies than the modern phylogenetic lineages, suggesting that the subspecies, rather than the phylogenetic lineages, is the unit of the current ecological divergence. The present study found little evidence that the LGM refugial retreat caused the currently observed ecological divergence and suggests that ecological divergence has occurred during postglacial expansion to the current distribution ranges.

Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

PREMISE OF THE STUDY: We conducted environmental niche modeling (ENM) of the Brachypodium distachyon s.l. complex, a model group of two diploid annual grasses ( B. distachyon , B. stacei ) and their derived allotetraploid ( B. hybridum) , native to the circum-Mediterranean region. We (1) investigated the ENMs of the three species in their native range based on present and past climate data; (2) identifi ed potential overlapping niches of the diploids and their hybrid across four Quaternary windows; (3) tested whether speciation was associated with niche divergence/conservatism in the complex species; and (4) tested for the potential of the polyploid outperforming the diploids in the native range. M ETHODS: Geo-referenced data, altitude, and 19 climatic variables were used to construct the ENMs. We used paleoclimate niche models to trace the potential existence of ancestral gene fl ow among the hybridizing species of the complex. KEY RESULTS: Brachypodium distachyon grows in higher, cooler, and wetter places, B. stacei in lower, warmer, and drier places, and B. hybridum in places with intermediate climatic features. Brachypodium hybridum had the largest niche overlap with its parent niches, but a similar distribution range and niche breadth. C ONCLUSIONS: Each species had a unique environmental niche though there were multiple niche overlapping areas for the diploids across time, suggesting the potential existence of several hybrid zones during the Pleistocene and the Holocene. No evidence of niche divergence was found, suggesting that species diversifi cation was not driven by ecological speciation but by evolutionary history, though it could be associated to distinct environmental adaptations.

Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions

Background: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. Methodology: We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Conclusions: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.

Resource partitioning and ecomorphological variation in two syntopic species of Lebiasinidae (Characiformes) in an Amazonian stream

ABSTRACTResource partitioning is important for species coexistence. Species with similar ecomorphology are potential competitors, especially when phylogenetically close, due to niche conservatism. The aim of this study was to investigate the resource partitioning among populations of two species of lebiasinids (Copella nigrofasciata and Pyrrhulina aff. brevis) that co-occur in a first-order Amazonian stream, analyzing the trophic ecology, feeding strategies and ecomorphological attributes related to the use of food and space by these species. Fish were captured in May and September 2010. The stomach contents of 60 individuals were analyzed and quantified volumetrically to characterize the feeding ecology of both species. Eleven morphological attributes were measured in 20 specimens and combined in nine ecomorphological indices. Both species had an omnivorous-invertivorous diet and consumed predominantly allochthonous items. Both showed a tendency to a generalist diet, but intrapopulational variation in resource use was also detected. Overall feeding niche overlap was high, but differed between seasons: low during the rainy season and high in the dry season. In the latter, the food niche overlap was asymmetric because C. nigrofasciata consumed several prey of P. aff. brevis, which reduced its food spectrum. The ecomorphological analysis suggests that C. nigrofasciatahas greater swimming capacity (greater relative length of caudal peduncle) than P. aff. brevis, which has greater maneuverability and tendency to inhabit lentic environments (greater relative depth of the body). Our results demonstrate that these species have similar trophic ecology and suggest a spatial segregation, given by morphological differences related to locomotion and occupation of habitat, favoring their coexistence.

Diet of the South American frog Leptodactylus ocellatus (Anura, Leptodactylidae) in Uruguay

The diet of Leptodactylus ocellatus (L., 1758) was studied in specimens collected at Maldonado Department (Uruguay), where monthly surveys were made between August 1998 and March 2000. A total of 143 frogs were collected, measured, sexed, and dissected, to assess stomach contents. The anurans were grouped into three age classes and four categories (considering sex and capture date). The trophic amplitude for each age class and sex-season category was quantified using Shannon-Weaver Index, and the trophic niche overlap between ages and categories by using the Pianka Index. Comparisons among treatments were made by G-tests. The most important prey items were coleopterans (IRI = 2547), and significant correlations were found between predator and prey sizes. The major differences on diet composition were found between extreme age classes (froglets and adults). Significant differences were also detected between sexes in the cold season but not in the warm season. Any of these changes in diet may be related with the availability of prey.