Kearney, Michael; Simpson, Stephen J.; Raubenheimer, David; Helmuth, Brian
The niche concept is central to ecology but is often depicted descriptively through observing associations between organisms and habitats. Here, we argue for the importance of mechanistically modelling niches based on functional traits of organisms and explore the possibilities for achieving this through the integration of three theoretical frameworks: biophysical ecology (BE), the geometric framework for nutrition (GF) and dynamic energy budget (DEB) models. These three frameworks are fundamentally based on the conservation laws of thermodynamics, describing energy and mass balance at the level of the individual and capturing the prodigious predictive power of the concepts of ‘homeostasis’ and ‘evolutionary fitness’. BE and the GF provide mechanistic multi-dimensional depictions of climatic and nutritional niches, respectively, providing a foundation for linking organismal traits (morphology, physiology, behaviour) with habitat characteristics. In turn, they provide driving inputs and cost functions for mass/energy allocation within the individual as determined by DEB models. We show how integration of the three frameworks permits calculation of activity constraints, vital rates (survival, development, growth, reproduction) and ultimately population growth rates and species distributions. When integrated with contemporary niche theory, functional trait niche models hold great promise for tackling major questions in ecology and evolutionary biology. PMID:20921046
Present approaches to species invasions are reactive in nature. This scenario results in management that perpetually lags behind the most recent invasion and makes control much more difficult. In contrast, spatially explicit ecological niche modeling provides an effective solut...
Escobar, Luis E; Craft, Meggan E
Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks.
Escobar, Luis E.; Craft, Meggan E.
Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks. PMID:27547199
Ikeda, Dana H; Max, Tamara L; Allan, Gerard J; Lau, Matthew K; Shuster, Stephen M; Whitham, Thomas G
We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, local adaptation. Local adaptation is common in species that span a range of environmental gradients (e.g., soils and climate). Moreover, common garden studies have demonstrated a covariance between neutral markers and functional traits associated with a species' ability to adapt to environmental change. We therefore predicted that genetically distinct populations would respond differently to climate change, resulting in predicted distributions with little overlap. To test whether genetic information improves our ability to predict a species' niche space, we created genetically informed ecological niche models (gENMs) using Populus fremontii (Salicaceae), a widespread tree species in which prior common garden experiments demonstrate strong evidence for local adaptation. Four major findings emerged: (i) gENMs predicted population occurrences with up to 12-fold greater accuracy than models without genetic information; (ii) tests of niche similarity revealed that three ecotypes, identified on the basis of neutral genetic markers and locally adapted populations, are associated with differences in climate; (iii) our forecasts indicate that ongoing climate change will likely shift these ecotypes further apart in geographic space, resulting in greater niche divergence; (iv) ecotypes that currently exhibit the largest geographic distribution and niche breadth appear to be buffered the most from climate change. As diverse agents of selection shape genetic variability and structure within species, we argue that gENMs will lead to more accurate predictions of species distributions under climate change.
Klawonn, M.; Dow, E. M.
Ecological Niche Modeling (ENM) is a collection of techniques to find a "fundamental niche", the range of environmental conditions suitable for a species' survival in the absence of inter-species interactions, given a set of environmental parameters. Traditional approaches to ENM face a number of obstacles including limited data accessibility, data management problems, computational costs, interface usability, and model validation. The MERGANSER system, which stands for Modeling Ecological Residency Given A Normalized Set of Environmental Records, addresses these issues through powerful data persistence and flexible data access, coupled with a clear presentation of results and fine-tuned control over model parameters. MERGANSER leverages data measuring 72 weather related phenomena, land cover, soil type, population, species occurrence, general species information, and elevation, totaling over 1.5 TB of data. To the best of the authors' knowledge, MERGANSER uses higher-resolution spatial data sets than previously published models. Since MERGANSER stores data in an instance of Apache SOLR, layers generated in support of niche models are accessible to users via simplified Apache Lucene queries. This is made even simpler via an HTTP front end that generates Lucene queries automatically. Specifically, a user need only enter the name of a place and a species to run a model. Using this approach to synthesizing model layers, the MERGANSER system has successfully reproduced previously published niche model results with a simplified user experience. Input layers for the model are generated dynamically using OpenStreetMap and SOLR's spatial search functionality. Models are then run using either user-specified or automatically determined parameters after normalizing them into a common grid. Finally, results are visualized in the web interface, which allows for quick validation. Model results and all surrounding metadata are also accessible to the user for further study.
Trends in Ecology & Evolution 14: 291. 29. Edwards JL, Lane MA, Nielsen ES (2000) Interoperability of biodiversity databases: biodiversity information on...Glor RE, Kolbe JJ (2006) Phylogenetic analysis of the evolution of the niche in lizards of the Anolis sagrei group. Ecology 87: S29–S38. 37. Jakob
Silva, Daniel P.; Vilela, Bruno; De Marco, Paulo; Nemésio, André
The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species. PMID:25422941
Silva, Daniel P; Vilela, Bruno; De Marco, Paulo; Nemésio, André
The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species.
Waltari, Eric; Hijmans, Robert J.; Peterson, A. Townsend; Nyári, Árpád S.; Perkins, Susan L.; Guralnick, Robert P.
Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution. PMID:17622339
Slagsvold, Tore; Wiebe, Karen L
A cornerstone of ecological theory is the ecological niche. Yet little is known about how individuals come to adopt it: whether it is innate or learned. Here, we report a cross-fostering experiment in the wild where we transferred eggs of blue tits, Cyanistes caeruleus, to nests of great tits, Parus major, and vice versa, to quantify the consequences of being reared in a different social context, but in an environment otherwise natural to the birds. We show that early learning causes a shift in the feeding niche in the direction of the foster species and that this shift lasts for life (foraging conservatism). Both species changed their feeding niches, but the change was greater in the great tit with its less specialized feeding behaviour. The study shows that cultural transmission through early learning is fundamental to the realization of ecological niches, and suggests a mechanism to explain learned habitat preference and sympatric speciation in animals. PMID:17015332
Slagsvold, Tore; Wiebe, Karen L
A cornerstone of ecological theory is the ecological niche. Yet little is known about how individuals come to adopt it: whether it is innate or learned. Here, we report a cross-fostering experiment in the wild where we transferred eggs of blue tits, Cyanistes caeruleus, to nests of great tits, Parus major, and vice versa, to quantify the consequences of being reared in a different social context, but in an environment otherwise natural to the birds. We show that early learning causes a shift in the feeding niche in the direction of the foster species and that this shift lasts for life (foraging conservatism). Both species changed their feeding niches, but the change was greater in the great tit with its less specialized feeding behaviour. The study shows that cultural transmission through early learning is fundamental to the realization of ecological niches, and suggests a mechanism to explain learned habitat preference and sympatric speciation in animals.
Lee-Yaw, Julie A; Kharouba, Heather M; Bontrager, Megan; Mahony, Colin; Csergő, Anna Mária; Noreen, Annika M E; Li, Qin; Schuster, Richard; Angert, Amy L
Global change has made it important to understand the factors that shape species' distributions. Central to this area of research is the question of whether species' range limits primarily reflect the distribution of suitable habitat (i.e. niche limits) or arise as a result of dispersal limitation. Over-the-edge transplant experiments and ecological niche models are commonly used to address this question, yet few studies have taken advantage of a combined approach for inferring the causes of range limits. Here, we synthesise results from existing transplant experiments with new information on the predicted suitability of sites based on niche models. We found that individual performance and habitat suitability independently decline beyond range limits across multiple species. Furthermore, inferences from transplant experiments and niche models were generally concordant within species, with 31 out of 40 cases fully supporting the hypothesis that range limits are niche limits. These results suggest that range limits are often niche limits and that the factors constraining species' ranges operate at scales detectable by both transplant experiments and niche models. In light of these findings, we outline an integrative framework for addressing the causes of range limits in individual species.
Drake, John M.
The ecological niche is the set of environments in which a population of a species can persist without introduction of individuals from other locations. A good mathematical or computational representation of the niche is a prerequisite to addressing many questions in ecology, biogeography, evolutionary biology and conservation. A particularly challenging question for ecological niche modelling is the problem of presence-only modelling. That is, can an ecological niche be identified from records drawn only from the set of niche environments without records from non-niche environments for comparison? Here, I introduce a new method for ecological niche modelling from presence-only data called range bagging. Range bagging draws on the concept of a species' environmental range, but was inspired by the empirical performance of ensemble learning algorithms in other areas of ecological research. This paper extends the concept of environmental range to multiple dimensions and shows that range bagging is computationally feasible even when the number of environmental dimensions is large. The target of the range bagging base learner is an environmental tolerance of the species in a projection of its niche and is therefore an ecologically interpretable property of a species' biological requirements. The computational complexity of range bagging is linear in the number of examples, which compares favourably with the main alternative, Qhull. In conclusion, range bagging appears to be a reasonable choice for niche modelling in applications in which a presence-only method is desired and may provide a solution to problems in other disciplines where one-class classification is required, such as outlier detection and concept learning. PMID:25948612
Peterson; Sober n J; Sanchez-Cordero
Theory predicts low niche differentiation between species over evolutionary time scales, but little empirical evidence is available. Reciprocal geographic predictions based on ecological niche models of sister taxon pairs of birds, mammals, and butterflies in southern Mexico indicate niche conservatism over several million years of independent evolution (between putative sister taxon pairs) but little conservatism at the level of families. Niche conservatism over such time scales indicates that speciation takes place in geographic, not ecological, dimensions and that ecological differences evolve later.
Raghavan, Ram K.; Goodin, Douglas G.; Hanzlicek, Gregg A.; Zolnerowich, Gregory; Dryden, Michael W.; Anderson, Gary A.; Ganta, Roman R.
Abstract The potential distribution of Amblyomma americanum ticks in Kansas was modeled using maximum entropy (MaxEnt) approaches based on museum and field-collected species occurrence data. Various bioclimatic variables were used in the model as potentially influential factors affecting the A. americanum niche. Following reduction of dimensionality among predictor variables using principal components analysis, which revealed that the first two principal axes explain over 87% of the variance, the model indicated that suitable conditions for this medically important tick species cover a larger area in Kansas than currently believed. Soil moisture, temperature, and precipitation were highly correlated with the first two principal components and were influential factors in the A. americanum ecological niche. Assuming that the niche estimated in this study covers the occupied distribution, which needs to be further confirmed by systematic surveys, human exposure to this known disease vector may be considerably under-appreciated in the state. PMID:26824880
Friedlaender, Ari S.; Johnston, David W.; Fraser, William R.; Burns, Jennifer; Halpin, Patrick N.; Costa, Daniel P.
Adélie penguins ( Pygoscelis adeliae), carabeater seals ( Lobodon carcinophagus), humpback ( Megaptera novaeangliae), and minke whales ( Balaenoptera bonaernsis) are found in the waters surrounding the Western Antarctic Peninsula. Each species relies primarily on Antarctic krill ( Euphausia superba) and has physiological constraints and foraging behaviors that dictate their ecological niches. Understanding the degree of ecological overlap between sympatric krill predators is critical to understanding and predicting the impacts on climate-driven changes to the Antarctic marine ecosystem. To explore ecological relationships amongst sympatric krill predators, we developed ecological niche models using a maximum entropy modeling approach (Maxent) that allows the integration of data collected by a variety of means (e.g. satellite-based locations and visual observations). We created spatially explicit probability distributions for the four krill predators in fall 2001 and 2002 in conjunction with a suite of environmental variables. We find areas within Marguerite Bay with high krill predator occurrence rates or biological hot spots. We find the modeled ecological niches for Adélie penguins and crabeater seals may be affected by their physiological needs to haul-out on substrate. Thus, their distributions may be less dictated by proximity to prey and more so by physical features that over time provide adequate access to prey. Humpback and minke whales, being fully marine and having greater energetic demands, occupy ecological niches more directly proximate to prey. We also find evidence to suggest that the amount of overlap between modeled niches is relatively low, even for species with similar energetic requirements. In a rapidly changing and variable environment, our modeling work shows little indication that krill predators maintain similar ecological niches across years around Marguerite Bay. Given the amount of variability in the marine environment around the
Marewski, Julian N; Schooler, Lael J
How do people select among different strategies to accomplish a given task? Across disciplines, the strategy selection problem represents a major challenge. We propose a quantitative model that predicts how selection emerges through the interplay among strategies, cognitive capacities, and the environment. This interplay carves out for each strategy a cognitive niche, that is, a limited number of situations in which the strategy can be applied, simplifying strategy selection. To illustrate our proposal, we consider selection in the context of 2 theories: the simple heuristics framework and the ACT-R (adaptive control of thought-rational) architecture of cognition. From the heuristics framework, we adopt the thesis that people make decisions by selecting from a repertoire of simple decision strategies that exploit regularities in the environment and draw on cognitive capacities, such as memory and time perception. ACT-R provides a quantitative theory of how these capacities adapt to the environment. In 14 simulations and 10 experiments, we consider the choice between strategies that operate on the accessibility of memories and those that depend on elaborate knowledge about the world. Based on Internet statistics, our model quantitatively predicts people's familiarity with and knowledge of real-world objects, the distributional characteristics of the associated speed of memory retrieval, and the cognitive niches of classic decision strategies, including those of the fluency, recognition, integration, lexicographic, and sequential-sampling heuristics. In doing so, the model specifies when people will be able to apply different strategies and how accurate, fast, and effortless people's decisions will be.
Qiao, Huijie; Lin, Congtian; Ji, Liqiang; Jiang, Zhigang
Background Predicting the ecological niche and potential habitat distribution of a given organism is one of the central domains of ecological and biogeographical research. A wide variety of modeling techniques have been developed for this purpose. In order to implement these models, the users must prepare a specific runtime environment for each model, learn how to use multiple model platforms, and prepare data in a different format each time. Additionally, often model results are difficult to interpret, and a standardized method for comparing model results across platforms does not exist. We developed a free and open source online platform, the multi-models web-based (mMWeb) platform, to address each of these problems, providing a novel environment in which the user can implement and compare multiple ecological niche model (ENM) algorithms. Methodology mMWeb combines 18 existing ENMs and their corresponding algorithms and provides a uniform procedure for modeling the potential habitat niche of a species via a common web browser. mMWeb uses Java Native Interface (JNI), Java R Interface to combine the different ENMs and executes multiple tasks in parallel on a super computer. The cross-platform, user-friendly interface of mMWeb simplifies the process of building ENMs, providing an accessible and efficient environment from which to explore and compare different model algorithms. PMID:22912854
This paper discusses the ecological niches, relationships and controls of Legionella derived from environmental sources. Only as clinical cases and studies relate directly to the ecological understanding of the bacterium will they be discussed. This review seeks to separate the ecological parameters associated with Legionella that are often incorporated into the medical literature as well as to highlight specific ecological studies. A series of ecological studies demonstrates the niches of Legionella, the ecological parameters that allow the bacterium to survive, grow and to be disseminated. Relationships among given habitats are explored along with biological relationships within a given habitat.
Parra-Henao, Gabriel; Suárez-Escudero, Laura C; González-Caro, Sebastián
Ecological niche modeling of Triatominae bugs allow us to establish the local risk of transmission of the parasite Trypanosoma cruzi, which causes Chagas disease. This information could help to guide health authority recommendations on infection monitoring, prevention, and control. In this study, we estimated the geographic distribution of triatomine species in Colombia and identified the relationship between landscape structure and climatic factors influencing their occurrence. A total of 2451 records of 4 triatomine species (Panstrongylus geniculatus, Rhodnius pallescens, R. prolixus, and Triatoma maculata) were analyzed. The variables that provided more information to explain the ecologic niche of these vectors were related to precipitation, altitude, and temperature. We found that the species with the broadest potential geographic distribution were P. geniculatus, R. pallescens, and R. prolixus. In general, the models predicted the highest occurrence probability of these vectors in the eastern slope of the Eastern Cordillera, the southern region of the Magdalena valley, and the Sierra Nevada of Santa Marta.
Suárez-Escudero, Laura C.; González-Caro, Sebastián
Ecological niche modeling of Triatominae bugs allow us to establish the local risk of transmission of the parasite Trypanosoma cruzi, which causes Chagas disease. This information could help to guide health authority recommendations on infection monitoring, prevention, and control. In this study, we estimated the geographic distribution of triatomine species in Colombia and identified the relationship between landscape structure and climatic factors influencing their occurrence. A total of 2451 records of 4 triatomine species (Panstrongylus geniculatus, Rhodnius pallescens, R. prolixus, and Triatoma maculata) were analyzed. The variables that provided more information to explain the ecologic niche of these vectors were related to precipitation, altitude, and temperature. We found that the species with the broadest potential geographic distribution were P. geniculatus, R. pallescens, and R. prolixus. In general, the models predicted the highest occurrence probability of these vectors in the eastern slope of the Eastern Cordillera, the southern region of the Magdalena valley, and the Sierra Nevada of Santa Marta. PMID:28115946
Anderson, Robert P
Recent advances allow harnessing enormous stores of biological and environmental data to model species niches and geographic distributions. Natural history museums hold specimens that represent the only information available for most species. Ecological niche models (sometimes termed species distribution models) combine such information with digital environmental data (especially climatic) to offer key insights for conservation biology, management of invasive species, zoonotic human diseases, and other pressing environmental problems. Five major pitfalls seriously hinder such research, especially for cross-space or cross-time uses: (1) incorrect taxonomic identifications; (2) lacking or inadequate databasing and georeferences; (3) effects of sampling bias across geography; (4) violation of assumptions related to selection of the study region; and (5) problems regarding model evaluation to identify optimal model complexity. Large-scale initiatives regarding data availability and quality, technological development, and capacity building should allow high-quality modeling on a scale commensurate with the enormous potential of and need for these techniques.
Jueterbock, Alexander; Smolina, Irina; Coyer, James A; Hoarau, Galice
Rising temperatures are predicted to melt all perennial ice cover in the Arctic by the end of this century, thus opening up suitable habitat for temperate and subarctic species. Canopy-forming seaweeds provide an ideal system to predict the potential impact of climate-change on rocky-shore ecosystems, given their direct dependence on temperature and their key role in the ecological system. Our primary objective was to predict the climate-change induced range-shift of Fucus distichus, the dominant canopy-forming macroalga in the Arctic and subarctic rocky intertidal. More specifically, we asked: which Arctic/subarctic and cold-temperate shores of the northern hemisphere will display the greatest distributional change of F. distichus and how will this affect niche overlap with seaweeds from temperate regions? We used the program MAXENT to develop correlative ecological niche models with dominant range-limiting factors and 169 occurrence records. Using three climate-change scenarios, we projected habitat suitability of F. distichus - and its niche overlap with three dominant temperate macroalgae - until year 2200. Maximum sea surface temperature was identified as the most important factor in limiting the fundamental niche of F. distichus. Rising temperatures were predicted to have low impact on the species' southern distribution limits, but to shift its northern distribution limits poleward into the high Arctic. In cold-temperate to subarctic regions, new areas of niche overlap were predicted between F. distichus and intertidal macroalgae immigrating from the south. While climate-change threatens intertidal seaweeds in warm-temperate regions, seaweed meadows will likely flourish in the Arctic intertidal. Although this enriches biodiversity and opens up new seaweed-harvesting grounds, it will also trigger unpredictable changes in the structure and functioning of the Arctic intertidal ecosystem.
Zhang, Yueyun; Chen, Chongtao; Li, Li; Zhao, Chengjian; Chen, Weicai; Huang, Yong
The black-spotted tokay and the red-spotted tokay are morphologically distinct and have largely allopatric distributions. The black-spotted tokay is characterized by a small body size and dark skin with sundry spots, while the red-spotted tokay has a relatively large body size and red spots. Based on morphological, karyotypic, genetic, and distribution differences, recent studies suggested their species status; however, their classifications remain controversial, and additional data such as ecological niches are necessary to establish firm hypotheses regarding their taxonomic status. We reconstructed their ecological niches models using climatic and geographic data. We then performed niche similarity tests (niche identity and background tests) and point-based analyses to explore whether ecological differentiation has occurred, and whether such differences are sufficient to explain the maintenance of their separate segments of environmental ranges. We found that both niche models of the black- and the red-spotted tokay had a good fit and a robust performance, as indicated by the high area under the curve (AUC) values (“black” = 0.982, SD = ± 0.002, “red” = 0.966 ± 0.02). Significant ecological differentiation across the entire geographic range was found, indicating that the involvement of ecological differentiation is important for species differentiation. Divergence along the environmental axes is highly associated with climatic conditions, with isothermality being important for the “black” form, while temperature seasonality, precipitation of warmest quarter, and annual temperature range together being important for the “red” form. These factors are likely important factors in niche differentiation between the two forms, which result in morphological replacement. Overall, beside morphological and genetic differentiation information, our results contribute to additional insights into taxonomic distinction and niche differentiation between the
Lisón, Fulgencio; Calvo, José F.
Wetlands and aquatic habitats in Mediterranean environments are very scarce in general, representing a limiting resource for all species. For pipistrelle bats, such environments are essential and so those species living in sympatry have to develop mechanisms of niche partitioning to avoid direct competition. We used ecological niche models and habitat suitability maps (HSMs) to study the ecological requirements and possible interspecific interactions between three sympatric species of pipistrelles in semiarid Mediterranean landscapes. The results point to differences between the three species: Pipistrellus kuhlii has the largest proportion of optimal habitat (despite being the least common), Pipistrellus pygmaeus has the highest value of marginality and the most common, Pipistrellus pipistrellus, is a habitat-tolerant and generalist species. However, all three species show a strong preference for aquatic habitats and there is a high degree of overlapping between them, so that their coexistence must obey fine-scale mechanisms of niche partitioning. The profound alterations that have occurred in Mediterranean ecosystems as a result of substantial changes in the landscape uses (intensive agriculture and urbanization) may favour P. pipistrellus and be detrimental to the other two species, especially P. kuhlii.
Aguilar, María; Lado, Carlos
Habitat availability and environmental preferences of species are among the most important factors in determining the success of dispersal processes and therefore in shaping the distribution of protists. We explored the differences in fundamental niches and potential distributions of an ecological guild of slime moulds-protosteloid amoebae-in the Iberian Peninsula. A large set of samples collected in a north-east to south-west transect of approximately 1000 km along the peninsula was used to test the hypothesis that, together with the existence of suitable microhabitats, climate conditions may determine the probability of survival of species. Although protosteloid amoebae share similar morphologies and life history strategies, canonical correspondence analyses showed that they have varied ecological optima, and that climate conditions have an important effect in niche differentiation. Maxent environmental niche models provided consistent predictions of the probability of presence of the species based on climate data, and they were used to generate maps of potential distribution in an 'everything is everywhere' scenario. The most important climatic factors were, in both analyses, variables that measure changes in conditions throughout the year, confirming that the alternation of fruiting bodies, cysts and amoeboid stages in the life cycles of protosteloid amoebae constitutes an advantage for surviving in a changing environment. Microhabitat affinity seems to be influenced by climatic conditions, which suggests that the micro-environment may vary at a local scale and change together with the external climate at a larger scale.
Larson, Scott R.; DeGroote, John P.; Bartholomay, Lyric C.; Sugumaran, Ramanathan
Ecological niche modeling (ENM) algorithms, Maximum Entropy Species Distribution Modeling (Maxent) and Genetic Algorithm for Rule-set Prediction (GARP), were used to develop models in Iowa for three species of mosquito — two significant, extant West Nile virus (WNV) vectors (Culex pipiens L and Culex tarsalis Coquillett (Diptera: Culicidae)), and the nuisance mosquito, Aedes vexans Meigen (Diptera: Culicidae), a potential WNV bridge vector. Occurrence data for the three mosquito species from a state-wide arbovirus surveillance program were used in combination with climatic and landscape layers. Maxent successfully created more appropriate niche models with greater accuracy than GARP. The three Maxent species' models were combined and the average values were statistically compared to human WNV incidence at the census block group level. The results showed that the Maxent-modeled species' niches averaged together were a useful indicator of WNV human incidence in the state of Iowa. This simple method for creating probability distribution maps proved useful for understanding WNV dynamics and could be applied to the study of other vector-borne diseases. PMID:20874412
Chalghaf, Bilel; Chlif, Sadok; Mayala, Benjamin; Ghawar, Wissem; Bettaieb, Jihène; Harrabi, Myriam; Benie, Goze Bertin; Michael, Edwin; Salah, Afif Ben
Cutaneous leishmaniasis is a very complex disease involving multiple factors that limit its emergence and spatial distribution. Prediction of cutaneous leishmaniasis epidemics in Tunisia remains difficult because most of the epidemiological tools used so far are descriptive in nature and mainly focus on a time dimension. The purpose of this work is to predict the potential geographic distribution of Phlebotomus papatasi and zoonotic cutaneous leishmaniasis caused by Leishmania major in Tunisia using Grinnellian ecological niche modeling. We attempted to assess the importance of environmental factors influencing the potential distribution of P. papatasi and cutaneous leishmaniasis caused by L. major. Vectors were trapped in central Tunisia during the transmission season using CDC light traps (John W. Hock Co., Gainesville, FL). A global positioning system was used to record the geographical coordinates of vector occurrence points and households tested positive for cutaneous leishmaniasis caused by L. major. Nine environmental layers were used as predictor variables to model the P. papatasi geographical distribution and five variables were used to model the L. major potential distribution. Ecological niche modeling was used to relate known species' occurrence points to values of environmental factors for these same points to predict the presence of the species in unsampled regions based on the value of the predictor variables. Rainfall and temperature contributed the most as predictors for sand flies and human case distributions. Ecological niche modeling anticipated the current distribution of P. papatasi with the highest suitability for species occurrence in the central and southeastern part of Tunisian. Furthermore, our study demonstrated that governorates of Gafsa, Sidi Bouzid, and Kairouan are at highest epidemic risk. PMID:26856914
number. 1. REPORT DATE 2010 2. REPORT TYPE 3. DATES COVERED 00-00-2010 to 00-00-2010 4. TITLE AND SUBTITLE Validation of Ecological Niche...prediction of species’ distributions from occurrence data. Ecography 29:129–151. Foley DH, Klein TA, Kim HC, Sames WJ, Wilkerson RC, Rueda LM. 2009. The...character- istics on performance of different species distribution modeling methods. Ecography 29:773–785. Kho WG, Jang JY, Hong ST, Lee HW, Lee WJ, Lee JS
Sandoval-Ruiz, C A; Zumaquero-Rios, J L; Rojas-Soto, O R
We analyzed the geographic distribution using ecological niche modeling of three species of triatomines distributed in the Mexican state of Puebla. Punctual records were gathered for a period of 5 yr of fieldwork sampling. We used the genetic algorithm for rule-set production (GARP) to achieve the potential distribution of the ecological niche of triatomines. The models showed that Triatoma barberi and Meccus pallidipennis are sympatric and widely distributed in the central-southern part of the state, whereas T. dimidata is restricted to the northern mountains of the state with no overlapping among other species, M. bassolsae was not modeled because of the scarce number of locality records. We highlighted the warm and dry conditions in southern Puebla as important potential areas for triatomine presence. Finally, we correlated the species potential presence with the human population at risk of acquiring Chagas disease by vector-borne transmission; it is showed that M. pallidipennis presents the highest values of both ecological and poverty risk scenarios representing the main potential vector in the state.
Samy, Abdallah M; van de Sande, Wendy W J; Fahal, Ahmed Hassan; Peterson, A Townsend
In 2013, the World Health Organization (WHO) recognized mycetoma as one of the neglected tropical conditions due to the efforts of the mycetoma consortium. This same consortium formulated knowledge gaps that require further research. One of these gaps was that very few data are available on the epidemiology and transmission cycle of the causative agents. Previous work suggested a soil-borne or Acacia thorn-prick-mediated origin of mycetoma infections, but no studies have investigated effects of soil type and Acacia geographic distribution on mycetoma case distributions. Here, we map risk of mycetoma infection across Sudan and South Sudan using ecological niche modeling (ENM). For this study, records of mycetoma cases were obtained from the scientific literature and GIDEON; Acacia records were obtained from the Global Biodiversity Information Facility. We developed ENMs based on digital GIS data layers summarizing soil characteristics, land-surface temperature, and greenness indices to provide a rich picture of environmental variation across Sudan and South Sudan. ENMs were calibrated in known endemic districts and transferred countrywide; model results suggested that risk is greatest in an east-west belt across central Sudan. Visualizing ENMs in environmental dimensions, mycetoma occurs under diverse environmental conditions. We compared niches of mycetoma and Acacia trees, and could not reject the null hypothesis of niche similarity. This study revealed contributions of different environmental factors to mycetoma infection risk, identified suitable environments and regions for transmission, signaled a potential mycetoma-Acacia association, and provided steps towards a robust risk map for the disease.
Xu, Min; Cao, Chunxiang; Li, Qun; Jia, Peng; Zhao, Jian
China was attacked by a serious influenza A (H7N9) virus in 2013. The first human infection case was confirmed in Shanghai City and soon spread across most of eastern China. Using the methods of Geographic Information Systems (GIS) and ecological niche modeling (ENM), this research quantitatively analyzed the relationships between the H7N9 occurrence and the main environmental factors, including meteorological variables, human population density, bird migratory routes, wetland distribution, and live poultry farms, markets, and processing factories. Based on these relationships the probability of the presence of H7N9 was predicted. Results indicated that the distribution of live poultry processing factories, farms, and human population density were the top three most important determinants of the H7N9 human infection. The relative contributions to the model of live poultry processing factories, farms and human population density were 39.9%, 17.7% and 17.7%, respectively, while the maximum temperature of the warmest month and mean relative humidity had nearly no contribution to the model. The paper has developed an ecological niche model (ENM) that predicts the spatial distribution of H7N9 cases in China using environmental variables. The area under the curve (AUC) values of the model were greater than 0.9 (0.992 for the training samples and 0.961 for the test data). The findings indicated that most of the high risk areas were distributed in the Yangtze River Delta. These findings have important significance for the Chinese government to enhance the environmental surveillance at multiple human poultry interfaces in the high risk area. PMID:27322296
Gholamrezaei, Mostafa; Mohebali, Mehdi; Hanafi-Bojd, Ahmad Ali; Sedaghat, Mohammad Mehdi; Shirzadi, Mohammad Reza
Zoonotic cutaneous leishmaniasis (ZCL), caused by Leishmania major, is a common zoonotic vector-borne disease in Iran. Close contact with infected reservoir hosts increases the probability of transmission of Leishmania parasite infections to susceptible humans. Four gerbil species (Rodentia: Gerbillidae) serve as the main reservoir hosts for ZCL in different endemic foci of Iran. These species include Rhombomys opimus, Meriones libycus, Meriones hurrianae and Tatera indica; while notable infection has been reported in Nesokia indica as well. The purpose of this study is to model the distribution of these reservoirs to identify the risk areas of ZCL. A data bank was developed including all published data during the period of 1970-2015. Maximum entropy model was used to find the most appropriate ecological niches for each species. The areas under curve obtained were 0.961, 0.927, 0.922, 0.997 and 0.899, instead of 1, for training test in R. opimus, M. libycus, T. indica, M. hurrianae and N. indica, respectively. The environmental variable with the highest gain when used in isolation was slope for R. opimus and N. indica, annual mean temperature for M. libycus, and seasonal precipitation for T. indica and M. hurrianae. Summation of presence probabilities for three main species, i.e., R. opimus, M. libycus and T. indica revealed favorable ecological niches in wide areas of 16 provinces. This is the first study to predict the distribution of ZCL reservoir hosts in Iran. Climatology and topography variables had high contributions toward the prediction of potential distribution of the main reservoir species; therefore, as climate changes, the models should be updated periodically with novel data, and the results should be used in disease-monitoring programs.
Sen, Sandeep; Gode, Ameya; Ramanujam, Srirama; Ravikanth, G; Aravind, N A
The center of diversity of Piper nigrum L. (Black Pepper), one of the highly valued spice crops is reported to be from India. Black pepper is naturally distributed in India in the Western Ghats biodiversity hotspot and is the only known existing source of its wild germplasm in the world. We used ecological niche models to predict the potential distribution of wild P. nigrum in the present and two future climate change scenarios viz (A1B) and (A2A) for the year 2080. Three topographic and nine uncorrelated bioclim variables were used to develop the niche models. The environmental variables influencing the distribution of wild P. nigrum across different climate change scenarios were identified. We also assessed the direction and magnitude of the niche centroid shift and the change in niche breadth to estimate the impact of projected climate change on the distribution of P. nigrum. The study shows a niche centroid shift in the future climate scenarios. Both the projected future climate scenarios predicted a reduction in the habitat of P. nigrum in Southern Western Ghats, which harbors many wild accessions of P. nigrum. Our results highlight the impact of future climate change on P. nigrum and provide useful information for designing sound germplasm conservation strategies for P. nigrum.
Liu, Huatao; Wang, Wenjuan; Song, Gang; Qu, Yanhua; Li, Shou-Hsien; Fjeldså, Jon; Lei, Fumin
An area of endemism (AOE) is a complex expression of the ecological and evolutionary history of a species. Here we aim to address the principal drivers of avian diversification in shaping patterns of endemism in China by integrating genetic, ecological, and distributional data on the Red-headed Tree Babbler (Stachyridopsis ruficeps), which is distributed across the eastern Himalayas and south China. We sequenced two mtDNA markers from 182 individuals representing all three of the primary AOEs in China. Phylogenetic inferences were used to reconstruct intraspecific phylogenetic relationships. Divergence time and population demography were estimated to gain insight into the evolutionary history of the species. We used Ecological niche modeling to predict species’ distributions during the Last Glacial Maximum (LGM) and in the present. Finally, we also used two quantitative tests, an identity test and background test to assess the similarity of ecological niche preferences between adjacent lineages. We found five primary reciprocally monophyletic clades, typically separated approximately 0.2–2.27 MYA, of which three were deeply isolated endemic lineages located in the three AOEs. All phylogroups were detected to have undergone population expansion during the past 0.3 MY. Niche models showed discontinuous habitats, and there were three barriers of less suitable habitat during the LGM and in modern times. Ecoclimatic niches may diverge significantly even over recent timescales, as each phylogroup had a unique distribution, and unique niche characteristics. Vicariant events associated with geographical and ecological barriers, glacial refuges and ecological differentiation may be the main drivers forming the pattern of endemism in China. PMID:23056441
Gurgel-Gonçalves, Rodrigo; Galvão, Cléber; Costa, Jane; Peterson, A. Townsend
Although Brazil was declared free from Chagas disease transmission by the domestic vector Triatoma infestans, human acute cases are still being registered based on transmission by native triatomine species. For a better understanding of transmission risk, the geographic distribution of Brazilian triatomines was analyzed. Sixteen out of 62 Brazilian species that both occur in >20 municipalities and present synanthropic tendencies were modeled based on their ecological niches. Panstrongylus geniculatus and P. megistus showed broad ecological ranges, but most of the species sort out by the biome in which they are distributed: Rhodnius pictipes and R. robustus in the Amazon; R. neglectus, Triatoma sordida, and T. costalimai in the Cerrado; R. nasutus, P. lutzi, T. brasiliensis, T. pseudomaculata, T. melanocephala, and T. petrocchiae in the Caatinga; T. rubrovaria in the southern pampas; T. tibiamaculata and T. vitticeps in the Atlantic Forest. Although most occurrences were recorded in open areas (Cerrado and Caatinga), our results show that all environmental conditions in the country are favorable to one or more of the species analyzed, such that almost nowhere is Chagas transmission risk negligible. PMID:22523500
Ochieng, Alfred O.; Nanyingi, Mark; Kipruto, Edwin; Ondiba, Isabella M.; Amimo, Fred A.; Oludhe, Christopher; Olago, Daniel O.; Nyamongo, Isaac K.; Estambale, Benson B. A.
Background Rift Valley fever (RVF) is a vector-borne zoonotic disease that has an impact on human health and animal productivity. Here, we explore the use of vector presence modelling to predict the distribution of RVF vector species under climate change scenario to demonstrate the potential for geographic spread of Rift Valley fever virus (RVFV). Objectives To evaluate the effect of climate change on RVF vector distribution in Baringo County, Kenya, with an aim of developing a risk map for spatial prediction of RVF outbreaks. Methodology The study used data on vector presence and ecological niche modelling (MaxEnt) algorithm to predict the effect of climatic change on habitat suitability and the spatial distribution of RVF vectors in Baringo County. Data on species occurrence were obtained from longitudinal sampling of adult mosquitoes and larvae in the study area. We used present (2000) and future (2050) Bioclim climate databases to model the vector distribution. Results Model results predicted potential suitable areas with high success rates for Culex quinquefasciatus, Culex univitattus, Mansonia africana, and Mansonia uniformis. Under the present climatic conditions, the lowlands were found to be highly suitable for all the species. Future climatic conditions indicate an increase in the spatial distribution of Cx. quinquefasciatus and M. africana. Model performance was statistically significant. Conclusion Soil types, precipitation in the driest quarter, precipitation seasonality, and isothermality showed the highest predictive potential for the four species. PMID:27863533
Carvalho, B M; Rangel, E F; Vale, M M
Vector-borne diseases are exceptionally sensitive to climate change. Predicting vector occurrence in specific regions is a challenge that disease control programs must meet in order to plan and execute control interventions and climate change adaptation measures. Recently, an increasing number of scientific articles have applied ecological niche modelling (ENM) to study medically important insects and ticks. With a myriad of available methods, it is challenging to interpret their results. Here we review the future projections of disease vectors produced by ENM, and assess their trends and limitations. Tropical regions are currently occupied by many vector species; but future projections indicate poleward expansions of suitable climates for their occurrence and, therefore, entomological surveillance must be continuously done in areas projected to become suitable. The most commonly applied methods were the maximum entropy algorithm, generalized linear models, the genetic algorithm for rule set prediction, and discriminant analysis. Lack of consideration of the full-known current distribution of the target species on models with future projections has led to questionable predictions. We conclude that there is no ideal 'gold standard' method to model vector distributions; researchers are encouraged to test different methods for the same data. Such practice is becoming common in the field of ENM, but still lags behind in studies of disease vectors.
Yañez-Arenas, Carlos; Peterson, A. Townsend; Mokondoko, Pierre; Rojas-Soto, Octavio; Martínez-Meyer, Enrique
Background Many authors have claimed that snakebite risk is associated with human population density, human activities, and snake behavior. Here we analyzed whether environmental suitability of vipers can be used as an indicator of snakebite risk. We tested several hypotheses to explain snakebite incidence, through the construction of models incorporating both environmental suitability and socioeconomic variables in Veracruz, Mexico. Methodology/Principal Findings Ecological niche modeling (ENM) was used to estimate potential geographic and ecological distributions of nine viper species' in Veracruz. We calculated the distance to the species' niche centroid (DNC); this distance may be associated with a prediction of abundance. We found significant inverse relationships between snakebites and DNCs of common vipers (Crotalus simus and Bothrops asper), explaining respectively 15% and almost 35% of variation in snakebite incidence. Additionally, DNCs for these two vipers, in combination with marginalization of human populations, accounted for 76% of variation in incidence. Conclusions/Significance Our results suggest that niche modeling and niche-centroid distance approaches can be used to mapping distributions of environmental suitability for venomous snakes; combining this ecological information with socioeconomic factors may help with inferring potential risk areas for snakebites, since hospital data are often biased (especially when incidences are low). PMID:24963989
Vessella, Federico; Simeone, Marco Cosimo; Schirone, Bartolomeo
Ecological Niche Modelling (ENM) is widely used to depict species potential occurrence according to environmental variables under different climatic scenarios. We tested the ENM approach to infer past range dynamics of cork oak, a keystone species of the Mediterranean Biome, from 130 ka to the present time. Hindcasting implications would deal with a better species risk assessment and conservation management for the future. We modelled present and past occurrence of cork oak using seven ENM algorithms, starting from 63,733 spatially unique presence points at 30 arc-second resolution. Fourteen environmental variables were used and four time slices were considered (Last Interglacial, Last Glacial Maximum, mid-Holocene and present time). A threshold-independent evaluation of the goodness-of-fit of the models was evaluated by means of ROC curve and fossil or historical evidences were used to validate the results. Four weighted average maps depicted the dynamics of area suitability for cork oak in the last 130 ka. The derived species autoecology allowed its long-term occurrence in the Mediterranean without striking range reduction or shifting. Fossil and historical post-processing validation support the modelled past spatial extension and a neglected species presence at Levantine until the recent time. Despite the severe climatic oscillation since the Last Glacial Maximum, cork oak potential distribution area experienced limited range changes, confirming its strong link with the Mediterranean Basin. The ecological amplitude of Quercus suber could be therefore adopted as a reference to trace the Mediterranean bioclimate area. A better knowledge of the past events of Mediterranean vegetation, a wider range of study species and environmental determinants are essential to inform us about its current state, its sensitivity to human impact and the potential responses to future changes.
Saupe, Erin E.; Papes, Monica; Selden, Paul A.; Vetter, Richard S.
Most spiders use venom to paralyze their prey and are commonly feared for their potential to cause injury to humans. In North America, one species in particular, Loxosceles reclusa (brown recluse spider, Sicariidae), causes the majority of necrotic wounds induced by the Araneae. However, its distributional limitations are poorly understood and, as a result, medical professionals routinely misdiagnose brown recluse bites outside endemic areas, confusing putative spider bites for other serious conditions. To address the issue of brown recluse distribution, we employ ecological niche modeling to investigate the present and future distributional potential of this species. We delineate range boundaries and demonstrate that under future climate change scenarios, the spider's distribution may expand northward, invading previously unaffected regions of the USA. At present, the spider's range is centered in the USA, from Kansas east to Kentucky and from southern Iowa south to Louisiana. Newly influenced areas may include parts of Nebraska, Minnesota, Wisconsin, Michigan, South Dakota, Ohio, and Pennsylvania. These results illustrate a potential negative consequence of climate change on humans and will aid medical professionals in proper bite identification/treatment, potentially reducing bite misdiagnoses. PMID:21464985
Meentemeyer, Ross K; Anacker, Brian L; Mark, Walter; Rizzo, David M
Distinguishing the manner in which dispersal limitation and niche requirements control the spread of invasive pathogens is important for prediction and early detection of disease outbreaks. Here, we use niche modeling augmented by dispersal estimation to examine the degree to which local habitat conditions vs. force of infection predict invasion of Phytophthora ramorum, the causal agent of the emerging infectious tree disease sudden oak death. We sampled 890 field plots for the presence of P. ramorum over a three-year period (2003-2005) across a range of host and abiotic conditions with variable proximities to known infections in California, USA. We developed and validated generalized linear models of invasion probability to analyze the relative predictive power of 12 niche variables and a negative exponential dispersal kernel estimated by likelihood profiling. Models were developed incrementally each year (2003, 2003-2004, 2003-2005) to examine annual variability in model parameters and to create realistic scenarios for using models to predict future infections and to guide early-detection sampling. Overall, 78 new infections were observed up to 33.5 km from the nearest known site of infection, with slightly increasing rates of prevalence across time windows (2003, 6.5%; 2003-2004, 7.1%; 2003-2005, 9.6%). The pathogen was not detected in many field plots that contained susceptible host vegetation. The generalized linear modeling indicated that the probability of invasion is limited by both dispersal and niche constraints. Probability of invasion was positively related to precipitation and temperature in the wet season and the presence of the inoculum-producing foliar host Umbellularia californica and decreased exponentially with distance to inoculum sources. Models that incorporated niche and dispersal parameters best predicted the locations of new infections, with accuracies ranging from 0.86 to 0.90, suggesting that the modeling approach can be used to forecast
Tedrow, Christine Atkins
The primary goal in this study was to explore remote sensing, ecological niche modeling, and Geographic Information Systems (GIS) as aids in predicting candidate Rift Valley fever (RVF) competent vector abundance and distribution in Virginia, and as means of estimating where risk of establishment in mosquitoes and risk of transmission to human populations would be greatest in Virginia. A second goal in this study was to determine whether the remotely-sensed Normalized Difference Vegetation Index (NDVI) can be used as a proxy variable of local conditions for the development of mosquitoes to predict mosquito species distribution and abundance in Virginia. As part of this study, a mosquito surveillance database was compiled to archive the historical patterns of mosquito species abundance in Virginia. In addition, linkages between mosquito density and local environmental and climatic patterns were spatially and temporally examined. The present study affirms the potential role of remote sensing imagery for species distribution prediction, and it demonstrates that ecological niche modeling is a valuable predictive tool to analyze the distributions of populations. The MaxEnt ecological niche modeling program was used to model predicted ranges for potential RVF competent vectors in Virginia. The MaxEnt model was shown to be robust, and the candidate RVF competent vector predicted distribution map is presented. The Normalized Difference Vegetation Index (NDVI) was found to be the most useful environmental-climatic variable to predict mosquito species distribution and abundance in Virginia. However, these results indicate that a more robust prediction is obtained by including other environmental-climatic factors correlated to mosquito densities (e.g., temperature, precipitation, elevation) with NDVI. The present study demonstrates that remote sensing and GIS can be used with ecological niche and risk modeling methods to estimate risk of virus establishment in mosquitoes and
Slater, Hannah; Michael, Edwin
Modelling the spatial distributions of human parasite species is crucial to understanding the environmental determinants of infection as well as for guiding the planning of control programmes. Here, we use ecological niche modelling to map the current potential distribution of the macroparasitic disease, lymphatic filariasis (LF), in Africa, and to estimate how future changes in climate and population could affect its spread and burden across the continent. We used 508 community-specific infection presence data collated from the published literature in conjunction with five predictive environmental/climatic and demographic variables, and a maximum entropy niche modelling method to construct the first ecological niche maps describing potential distribution and burden of LF in Africa. We also ran the best-fit model against climate projections made by the HADCM3 and CCCMA models for 2050 under A2a and B2a scenarios to simulate the likely distribution of LF under future climate and population changes. We predict a broad geographic distribution of LF in Africa extending from the west to the east across the middle region of the continent, with high probabilities of occurrence in the Western Africa compared to large areas of medium probability interspersed with smaller areas of high probability in Central and Eastern Africa and in Madagascar. We uncovered complex relationships between predictor ecological niche variables and the probability of LF occurrence. We show for the first time that predicted climate change and population growth will expand both the range and risk of LF infection (and ultimately disease) in an endemic region. We estimate that populations at risk to LF may range from 543 and 804 million currently, and that this could rise to between 1.65 to 1.86 billion in the future depending on the climate scenario used and thresholds applied to signify infection presence. PMID:22359670
Taboada, Angela; von Wehrden, Henrik; Assmann, Thorsten
Detailed understanding of a species’ natural history and environmental needs across spatial scales is a primary requisite for effective conservation planning, particularly for species with complex life cycles in which different life stages occupy different niches and respond to the environment at different scales. However, niche models applied to conservation often neglect early life stages and are mostly performed at broad spatial scales. Using the endangered heath tiger beetle (Cicindela sylvatica) as a model species, we relate presence/absence and abundance data of locally dispersing adults and sedentary larvae to abiotic and biotic variables measured in a multiscale approach within the geographic extent relevant to active conservation management. At the scale of hundreds of meters, fine-grained abiotic conditions (i.e., vegetation structure) are fundamental determinants of the occurrence of both life stages, whereas the effect of biotic factors is mostly contained in the abiotic signature. The combination of dense heath vegetation and bare ground areas is thus the first requirement for the species’ preservation, provided that accessibility to the suitable habitat is ensured. At a smaller scale (centimetres), the influence of abiotic factors on larval occurrence becomes negligible, suggesting the existence of important additional variables acting within larval proximity. Sustained significant correlations between neighbouring larvae in the models provide an indication of the potential impact of neighbourhood crowding on the larval niche within a few centimetres. Since the species spends the majority of its life cycle in the larval stage, it is essential to consider the hierarchical abiotic and biotic processes affecting the larvae when designing practical conservation guidelines for the species. This underlines the necessity for a more critical evaluation of the consequences of disregarding niche variation between life stages when estimating niches and
Barro, Alassane S; Fegan, Mark; Moloney, Barbara; Porter, Kelly; Muller, Janine; Warner, Simone; Blackburn, Jason K
The ecology and distribution of B. anthracis in Australia is not well understood, despite the continued occurrence of anthrax outbreaks in the eastern states of the country. Efforts to estimate the spatial extent of the risk of disease have been limited to a qualitative definition of an anthrax belt extending from southeast Queensland through the centre of New South Wales and into northern Victoria. This definition of the anthrax belt does not consider the role of environmental conditions in the distribution of B. anthracis. Here, we used the genetic algorithm for rule-set prediction model system (GARP), historical anthrax outbreaks and environmental data to model the ecological niche of B. anthracis and predict its potential geographic distribution in Australia. Our models reveal the niche of B. anthracis in Australia is characterized by a narrow range of ecological conditions concentrated in two disjunct corridors. The most dominant corridor, used to redefine a new anthrax belt, parallels the Eastern Highlands and runs from north Victoria to central east Queensland through the centre of New South Wales. This study has redefined the anthrax belt in eastern Australia and provides insights about the ecological factors that limit the distribution of B. anthracis at the continental scale for Australia. The geographic distributions identified can help inform anthrax surveillance strategies by public and veterinary health agencies.
Barro, Alassane S.; Fegan, Mark; Moloney, Barbara; Porter, Kelly; Muller, Janine; Warner, Simone; Blackburn, Jason K.
The ecology and distribution of B. anthracis in Australia is not well understood, despite the continued occurrence of anthrax outbreaks in the eastern states of the country. Efforts to estimate the spatial extent of the risk of disease have been limited to a qualitative definition of an anthrax belt extending from southeast Queensland through the centre of New South Wales and into northern Victoria. This definition of the anthrax belt does not consider the role of environmental conditions in the distribution of B. anthracis. Here, we used the genetic algorithm for rule-set prediction model system (GARP), historical anthrax outbreaks and environmental data to model the ecological niche of B. anthracis and predict its potential geographic distribution in Australia. Our models reveal the niche of B. anthracis in Australia is characterized by a narrow range of ecological conditions concentrated in two disjunct corridors. The most dominant corridor, used to redefine a new anthrax belt, parallels the Eastern Highlands and runs from north Victoria to central east Queensland through the centre of New South Wales. This study has redefined the anthrax belt in eastern Australia and provides insights about the ecological factors that limit the distribution of B. anthracis at the continental scale for Australia. The geographic distributions identified can help inform anthrax surveillance strategies by public and veterinary health agencies. PMID:27280981
Hawlitschek, Oliver; Porch, Nick; Hendrich, Lars; Balke, Michael
Background DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data. Methodology/Principal Findings The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n. Conclusion/Significance In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species. PMID:21347370
Santos, Xavier; Felicísimo, Ángel M.
Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks. PMID
Fernández, Miguel; Hamilton, Healy
Species distribution modeling is widely applied to predict invasive species distributions and species range shifts under climate change. Accurate predictions depend upon meeting the assumption that ecological niches are conserved, i.e., spatially or temporally transferable. Here we present a multi-taxon comparative analysis of niche conservatism using biological invasion events well documented in natural history museum collections. Our goal is to assess spatial transferability of the climatic niche of a range of noxious terrestrial invasive species using two complementary approaches. First we compare species' native versus invasive ranges in environmental space using two distinct methods, Principal Components Analysis and Mahalanobis distance. Second we compare species' native versus invaded ranges in geographic space as estimated using the species distribution modeling technique Maxent and the comparative index Hellinger's I. We find that species exhibit a range of responses, from almost complete transferability, in which the invaded niches completely overlap with the native niches, to a complete dissociation between native and invaded ranges. Intermediate responses included expansion of dimension attributable to either temperature or precipitation derived variables, as well as niche expansion in multiple dimensions. We conclude that the ecological niche in the native range is generally a poor predictor of invaded range and, by analogy, the ecological niche may be a poor predictor of range shifts under climate change. We suggest that assessing dimensions of niche transferability prior to standard species distribution modeling may improve the understanding of species' dynamics in the invaded range.
Kumar, Sunil; Neven, Lisa G; Yee, Wee L
Sweet cherries, Prunus avium (L.) L., grown in the western United States are exported to many countries around the world. Some of these countries have enforced strict quarantine rules and trade restrictions owing to concerns about the potential establishment and subsequent spread of western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), a major quarantine pest of sweet cherry. We used 1) niche models (CLIMEX and MaxEnt) to map the climatic suitability, 2) North Carolina State University-Animal and Plant Health Inspection Service Plant Pest Forecasting System to examine chilling requirement, and 3) host distribution and availability to assess the potential for establishment of R. indifferens in areas of western North America where it currently does not exist and eight current or potential fresh sweet cherry markets: Colombia, India, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam. Results from niche models conformed well to the current distribution of R. indifferens in western North America. MaxEnt and CLIMEX models had high performance and predicted climatic suitability in some of the countries (e.g., Andean range in Colombia and Venezuela, northern and northeastern India, central Taiwan, and parts of Vietnam). However, our results showed no potential for establishment of R. indifferens in Colombia, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam when the optimal chilling requirement to break diapause (minimum temperature < or = 3 degree C for at least 15 wk) was used as the criterion for whether establishment can occur. Furthermore, these countries have no host plant species available for R. indifferens. Our results can be used to make scientifically informed international trade decisions and negotiations by policy makers.
Wellenreuther, Maren; Larson, Keith W; Svensson, Erik I
The factors that determine species' range limits are of central interest to biologists. One particularly interesting group comprises odonates (dragonflies and damselflies), which show large differences in secondary sexual traits and respond quickly to climatic factors, but often have minor interspecific niche differences, challenging models of niche-based species coexistence. We quantified the environmental niches at two geographic scales to understand the ecological causes of northern range limits and the coexistence of two congeneric damselflies (Calopteryx splendens and C. virgo). Using environmental niche modeling, we quantified niche divergence first across the whole geographic range in Fennoscandia, and second only in the sympatric part of this range. We found evidence for interspecific divergence along the environmental axes of temperature and precipitation across the northern range in Fennoscandia, suggesting that adaptation to colder and wetter climate might have allowed C. virgo to expand farther north than C. splendens. However, in the sympatric zone in southern Fennoscandia we found only negligible and nonsignificant niche differences. Minor niche differences in sympatry lead to frequent encounters and intense interspecific sexual interactions at the local scale of populations. Nevertheless, niche differences across Fennoscandia suggest that species differences in physiological tolerances limit range expansions northward, and that current and future climate could have large effects on the distributional ranges of these and ecologically similar insects.
Wei, Lan; Qian, Quan; Wang, Zhi-Qiang; Glass, Gregory E.; Song, Shao-Xia; Zhang, Wen-Yi; Li, Xiu-Jun; Yang, Hong; Wang, Xian-Jun; Fang, Li-Qun; Cao, Wu-Chun
Hemorrhagic fever with renal syndrome (HFRS) is an important public health problem in Shandong Province, China. In this study, we combined ecologic niche modeling with geographic information systems (GIS) and remote sensing techniques to identify the risk factors and affected areas of hantavirus infections in rodent hosts. Land cover and elevation were found to be closely associated with the presence of hantavirus-infected rodent hosts. The averaged area under the receiver operating characteristic curve was 0.864, implying good performance. The predicted risk maps based on the model were validated both by the hantavirus-infected rodents' distribution and HFRS human case localities with a good fit. These findings have the applications for targeting control and prevention efforts. PMID:21363991
Boavida, Joana; Assis, Jorge; Silva, Inga; Serrão, Ester A.
Factors shaping the distribution of mesophotic octocorals (30–200 m depth) remain poorly understood, potentially leaving overlooked coral areas, particularly near their bathymetric and geographic distributional limits. Yet, detailed knowledge about habitat requirements is crucial for conservation of sensitive gorgonians. Here we use Ecological Niche Modelling (ENM) relating thirteen environmental predictors and a highly comprehensive presence dataset, enhanced by SCUBA diving surveys, to investigate the suitable habitat of an important structuring species, Paramuricea clavata, throughout its distribution (Mediterranean and adjacent Atlantic). Models showed that temperature (11.5–25.5 °C) and slope are the most important predictors carving the niche of P. clavata. Prediction throughout the full distribution (TSS 0.9) included known locations of P. clavata alongside with previously unknown or unreported sites along the coast of Portugal and Africa, including seamounts. These predictions increase the understanding of the potential distribution for the northern Mediterranean and indicate suitable hard bottom areas down to >150 m depth. Poorly sampled habitats with predicted presence along Algeria, Alboran Sea and adjacent Atlantic coasts encourage further investigation. We propose that surveys of target areas from the predicted distribution map, together with local expert knowledge, may lead to discoveries of new P. clavata sites and identify priority conservation areas. PMID:27841263
Boavida, Joana; Assis, Jorge; Silva, Inga; Serrão, Ester A
Factors shaping the distribution of mesophotic octocorals (30-200 m depth) remain poorly understood, potentially leaving overlooked coral areas, particularly near their bathymetric and geographic distributional limits. Yet, detailed knowledge about habitat requirements is crucial for conservation of sensitive gorgonians. Here we use Ecological Niche Modelling (ENM) relating thirteen environmental predictors and a highly comprehensive presence dataset, enhanced by SCUBA diving surveys, to investigate the suitable habitat of an important structuring species, Paramuricea clavata, throughout its distribution (Mediterranean and adjacent Atlantic). Models showed that temperature (11.5-25.5 °C) and slope are the most important predictors carving the niche of P. clavata. Prediction throughout the full distribution (TSS 0.9) included known locations of P. clavata alongside with previously unknown or unreported sites along the coast of Portugal and Africa, including seamounts. These predictions increase the understanding of the potential distribution for the northern Mediterranean and indicate suitable hard bottom areas down to >150 m depth. Poorly sampled habitats with predicted presence along Algeria, Alboran Sea and adjacent Atlantic coasts encourage further investigation. We propose that surveys of target areas from the predicted distribution map, together with local expert knowledge, may lead to discoveries of new P. clavata sites and identify priority conservation areas.
Bedia, Joaquín; Herrera, Sixto; Gutiérrez, José Manuel
Global bioclimatic datasets are being widely used in ecological research to estimate the potential distribution of species using Climate Envelope Models (CEMs). These datasets are easily available and offer high resolution information for all land areas globally. However, they have not been tested rigorously in smaller regions, and their use in regional CEM studies may pose problems derived from their poor representation of local climate features. Moreover, these problems may be enhanced when using CEMs for future climate projections—a topic of current active research—due to the uncertainty derived from the future altered climate scenarios.
Background The purpose of this study is to create distribution models of two sand fly species, Phlebotomus papatasi (Scopoli) and P. alexandri (Sinton), across the Middle East. Phlebotomus alexandri is a vector of visceral leishmaniasis, while P. papatasi is a vector of cutaneous leishmaniasis and sand fly fever. Collection records were obtained from literature reports from 1950 through 2007 and unpublished field collection records. Environmental layers considered in the model were elevation, precipitation, land cover, and WorldClim bioclimatic variables. Models were evaluated using the threshold-independent area under the curve (AUC) receiver operating characteristic analysis and the threshold-dependent minimum training presence. Results For both species, land cover was the most influential environmental layer in model development. The bioclimatic and elevation variables all contributed to model development; however, none influenced the model as strongly as land cover. Conclusion While not perfect representations of the absolute distribution of P. papatasi and P. alexandri, these models indicate areas with a higher probability of presence of these species. This information could be used to help guide future research efforts into the ecology of these species and epidemiology of the pathogens that they transmit. PMID:20089198
Nekaris, K. Anne-Isola; Arnell, Andrew P.; Svensson, Magdalena S.
Simple Summary Large “charismatic” animals (with widespread popular appeal) are often used as flagship species to raise awareness for conservation. Deforestation and forest fragmentation are among the main threats to biodiversity, and in many places such species are disappearing. In this paper we aim to find a suitable species among the less charismatic animal species left in the fragmented forests of South-western Sri Lanka. We selected ten candidates, using a questionnaire survey along with computer modelling of their distributions. The red slender loris and the fishing cat came out as finalists as they were both appealing to local people, and fulfilled selected ecological criteria. Abstract Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt) modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective
Fand, Babasaheb B; Kumar, Mahesh; Kamble, Ankush L
Mealybug, Phenacoccus solenopsis Tinsley has recently emerged as a serious insect pest of cotton in India. This study demonstrates the use of Maxent algorithm for modeling the potential geographic distribution of P. solenopsis in India with presence-only data. Predictions were made based on the analysis of the relationship between 111 occurrence records for P. solenopsis and the corresponding current and future climate data defined on the study area. The climate data from worldclim database for current (1950-2000) and future (SRES A2 emission scenario for 2050) conditions were used. DIVA-GIS, an open source software for conducting spatial analysis was used for mapping the predictions from Maxent. The algorithm provided reasonable estimates of the species range indicating better discrimination of suitable and unsuitable areas for its occurrence in India under both present and future climatic conditions. The fit for the model as measured by AUC was high, with value of 0.930 for the training data and 0.895 for the test data, indicating the high level of discriminatory power for the Maxent. A Jackknife test for variable importance indicated that mean temperature of coldest quarter with highest gain value was the most important environmental variable determining the potential geographic distribution of P. solenopsis. The approaches used for delineating the ecological niche and prediction of potential geographic distribution are described briefly. Possible applications and limitations of the present modeling approach in future research and as a decision making tool in integrated pest management are discussed.
Signorini, Manuela; Cassini, Rudi; Drigo, Michele; Frangipane di Regalbono, Antonio; Pietrobelli, Mario; Montarsi, Fabrizio; Stensgaard, Anna-Sofie
With respect to the epidemiology of leishmaniasis, it is crucial to take into account the ecoclimatic and environmental characteristics that influence the distribution patterns of the vector sand fly species. It is also important to consider the possible impact of on-going climate changes on the emergence of this disease. In order to map the potential distribution of Phlebotomus perniciosus, the main vector species of canine leishmaniasis in north-eastern Italy, geographical information systems tools, ecological niche models (ENM) and remotely sensed environmental data were applied for a retrospective analysis of an entomological survey conducted in north-eastern Italy over 12 years. Sand fly trapping was conducted from 2001 to 2012 in 175 sites in the provinces of Veneto, Friuli-Venezia Giulia and Trentino-Alto Adige. We developed a predictive model of potential distribution of P. perniciosus using the maximum entropy algorithm software, based on seasonal normalized difference vegetation index, day and night land surface temperature, the Corine land cover 2006, a digital elevation model (GTOPO30) and climate layers obtained from the WorldClim database. The MaxEnt prediction found the more suitable habitat for P. perniciosus to be hilly areas (100-300 m above the mean sea level) characterised by temperate climate during the winter and summer seasons, high winter vegetation cover and moderate rainfall during the activity season of vector sand fly. ENM provided a greater understanding of the geographical distribution and ecological requirements of P. perniciosus in the study area, which can be applied for the development of future surveillance strategies.
Cáceres, Nilton Carlos; de Moraes Weber, Marcelo; Melo, Geruza Leal; Meloro, Carlo; Sponchiado, Jonas; Carvalho, Renan dos Santos; Bubadué, Jamile de Moura
Didelphis albiventris and D. aurita are Neotropical marsupials that share a unique evolutionary history and both are largely distributed throughout South America, being primarily allopatric throughout their ranges. In the Araucaria moist forest of Southern Brazil these species are sympatric and they might potentially compete having similar ecology. For this reason, they are ideal biological models to address questions about ecological character displacement and how closely related species might share their geographic space. Little is known about how two morphologically similar species of marsupials may affect each other through competition, if by competitive exclusion and competitive release. We combined ecological niche modeling and geometric morphometrics to explore the possible effects of competition on their distributional ranges and skull morphology. Ecological niche modeling was used to predict their potential distribution and this method enabled us to identify a case of biotic exclusion where the habit generalist D. albiventris is excluded by the presence of the specialist D. aurita. The morphometric analyses show that a degree of shape discrimination occurs between the species, strengthened by allometric differences, which possibly allowed them to occupy marginally different feeding niches supplemented by behavioral shift in contact areas. Overlap in skull morphology is shown between sympatric and allopatric specimens and a significant, but weak, shift in shape occurs only in D. aurita in sympatric areas. This could be a residual evidence of a higher past competition between both species, when contact zones were possibly larger than today. Therefore, the specialist D. aurita acts a biotic barrier to D. albiventris when niche diversity is not available for coexistence. On the other hand, when there is niche diversification (e.g. habitat mosaic), both species are capable to coexist with a minimal competitive effect on the morphology of D. aurita. PMID
Sindato, Calvin; Stevens, Kim B.; Karimuribo, Esron D.; Mboera, Leonard E. G.; Paweska, Janusz T.; Pfeiffer, Dirk U.
Background Despite the long history of Rift Valley fever (RVF) in Tanzania, extent of its suitable habitat in the country remains unclear. In this study we investigated potential effects of temperature, precipitation, elevation, soil type, livestock density, rainfall pattern, proximity to wild animals, protected areas and forest on the habitat suitability for RVF occurrence in Tanzania. Materials and Methods Presence-only records of 193 RVF outbreak locations from 1930 to 2007 together with potential predictor variables were used to model and map the suitable habitats for RVF occurrence using ecological niche modelling. Ground-truthing of the model outputs was conducted by comparing the levels of RVF virus specific antibodies in cattle, sheep and goats sampled from locations in Tanzania that presented different predicted habitat suitability values. Principal Findings Habitat suitability values for RVF occurrence were higher in the northern and central-eastern regions of Tanzania than the rest of the regions in the country. Soil type and precipitation of the wettest quarter contributed equally to habitat suitability (32.4% each), followed by livestock density (25.9%) and rainfall pattern (9.3%). Ground-truthing of model outputs revealed that the odds of an animal being seropositive for RVFV when sampled from areas predicted to be most suitable for RVF occurrence were twice the odds of an animal sampled from areas least suitable for RVF occurrence (95% CI: 1.43, 2.76, p < 0.001). Conclusion/Significance The regions in the northern and central-eastern Tanzania were more suitable for RVF occurrence than the rest of the regions in the country. The modelled suitable habitat is characterised by impermeable soils, moderate precipitation in the wettest quarter, high livestock density and a bimodal rainfall pattern. The findings of this study should provide guidance for the design of appropriate RVF surveillance, prevention and control strategies which target areas with
Valle, Mireia; Borja, Ángel; Chust, Guillem; Galparsoro, Ibon; Garmendia, Joxe Mikel
Predicting species distribution and habitat suitability is of considerable use in supporting the implementation of environmental legislation, protection and conservation of marine waters and ecosystem-based management. As other seagrasses, Zostera noltii has declined worldwide, mainly due to human pressures, such as eutrophication and habitat loss. In the case of the Basque Country (northern Spain), the species is present only in 3 out of 12 estuaries. From the literature, it is known that at least 6 of these estuaries were formerly vegetated by this seagrass. Consequently, efforts to monitor and restore (potential) habitats have been enhanced. Therefore, we aim: (i) to determine the main environmental variables explaining Zostera noltii distribution, within the Basque estuaries based upon the Oka estuary; (ii) to model habitat suitability for this species, as a wider applicable management-decision tool for seagrass restoration; and (iii) to assess the applicability and predicted accuracy of the model by using internal and external validation methods. For this purpose, Ecological Niche Factor Analysis (ENFA) has been used to model habitat suitability, based upon topographical variables, obtained from bathymetric Light Detection And Ranging (LiDAR); sediment characteristics variables; and hydrodynamic variables. The results obtained from the ecological factors of the ENFA (Marginality: 1.00; Specialization: 2.59) indicate that the species habitat differs considerably from the mean environmental conditions over the study area; likewise, that the species is restrictive in the selection of the range of conditions within which it dwells. The main environmental variables relating to the species distribution, in order of importance, are: mean grain size; redox potential; intertidal height; sediment sorting; slope of intertidal flat; percentage of gravels; and percentage of organic matter content. The model has a high predicted accuracy (Boyce index: 0.92). Model
Abdel-Dayem, M S; Annajar, B B; Hanafi, H A; Obenauer, P J
The increased cases of cutaneous leishmaniasis vectored by Phlebotomus papatasi (Scopoli) in Libya have driven considerable effort to develop a predictive model for the potential geographical distribution of this disease. We collected adult P. papatasi from 17 sites in Musrata and Yefern regions of Libya using four different attraction traps. Our trap results and literature records describing the distribution of P. papatasi were incorporated into a MaxEnt algorithm prediction model that used 22 environmental variables. The model showed a high performance (AUC = 0.992 and 0.990 for training and test data, respectively). High suitability for P. papatasi was predicted to be largely confined to the coast at altitudes <600 m. Regions south of 300 degrees N latitude were calculated as unsuitable for this species. Jackknife analysis identified precipitation as having the most significant predictive power, while temperature and elevation variables were less influential. The National Leishmaniasis Control Program in Libya may find this information useful in their efforts to control zoonotic cutaneous leishmaniasis. Existing records are strongly biased toward a few geographical regions, and therefore, further sand fly collections are warranted that should include documentation of such factors as soil texture and humidity, land cover, and normalized difference vegetation index (NDVI) data to increase the model's predictive power.
Kumar, S.; Kulloli, R. N.; Tewari, J. C.; Singh, J. P.; Singh, A.
Ceropegia bulbosa Roxb. is a narrow endemic, tuberous twiner of Asclepiadaceae family. It is medicinally important: tubers are nutritive and edible, leaves are digestive and a cure for dysentery and diarrhea. Exploitation for its tubers and poor regeneration of this species has shrunk its distribution. In order to know its present status, we report here the results of its appraisal in Rajasthan, using remote sensing and ground truthing in the past five years (2009-14). A base map of C. bulbosa was prepared using Geographical Information System (GIS), open source software Quantum GIS, SAGA. The Landsat Enhanced Thematic Mapper (ETM) +Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), Global Digital Elevation Model (GDEM) Satellite Data were used in this study. ASTER and GDEM Data was clipped with district boundary and provided color range to get elevation information. A digital elevation model of Rajasthan physiography was developed from ASTER GDEM of 30-m resolution. GIS layers of Area of occurrences for C. bulbosa plant and elevation were created. This map along with topographic sheets of 1:50000 were used for field traversing and ground truthing as per GPS location inferred from map. Its geographic distribution was assessed using MaxEnt distribution modelling algorithm that employed 12 presence locality data, 19 bioclimatic variables, and elevation data. Results of this modelling predicted occurrence of C. bulbosa in the districts of Sirohi, Jalore, Barmer, Pali, Ajmer, Jhalawar, Dungarpur, Banswara, Baran, Kota, Bundi and Chittorgarh. Ground validation in these districts revealed its presence only at four places in three districts confirming its rarity. Analysis of dominance at their sites of occurrence revealed their poor populations and sub dominant status (RIV = 20-32) and very low density (2-12 plants per tenth ha).
Mudenda, Ntombi B; Malone, John B; Kearney, Michael T; Mischler, Paula D; Nieto, Prixia del Mar; McCarroll, Jennifer C; Vounatsou, Penelope
The distribution of hookworm in schistosomiasis-endemic areas in Brazil was mapped based on climate suitability. Known biological requirements of hookworm were fitted to data in a monthly long-term normal climate grid (18 x 18 km) using geographical information systems. Hookworm risk models were produced using the growing degree day (GDD) water budget (WB) concept. A moisture-adjusted model (MA-GDD) was developed based on accumulation of monthly temperatures above a base temperature of 15 °C (below which there is no lifecycle progression of Necator americanus) conditional on concurrent monthly values (rain/potential, evapotranspiration) of over 0.4. A second model, designated the gradient index, was calculated based on the monthly accumulation of the product of GDD and monthly WB values (GDD x WB). Both parameters had a significant positive correlation to hookworm prevalence. In the northeastern part of Brazil (the Caatinga), low hookworm prevalence was due to low soil moisture content, while the low prevalence in southern Brazil was related to low mean monthly temperatures. Both environmental temperature and soil moisture content were found to be important parameters for predicting the prevalence of N. americanus.
Gilichinsky, D; Rivkina, E; Shcherbakova, V; Laurinavichuis, K; Tiedje, J
This study describes brine lenses (cryopegs) found in Siberian permafrost derived from ancient marine sediment layers of the Arctic Ocean. The cryopegs were formed and isolated from sediment ~100,000-120,000 years ago. They remain liquid at the in situ temperature of -10 degrees C as a result of their high salt content (170-300 g/L). [(14)C] Glucose is taken up by the cryopeg biomass at -15 degrees C, indicating microbial metabolism at low temperatures in this habitat. Furthermore, aerobic, anaerobic heterotrophs, sulfate reducers, acetogens, and methanogens were detected by most probable number analysis. Two psychrophilic microbes were isolated from the cryopegs, a Clostridium and a Psychrobacter. The closest relatives of each were previously isolated from Antarctica. The cryopeg econiche might serve as a model for extraterrestrial life, and hence is of particular interest to astrobiology.
Mendoza-González, Gabriela; Martínez, M Luisa; Rojas-Soto, Octavio R; Vázquez, Gabriela; Gallego-Fernández, Juan B
Climate change (CC) and sea level rise (SLR) are phenomena that could have severe impacts on the distribution of coastal dune vegetation. To explore this we modeled the climatic niches of six coastal dunes plant species that grow along the shoreline of the Gulf of Mexico and the Yucatan Peninsula, and projected climatic niches to future potential distributions based on two CC scenarios and SLR projections. Our analyses suggest that distribution of coastal plants will be severely limited, and more so in the case of local endemics (Chamaecrista chamaecristoides, Palafoxia lindenii, Cakile edentula). The possibilities of inland migration to the potential 'new shoreline' will be limited by human infrastructure and ecosystem alteration that will lead to a 'coastal squeeze' of the coastal habitats. Finally, we identified areas as future potential refuges for the six species in central Gulf of Mexico, and northern Yucatán Peninsula especially under CC and SLR scenarios.
Miller-Coleman, Robin L.; Dodsworth, Jeremy A.; Ross, Christian A.; Shock, Everett L.; Williams, Amanda J.; Hartnett, Hilairy E.; McDonald, Austin I.; Havig, Jeff R.; Hedlund, Brian P.
Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7–8.5 at concentrations up to 6.6×106 16S rRNA gene copies g−1 wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to
Miller-Coleman, Robin L; Dodsworth, Jeremy A; Ross, Christian A; Shock, Everett L; Williams, Amanda J; Hartnett, Hilairy E; McDonald, Austin I; Havig, Jeff R; Hedlund, Brian P
Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7-8.5 at concentrations up to 6.6×10(6) 16S rRNA gene copies g(-1) wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to
Plague has been established in the western United States (US) since 1900 following the West Coast introduction of commensal rodents infected with Yersinia pestis via early industrial shipping. Over the last century, plague ecology has transitioned through cycles of widespread human transmission, urban domestic transmission among commensal rodents, and ultimately settled into the predominantly sylvan foci that remain today where it is maintained alternatively by enzootic and epizootic transmission. While zoonotic transmission to humans is much less common in modern times, significant plague risk remains in parts of the western US. Moreover, risk to some threatened species that are part of the epizootic cycle can be quite substantive. This investigation attempted to predict the risk of plague across the western US by modeling the ecologic niche of plague in sylvan and domestic animals identified between 2000 and 2015. A Maxent machine learning algorithm was used to predict this niche based on climate, altitude, land cover, and the presence of an important enzootic species, Peromyscus maniculatus. This model demonstrated good predictive ability (AUC = 86%) and identified areas of high risk in central Colorado, north-central New Mexico, and southwestern and northeastern California. The presence of P. maniculatus, altitude, precipitation during the driest and wettest quarters, and distance to artificial surfaces, all contributed substantively to maximizing the gain function. These findings add to the known landscape epidemiology and infection ecology of plague in the western US and may suggest locations of particular risk to be targeted for wild and domestic animal intervention. PMID:26713244
Banks, William E.; d'Errico, Francesco; Peterson, A. Townsend; Kageyama, Masa; Colombeau, Guillaume
A variety of approaches have been used to reconstruct glacial distributions of species, identify their environmental characteristics, and understand their influence on subsequent population expansions. Traditional methods, however, provide only rough estimates of past distributions, and are often unable to identify the ecological and geographic processes that shaped them. Recently, ecological niche modeling (ENM) methodologies have been applied to these questions in an effort to overcome such limitations. We apply ENM to the European faunal record of the Last Glacial Maximum (LGM) to reconstruct ecological niches and potential ranges for caribou ( Rangifer tarandus) and red deer ( Cervus elaphus), and evaluate whether their LGM distributions resulted from tracking the geographic footprint of their ecological niches (niche conservatism) or if ecological niche shifts between the LGM and present might be implicated. Results indicate that the LGM geographic ranges of both species represent distributions characterized by niche conservatism, expressed through geographic contraction of the geographic footprints of their respective ecological niches.
Williams, Richard J; Purves, Drew W
The structure of food webs, complex networks of interspecies feeding interactions, plays a crucial role in ecosystem resilience and function, and understanding food web structure remains a central problem in ecology. Previous studies have shown that key features of empirical food webs can be reproduced by low-dimensional "niche" models. Here we examine the form and variability of food web niche structure by fitting a probabilistic niche model to 37 empirical food webs, a much larger number of food webs than used in previous studies. The model relaxes previous assumptions about parameter distributions and hierarchy and returns parameter estimates for each species in each web. The model significantly outperforms previous niche model variants and also performs well for several webs where a body-size-based niche model performs poorly, implying that traits other than body size are important in structuring these webs' niche space. Parameter estimates frequently violate previous models' assumptions: in 19 of 37 webs, parameter values are not significantly hierarchical, 32 of 37 webs have nonuniform niche value distributions, and 15 of 37 webs lack a correlation between niche width and niche position. Extending the model to a two-dimensional niche space yields networks with a mixture of one- and two-dimensional niches and provides a significantly better fit for webs with a large number of species and links. These results confirm that food webs are strongly niche-structured but reveal substantial variation in the form of the niche structuring, a result with fundamental implications for ecosystem resilience and function.
Williams, Richard J; Anandanadesan, Ananthi; Purves, Drew
The niche model has been widely used to model the structure of complex food webs, and yet the ecological meaning of the single niche dimension has not been explored. In the niche model, each species has three traits, niche position, diet position and feeding range. Here, a new probabilistic niche model, which allows the maximum likelihood set of trait values to be estimated for each species, is applied to the food web of the Benguela fishery. We also developed the allometric niche model, in which body size is used as the niche dimension. About 80% of the links in the empirical data are predicted by the probabilistic niche model, a significant improvement over recent models. As in the niche model, species are uniformly distributed on the niche axis. Feeding ranges are exponentially distributed, but diet positions are not uniformly distributed below the predator. Species traits are strongly correlated with body size, but the allometric niche model performs significantly worse than the probabilistic niche model. The best-fit parameter set provides a significantly better model of the structure of the Benguela food web than was previously available. The methodology allows the identification of a number of taxa that stand out as outliers either in the model's poor performance at predicting their predators or prey or in their parameter values. While important, body size alone does not explain the structure of the one-dimensional niche.
Aguilée, Robin; Raoul, Gaël; Rousset, François; Ronce, Ophélie
Species may survive climate change by migrating to track favorable climates and/or adapting to different climates. Several quantitative genetics models predict that species escaping extinction will change their geographical distribution while keeping the same ecological niche. We introduce pollen dispersal in these models, which affects gene flow but not directly colonization. We show that plant populations may escape extinction because of both spatial range and ecological niche shifts. Exact analytical formulas predict that increasing pollen dispersal distance slows the expected spatial range shift and accelerates the ecological niche shift. There is an optimal distance of pollen dispersal, which maximizes the sustainable rate of climate change. These conclusions hold in simulations relaxing several strong assumptions of our analytical model. Our results imply that, for plants with long distance of pollen dispersal, models assuming niche conservatism may not accurately predict their future distribution under climate change. PMID:27621443
Micheletti, Steven J; Storfer, Andrew
The central-marginal hypothesis (CMH) predicts that population size, genetic diversity and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean centre on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core-to-edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.
Pauwels, Maxime; Pasierbinski, Andrzej; Przedpelska-Wasowicz, Ewa M.; Babst-Kostecka, Alicja A.; Saumitou-Laprade, Pierre; Rostanski, Adam
The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest. PMID:26835186
Jackson, S.T.; Betancourt, J.L.; Booth, R.K.; Gray, S.T.
Climate change in the coming centuries will be characterized by interannual, decadal, and multidecadal fluctuations superimposed on anthropogenic trends. Predicting ecological and biogeographic responses to these changes constitutes an immense challenge for ecologists. Perspectives from climatic and ecological history indicate that responses will be laden with contingencies, resulting from episodic climatic events interacting with demographic and colonization events. This effect is compounded by the dependency of environmental sensitivity upon life-stage for many species. Climate variables often used in empirical niche models may become decoupled from the proximal variables that directly influence individuals and populations. Greater predictive capacity, and morefundamental ecological and biogeographic understanding, will come from integration of correlational niche modeling with mechanistic niche modeling, dynamic ecological modeling, targeted experiments, and systematic observations of past and present patterns and dynamics.
Jackson, Stephen T.; Betancourt, Julio L.; Booth, Robert K.; Gray, Stephen T.
Climate change in the coming centuries will be characterized by interannual, decadal, and multidecadal fluctuations superimposed on anthropogenic trends. Predicting ecological and biogeographic responses to these changes constitutes an immense challenge for ecologists. Perspectives from climatic and ecological history indicate that responses will be laden with contingencies, resulting from episodic climatic events interacting with demographic and colonization events. This effect is compounded by the dependency of environmental sensitivity upon life-stage for many species. Climate variables often used in empirical niche models may become decoupled from the proximal variables that directly influence individuals and populations. Greater predictive capacity, and more-fundamental ecological and biogeographic understanding, will come from integration of correlational niche modeling with mechanistic niche modeling, dynamic ecological modeling, targeted experiments, and systematic observations of past and present patterns and dynamics. PMID:19805104
Jackson, Stephen T; Betancourt, Julio L; Booth, Robert K; Gray, Stephen T
Climate change in the coming centuries will be characterized by interannual, decadal, and multidecadal fluctuations superimposed on anthropogenic trends. Predicting ecological and biogeographic responses to these changes constitutes an immense challenge for ecologists. Perspectives from climatic and ecological history indicate that responses will be laden with contingencies, resulting from episodic climatic events interacting with demographic and colonization events. This effect is compounded by the dependency of environmental sensitivity upon life-stage for many species. Climate variables often used in empirical niche models may become decoupled from the proximal variables that directly influence individuals and populations. Greater predictive capacity, and more-fundamental ecological and biogeographic understanding, will come from integration of correlational niche modeling with mechanistic niche modeling, dynamic ecological modeling, targeted experiments, and systematic observations of past and present patterns and dynamics.
Jackson, Stephen T.; Betancourt, Julio L.; Booth, Robert K.; Gray, Stephen T.
Climate change in the coming centuries will be characterized by interannual, decadal, and multidecadal fluctuations superimposed on anthropogenic trends. Predicting ecological and biogeographic responses to these changes constitutes an immense challenge for ecologists. Perspectives from climatic and ecological history indicate that responses will be laden with contingencies, resulting from episodic climatic events interacting with demographic and colonization events. This effect is compounded by the dependency of environmental sensitivity upon life-stage for many species. Climate variables often used in empirical niche models may become decoupled from the proximal variables that directly influence individuals and populations. Greater predictive capacity, and more-fundamental ecological and biogeographic understanding, will come from integration of correlational niche modeling with mechanistic niche modeling, dynamic ecological modeling, targeted experiments, and systematic observations of past and present patterns and dynamics.
Simard, Frédéric; Ayala, Diego; Kamdem, Guy Colince; Pombi, Marco; Etouna, Joachim; Ose, Kenji; Fotsing, Jean-Marie; Fontenille, Didier; Besansky, Nora J; Costantini, Carlo
Background Speciation among members of the Anopheles gambiae complex is thought to be promoted by disruptive selection and ecological divergence acting on sets of adaptation genes protected from recombination by polymorphic paracentric chromosomal inversions. However, shared chromosomal polymorphisms between the M and S molecular forms of An. gambiae and insufficient information about their relationship with ecological divergence challenge this view. We used Geographic Information Systems, Ecological Niche Factor Analysis, and Bayesian multilocus genetic clustering to explore the nature and extent of ecological and chromosomal differentiation of M and S across all the biogeographic domains of Cameroon in Central Africa, in order to understand the role of chromosomal arrangements in ecological specialisation within and among molecular forms. Results Species distribution modelling with presence-only data revealed differences in the ecological niche of both molecular forms and the sibling species, An. arabiensis. The fundamental environmental envelope of the two molecular forms, however, overlapped to a large extent in the rainforest, where they occurred in sympatry. The S form had the greatest niche breadth of all three taxa, whereas An. arabiensis and the M form had the smallest niche overlap. Correspondence analysis of M and S karyotypes confirmed that molecular forms shared similar combinations of chromosomal inversion arrangements in response to the eco-climatic gradient defining the main biogeographic domains occurring across Cameroon. Savanna karyotypes of M and S, however, segregated along the smaller-scale environmental gradient defined by the second ordination axis. Population structure analysis identified three chromosomal clusters, each containing a mixture of M and S specimens. In both M and S, alternative karyotypes were segregating in contrasted environments, in agreement with a strong ecological adaptive value of chromosomal inversions. Conclusion Our
Collevatti, Rosane G.; Terribile, Levi C.; Rabelo, Suelen G.; Lima-Ribeiro, Matheus S.
Understanding the dispersal routes of Neotropical savanna tree species is an essential step to unravel the effects of past climate change on genetic patterns, species distribution and population demography. Here we reconstruct the demographic history and dispersal dynamics of the Neotropical savanna tree species Tabebuia aurea to understand the effects of Quaternary climate change on its current spatial patterns of genetic diversity. We sampled 285 individuals from 21 populations throughout Brazilian savannas and sequenced all individuals for three chloroplast intergenic spacers and ITS nrDNA. We analyzed data using a multi-model inference framework by coupling the relaxed random walk model (RRW), ecological niche modeling (ENM) and statistical phylogeography. The most recent common ancestor of T. aurea lineages dated from ~4.0 ± 2.5 Ma. T. aurea lineages cyclically dispersed from the West toward the Central-West Brazil, and from the Southeast toward the East and Northeast Brazil, following the paleodistribution dynamics shown by the ENMs through the last glacial cycle. A historical refugium through time may have allowed dispersal of lineages among populations of Central Brazil, overlapping with population expansion during interglacial periods and the diversification of new lineages. Range and population expansion through the Quaternary were, respectively, the most frequent prediction from ENMs and the most likely demographic scenario from coalescent simulations. Consistent phylogeographic patterns among multiple modeling inferences indicate a promising approach, allowing us to understand how cyclical climate changes through the Quaternary drove complex population dynamics and the current patterns of species distribution and genetic diversity. PMID:26379681
Ecological Niche Modelling Predicts Southward Expansion of Lutzomyia (Nyssomyia) flaviscutellata (Diptera: Psychodidae: Phlebotominae), Vector of Leishmania (Leishmania) amazonensis in South America, under Climate Change
Carvalho, Bruno M.; Ready, Paul D.
Vector borne diseases are susceptible to climate change because distributions and densities of many vectors are climate driven. The Amazon region is endemic for cutaneous leishmaniasis and is predicted to be severely impacted by climate change. Recent records suggest that the distributions of Lutzomyia (Nyssomyia) flaviscutellata and the parasite it transmits, Leishmania (Leishmania) amazonensis, are expanding southward, possibly due to climate change, and sometimes associated with new human infection cases. We define the vector’s climatic niche and explore future projections under climate change scenarios. Vector occurrence records were compiled from the literature, museum collections and Brazilian Health Departments. Six bioclimatic variables were used as predictors in six ecological niche model algorithms (BIOCLIM, DOMAIN, MaxEnt, GARP, logistic regression and Random Forest). Projections for 2050 used 17 general circulation models in two greenhouse gas representative concentration pathways: “stabilization” and “high increase”. Ensemble models and consensus maps were produced by overlapping binary predictions. Final model outputs showed good performance and significance. The use of species absence data substantially improved model performance. Currently, L. flaviscutellata is widely distributed in the Amazon region, with records in the Atlantic Forest and savannah regions of Central Brazil. Future projections indicate expansion of the climatically suitable area for the vector in both scenarios, towards higher latitudes and elevations. L. flaviscutellata is likely to find increasingly suitable conditions for its expansion into areas where human population size and density are much larger than they are in its current locations. If environmental conditions change as predicted, the range of the vector is likely to expand to southeastern and central-southern Brazil, eastern Paraguay and further into the Amazonian areas of Bolivia, Peru, Ecuador, Colombia and
Ecological Niche Modelling Predicts Southward Expansion of Lutzomyia (Nyssomyia) flaviscutellata (Diptera: Psychodidae: Phlebotominae), Vector of Leishmania (Leishmania) amazonensis in South America, under Climate Change.
Carvalho, Bruno M; Rangel, Elizabeth F; Ready, Paul D; Vale, Mariana M
Vector borne diseases are susceptible to climate change because distributions and densities of many vectors are climate driven. The Amazon region is endemic for cutaneous leishmaniasis and is predicted to be severely impacted by climate change. Recent records suggest that the distributions of Lutzomyia (Nyssomyia) flaviscutellata and the parasite it transmits, Leishmania (Leishmania) amazonensis, are expanding southward, possibly due to climate change, and sometimes associated with new human infection cases. We define the vector's climatic niche and explore future projections under climate change scenarios. Vector occurrence records were compiled from the literature, museum collections and Brazilian Health Departments. Six bioclimatic variables were used as predictors in six ecological niche model algorithms (BIOCLIM, DOMAIN, MaxEnt, GARP, logistic regression and Random Forest). Projections for 2050 used 17 general circulation models in two greenhouse gas representative concentration pathways: "stabilization" and "high increase". Ensemble models and consensus maps were produced by overlapping binary predictions. Final model outputs showed good performance and significance. The use of species absence data substantially improved model performance. Currently, L. flaviscutellata is widely distributed in the Amazon region, with records in the Atlantic Forest and savannah regions of Central Brazil. Future projections indicate expansion of the climatically suitable area for the vector in both scenarios, towards higher latitudes and elevations. L. flaviscutellata is likely to find increasingly suitable conditions for its expansion into areas where human population size and density are much larger than they are in its current locations. If environmental conditions change as predicted, the range of the vector is likely to expand to southeastern and central-southern Brazil, eastern Paraguay and further into the Amazonian areas of Bolivia, Peru, Ecuador, Colombia and Venezuela
Slatyer, Rachel A; Hirst, Megan; Sexton, Jason P
The range of resources that a species uses (i.e. its niche breadth) might determine the geographical area it can occupy, but consensus on whether a niche breadth-range size relationship generally exists among species has been slow to emerge. The validity of this hypothesis is a key question in ecology in that it proposes a mechanism for commonness and rarity, and if true, may help predict species' vulnerability to extinction. We identified 64 studies that measured niche breadth and range size, and we used a meta-analytic approach to test for the presence of a niche breadth-range size relationship. We found a significant positive relationship between range size and environmental tolerance breadth (z = 0.49), habitat breadth (z = 0.45), and diet breadth (z = 0.28). The overall positive effect persisted even when incorporating sampling effects. Despite significant variability in the strength of the relationship among studies, the general positive relationship suggests that specialist species might be disproportionately vulnerable to habitat loss and climate change due to synergistic effects of a narrow niche and small range size. An understanding of the ecological and evolutionary mechanisms that drive and cause deviations from this niche breadth-range size pattern is an important future research goal.
Mau, Martin; Lovell, John T.; Corral, José M.; Kiefer, Christiane; Koch, Marcus A.; Aliyu, Olawale M.; Sharbel, Timothy F.
Asexual reproduction is expected to reduce the adaptive potential to novel or changing environmental conditions, restricting or altering the ecological niche of asexual lineages. Asexual lineages of plants and animals are typically polyploid, an attribute that may influence their genetic variation, plasticity, adaptive potential, and niche breadth. The genus Boechera (Brassicaceae) represents an ideal model to test the relative ecological and biogeographic impacts of reproductive mode and ploidy because it is composed of diploid sexual and both diploid and polyploid asexual (i.e., apomictic) lineages. Here, we demonstrate a strong association between a transcriptionally conserved allele and apomictic seed formation. We then use this allele as a proxy apomixis marker in 1,649 accessions to demonstrate that apomixis is likely to be a common feature across the Boechera phylogeny. Phylogeographic analyses of these data demonstrate (i) species-specific niche differentiation in sexuals, (ii) extensive niche conservation between differing reproductive modes of the same species, (iii) ploidy-specific niche differentiation within and among species, and (iv) occasional niche drift between apomicts and their sexual ancestors. We conclude that ploidy is a substantially stronger and more common driver of niche divergence within and across Boechera species although variation in both traits may not necessarily lead to niche evolution on the species scale. PMID:25902513
Batalha, Helena R.; Ramos, Jaime A.; Cardoso, Gonçalo C.
Biological invasions often threaten biodiversity, yet their ecological effects are unpredictable and in some cases may be neutral. Assessing potential interactions between invasive and native species is thus important to understand community functioning and prioritize conservation efforts. With this purpose, we compared the ecological niche and occurrence of a successful avian invader in SW Europe, the common waxbill (Estrildidae: Estrilda astrild), with those of co-occurring native passerine species. We found that common waxbills occupy a marginal niche relative to the community of native passerines, with a larger average ecological distance to the remaining species in the community compared to the native species amongst themselves, and a nearest-neighbour ecological distance identical to those of native species. Furthermore, ecological similarity did not predict co-occurrence of waxbills with other bird species. This is consistent with the invasion using a vacant niche in unsaturated communities, which is likely related to invading waxbills occupying partly human-modified habitats. Similar explanations may apply to other biological invasions of human-modified environments. Results also suggest that detrimental ecological effects due to interspecific competition with native passerines are unlikely. Notwithstanding, the ecological nearest-neighbour of common waxbills was the reed bunting (Emberiza schoeniclus), whose SW European subspecies are endangered, and may justify conservation attention regarding possible interactions between these two species.
Purwandana, Deni; Ariefiandy, Achmad; Imansyah, M. Jeri; Seno, Aganto; Ciofi, Claudio; Letnic, Mike; Jessop, Tim S.
Ontogenetic allometries in ecological habits and niche use are key responses by which individuals maximize lifetime fitness. Moreover, such allometries have significant implications for how individuals influence population and community dynamics. Here, we examined how body size variation in Komodo dragons ( Varanus komodoensis) influenced ecological allometries in their: (1) prey size preference, (2) daily movement rates, (3) home range area, and (4) subsequent niche use across ontogeny. With increased body mass, Komodo dragons increased prey size with a dramatic switch from small (≤10 kg) to large prey (≥50 kg) in lizards heavier than 20 kg. Rates of foraging movement were described by a non-linear concave down response with lizard increasing hourly movement rates up until ˜20 kg body mass before decreasing daily movement suggesting reduced foraging effort in larger lizards. In contrast, home range area exhibited a sigmoid response with increased body mass. Intrapopulation ecological niche use and overlap were also strongly structured by body size. Thus, ontogenetic allometries suggest Komodo dragon's transition from a highly active foraging mode exploiting small prey through to a less active sit and wait feeding strategy focused on killing large ungulates. Further, our results suggest that as body size increases across ontogeny, the Komodo dragon exhibited marked ontogenetic niche shifts that enabled it to function as an entire vertebrate predator guild by exploiting prey across multiple trophic levels.
Purwandana, Deni; Ariefiandy, Achmad; Imansyah, M Jeri; Seno, Aganto; Ciofi, Claudio; Letnic, Mike; Jessop, Tim S
Ontogenetic allometries in ecological habits and niche use are key responses by which individuals maximize lifetime fitness. Moreover, such allometries have significant implications for how individuals influence population and community dynamics. Here, we examined how body size variation in Komodo dragons (Varanus komodoensis) influenced ecological allometries in their: (1) prey size preference, (2) daily movement rates, (3) home range area, and (4) subsequent niche use across ontogeny. With increased body mass, Komodo dragons increased prey size with a dramatic switch from small (≤10 kg) to large prey (≥50 kg) in lizards heavier than 20 kg. Rates of foraging movement were described by a non-linear concave down response with lizard increasing hourly movement rates up until ∼20 kg body mass before decreasing daily movement suggesting reduced foraging effort in larger lizards. In contrast, home range area exhibited a sigmoid response with increased body mass. Intrapopulation ecological niche use and overlap were also strongly structured by body size. Thus, ontogenetic allometries suggest Komodo dragon's transition from a highly active foraging mode exploiting small prey through to a less active sit and wait feeding strategy focused on killing large ungulates. Further, our results suggest that as body size increases across ontogeny, the Komodo dragon exhibited marked ontogenetic niche shifts that enabled it to function as an entire vertebrate predator guild by exploiting prey across multiple trophic levels.
Wogan, Guinevere O.U.; Richmond, Jonathan Q.
Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by-product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size-divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.
Ye, Zhen; Zhu, Gengping; Chen, Pingping; Zhang, Danli; Bu, Wenjun
This study investigated the Pleistocene history of a semi-aquatic bug, Microvelia douglasi douglasi Scott, 1874 (Hemiptera: Veliidae) in East Asia. We used M. douglasi douglasi as a model species to explore the effects of historical climatic fluctuations on montane semi-aquatic invertebrate species. Two hypotheses were developed using ecological niche models (ENMs). First, we hypothesized that M. douglasi douglasi persisted in suitable habitats in southern Guizhou, southern Yunnan, Hainan, Taiwan and southeast China during the LIG. After that, the populations expanded (Hypothesis 1). As the spatial prediction in the LGM was significantly larger than in the LIG, we then hypothesized that the population expanded during the LIG to LGM transition (Hypothesis 2). We tested these hypotheses using mitochondrial data (COI+COII) and nuclear data (ITS1+5.8S+ITS2). Young lineages, relatively deep splits, lineage differentiation among mountain ranges in central, south and southwest China and high genetic diversities were observed in these suitable habitats. Evidence of mismatch distributions and neutrality tests indicate that a population expansion occurred in the late Pleistocene. The Bayesian skyline plot (BSP) revealed an unusual population expansion that likely happened during the cooling transition between LIG and LGM. The results of genetic data were mostly consistent with the spatial predictions from ENM, a finding that can profoundly improve phylogeographic research. The ecological requirements of M. douglasi douglasi, together with the geographical heterogeneity and climatic fluctuations of Pleistocene in East Asia, could have shaped this unusual demographic history. Our study contributes to our knowledge of semi-aquatic bug/invertebrate responses to Pleistocene climatic fluctuations in East Asia.
Praca, E.; Gannier, A.
In the northwestern Mediterranean Sea, sperm whales, pilot whales and Risso's dolphins prey on cephalopods exclusively or preferentially. In order to evaluate their competition, we modelled their habitat suitability with the Ecological Niche Factor Analysis (ENFA) and compared their ecological niche using a discriminant analysis. We used a long term (1995-2005) small boat data set, with visual and acoustic (sperm whale) detections. Risso's dolphin had the shallowest and the more spatially restricted principal habitat, mainly located on the upper part of the continental slope (640 m mean depth). With a wider principal habitat, at 1750 m depth in average, the sperm whale used a deeper part of the slope as well as close offshore waters. Finally, the pilot whale has the most oceanic habitat (2500 m mean depth) mainly located in the central Ligurian Sea and Provençal basin. Therefore, potential competition for food between these species may be reduced by the differentiation of their ecological niches.
Fort, Florian; Jouany, Claire; Cruz, Pablo
Fabaceae species play a key role in ecosystem functioning through their capacity to fix atmospheric nitrogen via their symbiosis with Rhizobium bacteria. To increase benefits of using Fabaceae in agricultural systems, it is necessary to find ways to evaluate species or genotypes having potential adaptations to sub-optimal growth conditions. We evaluated the relevance of phylogenetic distance, absolute trait distance and hierarchical trait distance for comparing the adaptation of 13 grassland Fabaceae species to different habitats, i.e., ecological niches. We measured a wide range of functional traits (root traits, leaf traits, and whole plant traits) in these species. Species phylogenetic and ecological distances were assessed from a species-level phylogenetic tree and species' ecological indicator values, respectively. We demonstrated that differences in ecological niches between grassland Fabaceae species were related more to their hierarchical trait distances than to their phylogenetic distances. We showed that grassland Fabaceae functional traits tend to converge among species with the same ecological requirements. Species with acquisitive root strategies (thin roots, shallow root systems) are competitive species adapted to non-stressful meadows, while conservative ones (coarse roots, deep root systems) are able to tolerate stressful continental climates. In contrast, acquisitive species appeared to be able to tolerate low soil-P availability, while conservative ones need high P availability. Finally we highlight that traits converge along the ecological gradient, providing the assumption that species with similar root-trait values are better able to coexist, regardless of their phylogenetic distance. PMID:25741353
Hardy, Sarah M; Lindgren, Michael; Konakanchi, Hanumantharao; Huettmann, Falk
Populations of the snow crab (Chionoecetes opilio) are widely distributed on high-latitude continental shelves of the North Pacific and North Atlantic, and represent a valuable resource in both the United States and Canada. In US waters, snow crabs are found throughout the Arctic and sub-Arctic seas surrounding Alaska, north of the Aleutian Islands, yet commercial harvest currently focuses on the more southerly population in the Bering Sea. Population dynamics are well-monitored in exploited areas, but few data exist for populations further north where climate trends in the Arctic appear to be affecting species' distributions and community structure on multiple trophic levels. Moreover, increased shipping traffic, as well as fisheries and petroleum resource development, may add additional pressures in northern portions of the range as seasonal ice cover continues to decline. In the face of these pressures, we examined the ecological niche and population distribution of snow crabs in Alaskan waters using a GIS-based spatial modeling approach. We present the first quantitative open-access model predictions of snow-crab distribution, abundance, and biomass in the Chukchi and Beaufort Seas. Multi-variate analysis of environmental drivers of species' distribution and community structure commonly rely on multiple linear regression methods. The spatial modeling approach employed here improves upon linear regression methods in allowing for exploration of nonlinear relationships and interactions between variables. Three machine-learning algorithms were used to evaluate relationships between snow-crab distribution and environmental parameters, including TreeNet, Random Forests, and MARS. An ensemble model was then generated by combining output from these three models to generate consensus predictions for presence-absence, abundance, and biomass of snow crabs. Each algorithm identified a suite of variables most important in predicting snow-crab distribution, including
Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos
Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784
Ning, Shuoying; Wei, Jiufeng; Feng, Jinian
Climate change will markedly impact biology, population ecology, and spatial distribution patterns of insect pests because of the influence of future greenhouse effects on insect development and population dynamics. Onion maggot, Delia antiqua, larvae are subterranean pests with limited mobility, that directly feed on bulbs of Allium sp. and render them completely unmarketable. Modeling the spatial distribution of such a widespread and damaging pest is crucial not only to identify current potentially suitable climactic areas but also to predict where the pest is likely to spread in the future so that appropriate monitoring and management programs can be developed. In this study, Maximum Entropy Niche Modeling was used to estimate the current potential distribution of D. antiqua and to predict the future distribution of this species in 2030, 2050, 2070 and 2080 by using emission scenario (A2) with 7 climate variables. The results of this study show that currently highly suitable habitats for D.antiqua occur throughout most of East Asia, some regions of North America, Western Europe, and Western Asian countries near the Caspian sea and Black Sea. In the future, we predict an even broader distribution of this pest spread more extensively throughout Asia, North America and Europe, particularly in most of European countries, Central regions of United States and much of East Asia. Our present day and future predictions can enhance strategic planning of agricultural organizations by identifying regions that will need to develop Integrated Pest Management programs to manage the onion maggot. The distribution forecasts will also help governments to optimize economic investments in management programs for this pest by identifying regions that are or will become less suitable for current and future infestations.
Climate change will markedly impact biology, population ecology, and spatial distribution patterns of insect pests because of the influence of future greenhouse effects on insect development and population dynamics. Onion maggot, Delia antiqua, larvae are subterranean pests with limited mobility, that directly feed on bulbs of Allium sp. and render them completely unmarketable. Modeling the spatial distribution of such a widespread and damaging pest is crucial not only to identify current potentially suitable climactic areas but also to predict where the pest is likely to spread in the future so that appropriate monitoring and management programs can be developed. In this study, Maximum Entropy Niche Modeling was used to estimate the current potential distribution of D. antiqua and to predict the future distribution of this species in 2030, 2050, 2070 and 2080 by using emission scenario (A2) with 7 climate variables. The results of this study show that currently highly suitable habitats for D.antiqua occur throughout most of East Asia, some regions of North America, Western Europe, and Western Asian countries near the Caspian sea and Black Sea. In the future, we predict an even broader distribution of this pest spread more extensively throughout Asia, North America and Europe, particularly in most of European countries, Central regions of United States and much of East Asia. Our present day and future predictions can enhance strategic planning of agricultural organizations by identifying regions that will need to develop Integrated Pest Management programs to manage the onion maggot. The distribution forecasts will also help governments to optimize economic investments in management programs for this pest by identifying regions that are or will become less suitable for current and future infestations. PMID:28158259
Wang, Wenjuan; Lin, Congtian; Gao, Bin; Yang, Xiaojun; Zhang, Zhengwang; Lei, Fumin
Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis–concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis–concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory. PMID:22195047
Cantrell, Sharon A.; Duval-Pérez, Lisabeth
Fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance – EPS) was explored. Fungal diversity is higher during the wet season with Acremonium, Aspergillus, Cladosporium, and Penicillium among the more common genera. Diversity is also higher in the oxic layer and in young and transient mats. Enrichments with xanthan (a model EPS) show that without antibiotics (full community) degradation is faster than enrichments with antibacterial (fungal community) and antifungal (bacterial community) agents, suggesting that degradation is performed by a consortium of organisms (bacteria and fungi). The combined evidence from all experiments indicates that bacteria carried out approximately two-third of the xanthan degradation. The pattern of degradation is similar between seasons and layers but degradation is faster in enrichments from the wet season. The research suggests that fungi thrive in these hypersaline consortia and may participate in the carbon cycle through the degradation of complex carbohydrates. PMID:23577004
Moo-Llanes, D A; Arque-Chunga, W; Carmona-Castro, O; Yañez-Arenas, C; Yañez-Trujillano, H H; Cheverría-Pacheco, L; Baak-Baak, C M; Cáceres, A G
The Peruvian Andes presents a climate suitable for many species of sandfly that are known vectors of leishmaniasis or bartonellosis, including Lutzomyia peruensis (Diptera: Psychodidae), among others. In the present study, occurrences data for Lu. peruensis were compiled from several items in the scientific literature from Peru published between 1927 and 2015. Based on these data, ecological niche models were constructed to predict spatial distributions using three algorithms [Support vector machine (SVM), the Genetic Algorithm for Rule-set Prediction (GARP) and Maximum Entropy (MaxEnt)]. In addition, the environmental requirements of Lu. peruensis and three niche characteristics were modelled in the context of future climate change scenarios: (a) potential changes in niche breadth; (b) shifts in the direction and magnitude of niche centroids, and (c) shifts in elevation range. The model identified areas that included environments suitable for Lu. peruensis in most regions of Peru (45.77%) and an average altitude of 3289 m a.s.l. Under climate change scenarios, a decrease in the distribution areas of Lu. peruensis was observed for all representative concentration pathways. However, the centroid of the species' ecological niche showed a northwest direction in all climate change scenarios. The information generated in this study may help health authorities responsible for the supervision of strategies to control leishmaniasis to coordinate, plan and implement appropriate strategies for each area of risk, taking into account the geographic distribution and potential dispersal of Lu. peruensis.
Pech-May, Angélica; Moo-Llanes, David A; Puerto-Avila, María Belem; Casas, Mauricio; Danis-Lozano, Rogelio; Ponce, Gustavo; Tun-Ku, Ezequiel; Pinto-Castillo, José Francisco; Villegas, Alejandro; Ibáñez-Piñon, Clemente R; González, Cassandra; Ramsey, Janine M
The Asian tiger mosquito Aedes albopictus (Skuse), is one of the most invasive mosquito species worldwide. In Mexico it is now recorded in 12 states and represents a serious public health problem, given the recent introduction of Chikungunya on the southern border. The aim of this study was to analyze the population genetics of A. albopictus from all major recorded foci, and model its ecological niche. Niche similarity with that from its autochthonous distribution in Asia and other invaded countries were analyzed and its potential future expansion and potential human exposure in climate change scenarios measured. We analyzed 125 sequences of a 317 bp fragment of the cyt b gene from seven A. albopictus populations across Mexico. The samples belong to 25 haplotypes with moderate population structuring (Fst=0.081, p<0.02) and population expansion. The most prevalent haplotype, found in all principal sites, was shared with the USA, Brazil, France, Madagascar, and Reunion Island. The ecological niche model using Mexican occurrence records covers 79.7% of the country, and has an 83% overlap with the Asian niche projected to Mexico. Both Neotropical and Nearctic regions are included in the Mexican niche model. Currently in Mexico, 38.6 million inhabitants are exposed to A. albopictus, which is expected to increase to 45.6 million by 2070. Genetic evidence supports collection information that A. albopictus was introduced to Mexico principally by land from the USA and Central and South America. Prevalent haplotypes from Mexico are shared with most invasive regions across the world, just as there was high niche similarity with both natural and invaded regions. The important overlap with the Asian niche model suggests a high potential for the species to disperse to sylvatic regions in Mexico.
An, Miao; Zeng, Liyan; Zhang, Ticao; Zhong, Yang
Thlaspi arvense is a well-known annual farmland weed with worldwide distribution, which can be found from sea level to above 4000 m high on the Qinghai-Tibetan Plateau (QTP). In this paper, a phylogeographic history of T. arvense including 19 populations from China was inferred by using three chloroplast (cp) DNA segments (trnL-trnF, rpl32-trnL and rps16) and one nuclear (n) DNA segment (Fe-regulated transporter-like protein, ZIP). A total of 11 chloroplast haplotypes and six nuclear alleles were identified, and haplotypes unique to the QTP were recognized (C4, C5, C7 and N4). On the basis of molecular dating, haplotypes C4, C5 and C7 have separated from others around 1.58 Ma for cpDNA, which corresponds to the QTP uplift. In addition, this article suggests that the T. arvense populations in China are a mixture of diverged subpopulations as inferred by hT/vT test (hT ≤ vT, cpDNA) and positive Tajima’s D values (1.87, 0.05 < p < 0.10 for cpDNA and 3.37, p < 0.01 for nDNA). Multimodality mismatch distribution curves and a relatively large shared area of suitable environmental conditions between the Last Glacial Maximum (LGM) as well as the present time recognized by MaxEnt software reject the sudden expansion population model. PMID:26110380
Henry, Lee M.; Peccoud, Jean; Simon, Jean-Christophe; Hadfield, Jarrod D.; Maiden, Martin J.C.; Ferrari, Julia; Godfray, H. Charles J.
Summary Facultative or “secondary” symbionts are common in eukaryotes, particularly insects. While not essential for host survival, they often provide significant fitness benefits [1-5]. It has been hypothesized that secondary symbionts form a “horizontal gene pool” shuttling adaptive genes among host lineages in an analogous manner to plasmids and other mobile genetic elements in bacteria [6, 7]. However, we do not know whether the distributions of symbionts across host populations reflect random acquisitions followed by vertical inheritance or whether the associations have occurred repeatedly in a manner consistent with a dynamic horizontal gene pool. Here we explore these questions using the phylogenetic and ecological distributions of secondary symbionts carried by 1,104 pea aphids, Acyrthosiphon pisum. We find that not only is horizontal transfer common, but it is also associated with aphid lineages colonizing new ecological niches, including novel plant species and climatic regions. Moreover, aphids that share the same ecologies worldwide have independently acquired related symbiont genotypes, suggesting significant involvement of symbionts in their host’s adaptation to different niches. We conclude that the secondary symbiont community forms a horizontal gene pool that influences the adaptation and distribution of their insect hosts. These findings highlight the importance of symbiotic microorganisms in the radiation of eukaryotes. PMID:23993843
Alahuhta, Janne; Virtala, Antti; Hjort, Jan; Ecke, Frauke; Johnson, Lucinda B; Sass, Laura; Heino, Jani
Different species' niche breadths in relation to ecological gradients are infrequently examined within the same study and, moreover, species niche breadths have rarely been averaged to account for variation in entire ecological communities. We investigated how average environmental niche breadths (climate, water quality and climate-water quality niches) in aquatic macrophyte communities are related to ecological gradients (latitude, longitude, altitude, species richness and lake area) among four distinct regions (Finland, Sweden and US states of Minnesota and Wisconsin) on two continents. We found that correlations between the three different measures of average niche breadths and ecological gradients varied considerably among the study regions, with average climate and average water quality niche breadth models often showing opposite trends. However, consistent patterns were also found, such as widening of average climate niche breadths and narrowing of average water quality niche breadths of aquatic macrophytes along increasing latitudinal and altitudinal gradients. This result suggests that macrophyte species are generalists in relation to temperature variations at higher latitudes and altitudes, whereas species in southern, lowland lakes are more specialised. In contrast, aquatic macrophytes growing in more southern nutrient-rich lakes were generalists in relation to water quality, while specialist species are adapted to low-productivity conditions and are found in highland lakes. Our results emphasise that species niche breadths should not be studied using only coarse-scale data of species distributions and corresponding environmental conditions, but that investigations on different kinds of niche breadths (e.g., climate vs. local niches) also require finer resolution data at broad spatial extents.
Batalden, Rebecca V; Oberhauser, Karen; Peterson, A Townsend
Eastern North American monarch butterflies (Danaus plexippus L.) show a series of range shifts during their breeding season. Using ecological niche modeling, we studied the environmental context of these shifts by identifying the ecological conditions that monarchs use in successive summer months. Monarchs use a consistent ecological regimen through the summer, but these conditions contrast strikingly with those used during the winter. Hence, monarchs exhibit niche-following among sequential breeding generations but niche-switching between the breeding and overwintering stages of their annual cycle. We projected their breeding ecological niche onto monthly future climate scenarios, which indicated northward shifts, particularly at the northern extreme of their summer movements, over the next 50 yrs; if both monarchs and their milkweed host plants cannot track these changing climates, monarchs could lose distributional area during critical breeding months.
Chase, Jonathan M.; Myers, Jonathan A.
Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity and composition. In contrast, more stochastic theories emphasize the importance of chance colonization, random extinction and ecological drift. The schisms between deterministic and stochastic perspectives, which date back to the earliest days of ecology, continue to fuel contemporary debates (e.g. niches versus neutrality). As illustrated by the pioneering studies of Robert H. MacArthur and co-workers, resolution to these debates requires consideration of how the importance of local processes changes across scales. Here, we develop a framework for disentangling the relative importance of deterministic and stochastic processes in generating site-to-site variation in species composition (β-diversity) along ecological gradients (disturbance, productivity and biotic interactions) and among biogeographic regions that differ in the size of the regional species pool. We illustrate how to discern the importance of deterministic processes using null-model approaches that explicitly account for local and regional factors that inherently create stochastic turnover. By embracing processes across scales, we can build a more synthetic framework for understanding how niches structure patterns of biodiversity in the face of stochastic processes that emerge from local and biogeographic factors. PMID:21768151
Praca, E.; Gannier, A.
In the northwestern Mediterranean Sea, sperm whales, pilot whales and Risso's dolphins prey exclusively or preferentially on cephalopods. In order to evaluate their competition, we modelled their habitat suitability with the Ecological Niche Factor Analysis (ENFA) and compared their ecological niches using a discriminant analysis. We used a long term (1995-2005) small boat data set, with visual and acoustic (sperm whale) detections. Risso's dolphin had the shallowest and the more spatially restricted principal habitat, mainly located on the upper part of the continental slope (640 m mean depth). With a wider principal habitat, at 1750 m depth in average, the sperm whale used a deeper part of the slope as well as the closest offshore waters. Finally, the pilot whale has the most oceanic habitat (2500 m mean depth) mainly located in the central Ligurian Sea and Provençal basin. Therefore, potential competition for food between these species may be reduced by the differentiation of their habitats.
Sun, Hao; Huang, Lu-ming; Huang, Lu-qi; Guo, Lan-ping; Zhou, Jie; Lv, Dong-mei; Zeng, Yan
Based on the conception and theory of ecological niche, authors analyzed the cause of the allelopathy and soil sickness of medicinal plants and the relationship between them. Methods to resolve problems in the cultivating medicinal plant was found, that is to construct the ecological niche based on allelopathy theory and avoid the soil sickness.
Martínez-Meyer, Enrique; Peterson, A Townsend; Navarro-Sigüenza, Adolfo G
The evolution of migration has long been considered complex and recent work has demonstrated additional complexity: some species follow the same ecological conditions throughout the year, whereas others 'switch niches' between breeding and wintering ranges. Hypotheses regarding the evolution of migration would generally predict niche-following as primitive, and niche-switching as derived. However, no test has, to our knowledge, yet determined the directionality of evolution of these states within a lineage. We present an analysis of phylogenetic dimensions of seasonal niches in the Passerina buntings that indicates greater evolutionary change in the niches of breeding populations than among those of wintering populations. These results are consistent with hypotheses of (i) niche conservatism (in winter, at least) across a recently speciated lineage; and (ii) the derived state of the breeding (rather than winter) ecological niches of each species.
Martínez-Meyer, Enrique; Peterson, A. Townsend; Navarro-Sigüenza, Adolfo G.
The evolution of migration has long been considered complex and recent work has demonstrated additional complexity: some species follow the same ecological conditions throughout the year, whereas others 'switch niches' between breeding and wintering ranges. Hypotheses regarding the evolution of migration would generally predict niche-following as primitive, and niche-switching as derived. However, no test has, to our knowledge, yet determined the directionality of evolution of these states within a lineage. We present an analysis of phylogenetic dimensions of seasonal niches in the Passerina buntings that indicates greater evolutionary change in the niches of breeding populations than among those of wintering populations. These results are consistent with hypotheses of (i) niche conservatism (in winter, at least) across a recently speciated lineage; and (ii) the derived state of the breeding (rather than winter) ecological niches of each species. PMID:15306365
Li, Xian-sen; Yu, Zhen-hai; Sun, Shan; Jin, Xian-shi
Based on the fishery resources data from the bottom trawl surveys conducted on the R/V Beidou in the Yangtze River estuary and its adjacent waters in June, August and October of 2006, the index of relative importance (IRI) was measured to determine the dominant species of fish assemblage, and the niche indicators and their seasonal variations of the dominant species were analyzed. A total of 10 dominant species in the 3 survey cruises were recorded, which were divided into two groups by the Bray-curtis similarity clustering and non-metric multidimensional scaling (MDS) analysis, with a significant seasonal variation of niche breadth and niche overlap. One group included Engraulis japonicus, Champsodon capensis, and Acropoma japonicum, whose niche breadth and niche overlap were larger in summer than in autumn, with a migration from the Yangtze River estuary and its adjacent waters to outer deeper waters, while the other group included Trichiurus haumela, Chaeturichthys stigmatias, Apogon lineatus, Larimichthys polyactis, Psenopsis anomala, Argyrosomus argentatus, and Benthosema pterotum, whose niche breadth and niche overlap were larger in autumn than in summer, with a reverse migration from southern Yellow Sea and northern East China Sea to the Yangtze River estuary and its adjacent waters. The different migration direction of the two groups was related to their ecological habits and environmental factors.
Sen, Sandeep; Shivaprakash, Kadukothanahally Nagaraju; Aravind, Neelavara A; Ravikanth, Gudasalamani; Dayanandan, Selvadurai
Conservation managers and policy makers are often confronted with a challenging dilemma of devising suitable strategies to maintain agricultural productivity while conserving endemic species that at the early stages of becoming pests of agricultural crops. Identification of environmental factors conducive to species range expansion for forecasting species distribution patterns will play a central role in devising management strategies to minimize the conflict between the agricultural productivity and biodiversity conservation. Here, we present results of a study that predicts the distribution of Indrella ampulla, a snail endemic to the Western Ghats biodiversity hotspot, which is becoming a pest in cardamom (Ellettaria cardamomum) plantations. We determined the distribution patterns and niche overlap between I. ampulla and Ellettaria cardamomum using maximum entropy (MaxEnt) niche modeling techniques under current and future (2020-2080) climatic scenarios. The results showed that climatic (precipitation of coldest quarter and isothermality) and soil (cation exchange capacity of soil [CEC]) parameters are major factors that determine the distribution of I. ampulla in Western Ghats. The model predicted cardamom cultivation areas in southern Western Ghats are highly sensitive to invasion of I. ampulla under both present and future climatic conditions. While the land area in the central Western Ghats is predicted to become unsuitable for I. ampulla and Ellettaria cardamomum in future, we found 71% of the Western Ghats land area is suitable for Ellettaria cardamomum cultivation and 45% suitable for I. ampulla, with an overlap of 35% between two species. The resulting distribution maps are invaluable for policy makers and conservation managers to design and implement management strategies minimizing the conflicts to sustain agricultural productivity while maintaining biodiversity in the region.
Predicting the Distribution of Phlebotomus papatasi (Diptera: Psychodidae), the Primary Vector of Zoonotic Cutaneous Leishmaniasis, in Golestan Province of Iran Using Ecological Niche Modeling: Comparison of MaxEnt and GARP Models.
Sofizadeh, Aioub; Rassi, Yavar; Vatandoost, Hassan; Hanafi-Bojd, Ahmad Ali; Mollalo, Abolfazl; Rafizadeh, Sayena; Akhavan, Amir Ahmad
Zoonotic cutaneous leishmaniasis (ZCL) is a prevalent vector-borne disease in the Golestan province of Iran, with Phlebotomus papatasi (Scopoli, 1786) serving as the main vector. The aim of this study was to model the probability of presence of this species in the study area, and to determine the underlying factors affecting its distribution. Three villages were selected from each county of the province and visited monthly for investigating ZCL. Sticky paper traps were used for collecting the sand flies to determine the species present. The presence of Ph. papatasi was modeled using genetic algorithm for rule-set production (GARP) and maximum entropy (MaxEnt) techniques. Both models showed the central and northern parts of the province with lowland areas were more vulnerable to Ph. papatasi propagation, in comparison with the southern parts with mountainous and forest areas. The area under curve (AUC) of MaxEnt model for the training points was calculated as 0.90, indicating excellent performance of the model in predicting Ph. papatasi distribution. Jackknife test showed that the factors with the greatest influence in vector distribution were slope, vegetation cover, annual mean temperature, and altitude. By using ecological niche models, it is possible to identify areas with higher probability of presence of Ph. papatasi, which guides public health policy makers for planning better vector control interventions.
Aubier, Thomas G; Elias, Marianne; Llaurens, Violaine; Chazot, Nicolas
Species richness varies among clades, yet the drivers of diversification creating this variation remain poorly understood. While abiotic factors likely drive some of the variation in species richness, ecological interactions may also contribute. Here, we examine one class of potential contributors to species richness variation that is particularly poorly understood: mutualistic interactions. We aim to elucidate large-scale patterns of diversification mediated by mutualistic interactions using a spatially-explicit population-based model. We focus on mutualistic Müllerian mimicry between conspicuous toxic prey species, where convergence in colour patterns emerges from predators' learning process. To investigate the effects of Müllerian mimicry on species diversification, we assume that some speciation events stem from shifts in ecological niches, and can also be associated with shift in mimetic colour pattern. Through the emergence of spatial mosaics of mimetic colour patterns, Müllerian mimicry constrains the geographical distribution of species and allows different species with similar ecological niches to exist simultaneously in different regions. Müllerian mimicry and the resulting spatial segregation of mimetic colour patterns thus generate more balanced phylogenetic trees and increase overall species diversity. Our study sheds light on complex effects of Müllerian mimicry on ecological, spatial and phylogenetic diversification. This article is protected by copyright. All rights reserved.
Kearney, Michael R; Matzelle, Allison; Helmuth, Brian
The emerging field of mechanistic niche modelling aims to link the functional traits of organisms to their environments to predict survival, reproduction, distribution and abundance. This approach has great potential to increase our understanding of the impacts of environmental change on individuals, populations and communities by providing functional connections between physiological and ecological response to increasingly available spatial environmental data. By their nature, such mechanistic models are more data intensive in comparison with the more widely applied correlative approaches but can potentially provide more spatially and temporally explicit predictions, which are often needed by decision makers. A poorly explored issue in this context is the appropriate level of temporal resolution of input data required for these models, and specifically the error in predictions that can be incurred through the use of temporally averaged data. Here, we review how biomechanical principles from heat-transfer and metabolic theory are currently being used as foundations for mechanistic niche models and consider the consequences of different temporal resolutions of environmental data for modelling the niche of a behaviourally thermoregulating terrestrial lizard. We show that fine-scale temporal resolution (daily) data can be crucial for unbiased inference of climatic impacts on survival, growth and reproduction. This is especially so for species with little capacity for behavioural buffering, because of behavioural or habitat constraints, and for detecting temporal trends. However, coarser-resolution data (long-term monthly averages) can be appropriate for mechanistic studies of climatic constraints on distribution and abundance limits in thermoregulating species at broad spatial scales.
Vogt, Meike; Brun, Philipp; Payne, Mark R.; O'Brien, Colleen J.; Bednaršek, Nina; Buitenhuis, Erik T.; Doney, Scott C.; Leblanc, Karine; Le Quéré, Corinne; Luo, Yawei; Moriarty, Róisín; O'Brien, Todd D.; Schiebel, Ralf; Swan, Chantal
Marine plankton play a central role in the biogeochemical cycling of important elements such as carbon, nitrogen, and sulphur. While our knowledge about marine ecosystem structure and functioning is still scarce and episodic, several recent observational studies confirm that marine ecosystems have been changing due to recent climate change, overfishing, and coastal eutrophication. In order to better understand marine ecosystem dynamics, the MAREDAT initiative has recently collected abundance and biomass data for 5 autotrophic (diatoms, Phaeocystis, coccolithophores, nitrogen fixers, picophytoplankton), and 6 heterotrophic plankton functional types (PFTs; bacteria, micro-, meso- and macrozooplankton, foraminifera and pteropods). Species distribution models (SDMs) are statistical tools that can be used to derive information about species habitats in space and time. They have been used extensively for a wide range of ecological applications in terrestrial ecosystems, but here we present the first global application in the marine realm, which was made possible by the MAREDAT data synthesis effort. We use a maximum entropy SDM to simulate global habitat suitability, habitat extent and ecological niches for different PFTs in the modern ocean. Present habitat suitability is derived from presence-only MAREDAT data and the observed annual and monthly mean levels of physiologically relevant variables such as SST, nutrient concentration or photosynthetic active radiation received in the mixed layer. This information can then be used to derive ecological niches for different species or taxa within each PFT, and to compare the ecological niches of different PFTs. While these results still need verification because data was not available for all ocean regions for all PFTs, they can give a first indication what present and future plankton habitats may look like, and what consequences we may have to expect for future marine ecosystem functioning and service provision in a warmer
Tanigawa, Shunsuke; Perantoni, Alan O.
Significant recent advances in methodologies for the differentiation of pluripotent stem cells to renal progenitors as well as the definition of niche conditions for sustaining those progenitors have dramatically enhanced our understanding of their biology and developmental programing, prerequisites for establishing viable approaches to renal regeneration. In this article, we review the evolution of culture techniques and models for the study of metanephric development, describe the signaling mechanisms likely to be driving progenitor self-renewal, and discuss current efforts to generate de novo functional tissues, providing in depth protocols and niche conditions for the stabilization of the nephronic Six2+ progenitor. PMID:26856661
Nieto, Prixia; Malone, John B; Bavia, Maria E
Two predictive models were developed within a geographic information system using Genetic Algorithm Rule-Set Prediction (GARP) and the growing degree day (GDD)-water budget (WB) concept to predict the distribution and potential risk of visceral leishmaniasis (VL) in the State of Bahia, Brazil. The objective was to define the environmental suitability of the disease as well as to obtain a deeper understanding of the eco-epidemiology of VL by associating environmental and climatic variables with disease prevalence. Both the GARP model and the GDDWB model, using different analysis approaches and with the same human prevalence database, predicted similar distribution and abundance patterns for the Lutzomyia longipalpis-Leishmania chagasi system in Bahia. High and moderate prevalence sites for VL were significantly related to areas of high and moderate risk prediction by: (i) the area predicted by the GARP model, depending on the number of pixels that overlapped among eleven annual model years, and (ii) the number of potential generations per year that could be completed by the Lu. longipalpis-L. chagasi system by GDD-WB analysis. When applied to the ecological zones of Bahia, both the GARP and the GDD-WB prediction models suggest that the highest VL risk is in the interior region of the state, characterized by a semi-arid and hot climate known as Caatinga, while the risk in the Bahia interior forest and the Cerrado ecological regions is lower. The Bahia coastal forest was predicted to be a low-risk area due to the unsuitable conditions for the vector and VL transmission.
Adegboye, Oyelola A; Adegboye, Majeed
Leishmaniasis is the third most common vector-borne disease and a very important protozoan infection. Cutaneous leishmaniasis is one of the most common types of leishmaniasis infectious diseases with up to 1.2 million occurrences of new cases each year worldwide. A dynamic transmission multivariate time series model was applied to the data to account for overdispersion and evaluate the effects of three environmental layers as well as seasonality in the data. Furthermore, ecological niche modeling was used to study the geographically suitable conditions for cutaneous leishmaniasis using temperature, precipitation and altitude as environmental layers, together with the leishmaniasis presence data. A retrospective analysis of the cutaneous leishmaniasis spatial data in Afghanistan between 2003 and 2009 indicates a steady increase from 2003 to 2007, a small decrease in 2008, and then another increase in 2009. An upward trend and regularly repeating patterns of highs and lows were observed related to the months of the year, which suggests seasonality effect in the data. Two peaks were observed in the disease occurrence-January to March and September to December-which coincide with the cold period. Ecological niche modelling indicates that precipitation has the greatest contribution to the potential distribution of leishmaniasis.
Adegboye, Oyelola A.; Adegboye, Majeed
Leishmaniasis is the third most common vector-borne disease and a very important protozoan infection. Cutaneous leishmaniasis is one of the most common types of leishmaniasis infectious diseases with up to 1.2 million occurrences of new cases each year worldwide. A dynamic transmission multivariate time series model was applied to the data to account for overdispersion and evaluate the effects of three environmental layers as well as seasonality in the data. Furthermore, ecological niche modeling was used to study the geographically suitable conditions for cutaneous leishmaniasis using temperature, precipitation and altitude as environmental layers, together with the leishmaniasis presence data. A retrospective analysis of the cutaneous leishmaniasis spatial data in Afghanistan between 2003 and 2009 indicates a steady increase from 2003 to 2007, a small decrease in 2008, and then another increase in 2009. An upward trend and regularly repeating patterns of highs and lows were observed related to the months of the year, which suggests seasonality effect in the data. Two peaks were observed in the disease occurrence—January to March and September to December—which coincide with the cold period. Ecological niche modelling indicates that precipitation has the greatest contribution to the potential distribution of leishmaniasis. PMID:28304356
Olson, R J; Young, J W; Ménard, F; Potier, M; Allain, V; Goñi, N; Logan, J M; Galván-Magaña, F
Tunas are highly specialized predators that have evolved numerous adaptations for a lifestyle that requires large amounts of energy consumption. Here we review our understanding of the bioenergetics and feeding dynamics of tunas on a global scale, with an emphasis on yellowfin, bigeye, skipjack, albacore, and Atlantic bluefin tunas. Food consumption balances bioenergetics expenditures for respiration, growth (including gonad production), specific dynamic action, egestion, and excretion. Tunas feed across the micronekton and some large zooplankton. Some tunas appear to time their life history to take advantage of ephemeral aggregations of crustacean, fish, and molluscan prey. Ontogenetic and spatial diet differences are substantial, and significant interdecadal changes in prey composition have been observed. Diet shifts from larger to smaller prey taxa highlight ecosystem-wide changes in prey availability and diversity and provide implications for changing bioenergetics requirements into the future. Where tunas overlap, we show evidence of niche separation between them; resources are divided largely by differences in diet percentages and size ranges of prey taxa. The lack of long-term data limits the ability to predict impacts of climate change on tuna feeding behaviour. We note the need for systematic collection of feeding data as part of routine monitoring of these species, and we highlight the advantages of using biochemical techniques for broad-scale analyses of trophic relations. We support the continued development of ecosystem models, which all too often lack the regional-specific trophic data needed to adequately investigate climate and fishing impacts.
Wolf, N.; Siegmund, A.; del Río, C.; Osses, P.; García, J. L.
In the coastal Atacama Desert in Northern Chile plant growth is constrained to so-called `fog oases' dominated by monospecific stands of the genus Tillandsia. Adapted to the hyperarid environmental conditions, these plants specialize on the foliar uptake of fog as main water and nutrient source. It is this characteristic that leads to distinctive macro- and micro-scale distribution patterns, reflecting complex geo-ecological gradients, mainly affected by the spatiotemporal occurrence of coastal fog respectively the South Pacific Stratocumulus clouds reaching inlands. The current work employs remote sensing, machine learning and spatial pattern/GIS analysis techniques to acquire detailed information on the presence and state of Tillandsia spp. in the Tarapacá region as a base to better understand the bioclimatic and topographic constraints determining the distribution patterns of Tillandsia spp. Spatial and spectral predictors extracted from WorldView-3 satellite data are used to map present Tillandsia vegetation in the Tarapaca region. Regression models on Vegetation Cover Fraction (VCF) are generated combining satellite-based as well as topographic variables and using aggregated high spatial resolution information on vegetation cover derived from UAV flight campaigns as a reference. The results are a first step towards mapping and modelling the topographic as well as bioclimatic factors explaining the spatial distribution patterns of Tillandsia fog oases in the Atacama, Chile.
Fields, William R.; Grant, Evan; Lowe, Winsor H.
Ontogenetic niche shifts (ONS) are important drivers of population and community dynamics, but they can be difficult to identify for species with prolonged larval or juvenile stages, or for species that inhabit continuous habitats. Most studies of ONS focus on single transitions among discrete habitat patches at local scales. However, for species with long larval or juvenile periods, affinity for particular locations within connected habitat networks may differ among cohorts. The resulting spatial patterns of distribution can result from a combination of landscape-scale habitat structure, position of a habitat patch within a network, and local habitat characteristics—all of which may interact and change as individuals grow. We estimated such spatial ONS for spring salamanders (Gyrinophilus porphyriticus), which have a larval period that can last 4 years or more. Using mixture models to identify larval cohorts from size frequency data, we fit occupancy models for each age class using two measures of the branching structure of stream networks and three measures of stream network position. Larval salamander cohorts showed different preferences for the position of a site within the stream network, and the strength of these responses depended on the basin-wide spatial structure of the stream network. The isolation of a site had a stronger effect on occupancy in watersheds with more isolated headwater streams, while the catchment area, which is associated with gradients in stream habitat, had a stronger effect on occupancy in watersheds with more paired headwater streams. Our results show that considering the spatial structure of habitat networks can provide new insights on ONS in long-lived species.
Carretero, Miguel A.; Sillero, Neftalí
Ecological niche models (ENMs) will successfully identify a species' ecological niche, provided that important assumptions are fulfilled, namely environment equilibrium and niche equality across the distribution. Violations may seriously affect ENM reliability, leading to erroneous biogeographic conclusions and inappropriate conservation prioritisation. We evaluate the robustness of ENMs against incomplete knowledge of distribution with a real example, the threatened Iberian lizard Podarcis carbonelli, whose distribution was gradually discovered over a long time period. We used several ENM methods for presence-only data (Maxent, ENFA, Bioclim, and Domain) to infer the realised ecological niche at two spatial resolutions (1 km and 200 m). The distribution data were split into four partial datasets corresponding to separate subranges: Central System (CS); Viseu-Aveiro (VA); Atlantic coast (AC); and Doñana (DO). We then accumulated the datasets following the species discovery sequence: CS + VA, CS + VA + AC, and CS + VA + AC + DO. Niche equivalence and similarity between partial models were compared using Ecospat. ENMs were strongly affected by the violation of niche equilibrium; only the VA subrange forecasts the complete species range. ENMs were also sensitive to the violation of niche equality: only VA models were similar to the Iberian model, altitude being the most important variable followed by annual precipitation, maximum temperature in July, and annual radiation. When the ENMs were applied only to the first subrange discovered (CS), only the VA area was predicted, while the other subranges might have remained unknown, thus compromising conservation strategies. As assumptions of niche equilibrium and equality were violated, likely owing to the species' ecological multimodality, the models generated were biased and of limited predictive value. ENMs are useful tools in biogeography and conservation, but only if their basal assumptions are achieved. Partial
Wang, Meirong; Liu, Fei; Lin, Pengcheng; Yang, Shaorong; Liu, Huanzhang
In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus,R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism.
Wang, Meirong; Liu, Fei; Lin, Pengcheng; Yang, Shaorong; Liu, Huanzhang
In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus,R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism. PMID:25691981
Gross, Robert; Winiwarter, Verena
White belts of snow clad mountains all over the world each winter. Even if there is no snow, the tourism industry is able to produce the white finery at the push of the button, thereby consuming large amounts of water. Studying Damüls, a well-known ski resort in Austria's westernmost province Vorarlberg, we can show that the development of a service sector within agro-pastoral landscapes was connected with novel water uses and massive interventions into Alpine landscapes. Human niche construction theory offers a unique avenue for studying the development of Alpine communities, but also highlights side effects accompanying the change from agrarian to tourism livelihoods. One aim of this paper is to broaden the scope of human niche construction theory. Inceptive, counteractive and relocational niche construction activities were coupled to the differentiation of actor groups. To incorporate social dynamics, indispensable for studies in environmental history, we propose the concept of socio-ecological niche construction. The paper investigates how villagers balanced resource limitations typical for an agrarian society with the differentiation of sub-niches, mediating selective forces on the population. When the valleys were industrialized, Damüls was almost given up as a permanent settlement. Then, tourists entered the stage, by and by turning the wheel of local development into a different direction. A tourism niche based on natural snow evolved from the 1930s onwards. While the socio-ecological niches of agriculture and tourism coexisted in the interwar years, this changed when ski lifts were built, embedded into a debt-based economy that made the tourism niche vulnerable to snow availability. Snow-dependency became a powerful selective force. It was mediated by the ski lift companies through a range of niche construction activities that turned water into an important resource of snowmaking systems.
Macho, Gabriele A.
Hominins are generally considered eclectic omnivores like baboons, but recent isotope studies call into question the generalist status of some hominins. Paranthropus boisei and Australopithecus bahrelghazali derived 75%–80% of their tissues’ δ13C from C4 sources, i.e. mainly low-quality foods like grasses and sedges. Here I consider the energetics of P. boisei and the nutritional value of C4 foods, taking into account scaling issues between the volume of food consumed and body mass, and P. boisei’s food preference as inferred from dento-cranial morphology. Underlying the models are empirical data for Papio cynocephalus dietary ecology. Paranthropus boisei only needed to spend some 37%–42% of its daily feeding time (conservative estimate) on C4 sources to meet 80% of its daily requirements of calories, and all its requirements for protein. The energetic requirements of 2–4 times the basal metabolic rate (BMR) common to mammals could therefore have been met within a 6-hour feeding/foraging day. The findings highlight the high nutritional yield of many C4 foods eaten by baboons (and presumably hominins), explain the evolutionary success of P. boisei, and indicate that P. boisei was probably a generalist like other hominins. The diet proposed is consistent with the species’ derived morphology and unique microwear textures. Finally, the results highlight the importance of baboon/hominin hand in food acquisition and preparation. PMID:24416315
Macho, Gabriele A
Hominins are generally considered eclectic omnivores like baboons, but recent isotope studies call into question the generalist status of some hominins. Paranthropus boisei and Australopithecus bahrelghazali derived 75%-80% of their tissues' δ(13)C from C4 sources, i.e. mainly low-quality foods like grasses and sedges. Here I consider the energetics of P. boisei and the nutritional value of C4 foods, taking into account scaling issues between the volume of food consumed and body mass, and P. boisei's food preference as inferred from dento-cranial morphology. Underlying the models are empirical data for Papio cynocephalus dietary ecology. Paranthropus boisei only needed to spend some 37%-42% of its daily feeding time (conservative estimate) on C4 sources to meet 80% of its daily requirements of calories, and all its requirements for protein. The energetic requirements of 2-4 times the basal metabolic rate (BMR) common to mammals could therefore have been met within a 6-hour feeding/foraging day. The findings highlight the high nutritional yield of many C4 foods eaten by baboons (and presumably hominins), explain the evolutionary success of P. boisei, and indicate that P. boisei was probably a generalist like other hominins. The diet proposed is consistent with the species' derived morphology and unique microwear textures. Finally, the results highlight the importance of baboon/hominin hand in food acquisition and preparation.
A strong ‘filter’ effect of the East China Sea land bridge for East Asia’s temperate plant species: inferences from molecular phylogeography and ecological niche modelling of Platycrater arguta (Hydrangeaceae)
Background In East Asia, an increasing number of studies on temperate forest tree species find evidence for migration and gene exchange across the East China Sea (ECS) land bridge up until the last glacial maximum (LGM). However, it is less clear when and how lineages diverged in this region, whether in full isolation or in the face of post-divergence gene flow. Here, we investigate the effects of Quaternary changes in climate and sea level on the evolutionary and demographic history of Platycrater arguta, a rare temperate understorey shrub with disjunct distributions in East China (var. sinensis) and South Japan (var. arguta). Molecular data were obtained from 14 P. arguta populations to infer current patterns of molecular structure and diversity in relation to past (Last Interglacial and Last Glacial Maximum) and present distributions based on ecological niche modelling (ENM). A coalescent-based isolation-with-migration (IM) model was used to estimate lineage divergence times and population demographic parameters. Results Combining information from nuclear/chloroplast sequence data with nuclear microsatellites, our IM analyses identify the two varieties as genetically distinct units that evolved in strict allopatry since the mid-Pleistocene, c. 0.89 (0.51–1.2) Ma. Together with Bayesian Skyeline Plots, our data further suggest that both lineages experienced post-divergence demographic growth, followed by refugial isolation, divergence, and in the case of var. arguta post-glacial admixture. However, past species distribution modelling indicates that the species’ overall distribution has not greatly changed over the last glacial cycles. Conclusions Our findings highlight the important influence of ancient sea-level changes on the diversification of East Asia’s temperate flora. Implicitly, they challenge the notion of general temperate forest expansion across the ECS land bridge, demonstrating instead its ‘filter’ effect owing to an unsuitable environment
Kostikova, Anna; Litsios, Glenn; Salamin, Nicolas; Pearman, Peter B
Macroevolutionary and microevolutionary studies provide complementary explanations of the processes shaping the evolution of niche breadth. Macroevolutionary approaches scrutinize factors such as the temporal and spatial environmental heterogeneities that drive differentiation among species. Microevolutionary studies, in contrast, focus on the processes that affect intraspecific variability. We combine these perspectives by using macroevolutionary models in a comparative study of intraspecific variability. We address potential differences in rates of evolution of niche breadth and position in annual and perennial plants of the Eriogonoideae subfamily of the Polygonaceae. We anticipated higher rates of evolution in annuals than in perennials owing to differences in generation time that are paralleled by rates of molecular evolution. Instead, we found that perennial eriogonoid species present greater environmental tolerance (wider climate niche) than annual species. Niche breadth of perennial species has evolved two to four times faster than in annuals, while niche optimum has diversified more rapidly among annual species than among perennials. Niche breadth and average elevation of species are correlated. Moreover, niche breadth increases more rapidly with mean species elevation in perennials than in annuals. Our results suggest that both environmental gradients and life-history strategy influence rates and patterns of niche breadth evolution.
Ecological niche modeling was used to assess the risk of establishment of western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), in sweet cherry, Prunus avium (L.) L., in the commercial cherry-growing areas of California. We integrated species occurrence records and spatial...
Ford, Antonia G. P.; Rüber, Lukas; Newton, Jason; Dasmahapatra, Kanchon K.; Balarin, John D.; Bruun, Kristoffer; Day, Julia J.
Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype‐environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large‐scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi. PMID:27659769
Rotenberry, J.T.; Preston, K.L.; Knick, S.
Ecological a??niche modelinga?? using presence-only locality data and large-scale environmental variables provides a powerful tool for identifying and mapping suitable habitat for species over large spatial extents. We describe a niche modeling approach that identifies a minimum (rather than an optimum) set of basic habitat requirements for a species, based on the assumption that constant environmental relationships in a species' distribution (i.e., variables that maintain a consistent value where the species occurs) are most likely to be associated with limiting factors. Environmental variables that take on a wide range of values where a species occurs are less informative because they do not limit a species' distribution, at least over the range of variation sampled. This approach is operationalized by partitioning Mahalanobis D2 (standardized difference between values of a set of environmental variables for any point and mean values for those same variables calculated from all points at which a species was detected) into independent components. The smallest of these components represents the linear combination of variables with minimum variance; increasingly larger components represent larger variances and are increasingly less limiting. We illustrate this approach using the California Gnatcatcher (Polioptila californica Brewster) and provide SAS code to implement it.
Camargo, Arley; Werneck, Fernanda P; Morando, Mariana; Sites, Jack W; Avila, Luciano J
Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo-distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo-distribution models can shed light on both demographic and range expansion processes and their potential causes.
Lv, Xue; Xia, Lin; Ge, Deyan; Wu, Yongjie; Yang, Qisen
Climatic niche conservatism shapes patterns of diversity in many taxonomic groups, while ecological opportunity (EO) can trigger rapid speciation that is less constrained by the amount of time a lineage has occupied a given habitat. These two processes are well studied, but limited research has considered their joint and relative roles in shaping diversity patterns. We characterized climatic and biogeographic variables for 102 species of arvicoline rodents (Arvicolinae, Cricetidae), testing the effects of climatic niche conservatism and EO on arvicoline diversification as lineages transitioned between biogeographic regions. We found that the amount of time a lineage has occupied a precipitation niche is positively correlated with diversity along a precipitation gradient, suggesting climatic niche conservatism. In contrast, shift in diversification rate explained diversity patterns along a temperature gradient. Our results suggest that an indirect relationship exists between temperature and diversification that is associated with EO as arvicoline rodents colonized warm Palearctic environments. Climatic niche conservatism alone did not fully explain diversity patterns under density-dependence, highlighting the additional importance of EO-related processes in promoting the explosive radiation in arvicoline rodents and shaping diversity pattern among biogeographic regions and along climatic gradients.
Laiolo, Paola; Seoane, Javier; Illera, Juan Carlos; Bastianelli, Giulia; Carrascal, Luis María; Obeso, José Ramón
The fit between life histories and ecological niche is a paradigm of phenotypic evolution, also widely used to explain patterns of species co-occurrence. By analysing the lifestyles of a sympatric avian assemblage, we show that species' solutions to environmental problems are not unbound. We identify a life-history continuum structured on the cost of reproduction along a temperature gradient, as well as habitat-driven parental behaviour. However, environmental fit and trait convergence are limited by niche filling and by within-species variability of niche traits, which is greater than variability of life histories. Phylogeny, allometry and trade-offs are other important constraints: lifetime reproductive investment is tightly bound to body size, and the optimal allocation to reproduction for a given size is not established by niche characteristics but by trade-offs with survival. Life histories thus keep pace with habitat and climate, but under the limitations imposed by metabolism, trade-offs among traits and species' realized niche. PMID:26674945
Lloyd-Smith, James O
A recurring theme in the epidemiological literature on disease eradication is that each pathogen occupies an ecological niche, and eradication of one pathogen leaves a vacant niche that favours the emergence of new pathogens to replace it. However, eminent figures have rejected this view unequivocally, stating that there is no basis to fear pathogen replacement and even that pathogen niches do not exist. After exploring the roots of this controversy, I propose resolutions to disputed issues by drawing on broader ecological theory, and advance a new consensus based on robust mechanistic principles. I argue that pathogen eradication (and cessation of vaccination) leads to a 'vacated niche', which could be re-invaded by the original pathogen if introduced. Consequences for other pathogens will vary, with the crucial mechanisms being competitive release, whereby the decline of one species allows its competitors to perform better, and evolutionary adaptation. Hence, eradication can cause a quantitative rise in the incidence of another infection, but whether this leads to emergence as an endemic pathogen depends on additional factors. I focus on the case study of human monkeypox and its rise following smallpox eradication, but also survey how these ideas apply to other pathogens and discuss implications for eradication policy.
Summary Enterotoxigenic E scherichia coli (ETEC) is a water and food‐borne pathogen that infects the small intestine of the human gut and causes diarrhoea. Enterotoxigenic E. coli adheres to the epithelium by means of colonization factors and secretes two enterotoxins, the heat labile toxin and/or the heat stable toxin that both deregulate ion channels and cause secretory diarrhoea. Enterotoxigenic E. coli as all E. coli, is a versatile organism able to survive and grow in different environments. During transmission and infection, ETEC is exposed to various environmental cues that have an impact on survivability and virulence. The ability to cope with exposure to different stressful habitats is probably shaping the pool of virulent ETEC strains that cause both endemic and epidemic infections. This review will focus on the ecology of ETEC in its different habitats and interactions with other organisms as well as abiotic factors. PMID:26522129
Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats. PMID:20370917
Semmens, Brice X; Ward, Eric J; Moore, Jonathan W; Darimont, Chris T
Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population.
Zhang, Lei; Liu, Shirong; Sun, Pengsen; Wang, Tongli; Wang, Guangyu; Zhang, Xudong; Wang, Linlin
Ensemble forecasting is advocated as a way of reducing uncertainty in species distribution modeling (SDM). This is because it is expected to balance accuracy and robustness of SDM models. However, there are little available data regarding the spatial similarity of the combined distribution maps generated by different consensus approaches. Here, using eight niche-based models, nine split-sample calibration bouts (or nine random model-training subsets), and nine climate change scenarios, the distributions of 32 forest tree species in China were simulated under current and future climate conditions. The forecasting ensembles were combined to determine final consensual prediction maps for target species using three simple consensus approaches (average, frequency, and median [PCA]). Species’ geographic ranges changed (area change and shifting distance) in response to climate change, but the three consensual projections did not differ significantly with respect to how much or in which direction, but they did differ with respect to the spatial similarity of the three consensual predictions. Incongruent areas were observed primarily at the edges of species’ ranges. Multiple stepwise regression models showed the three factors (niche marginality and specialization, and niche model accuracy) to be related to the observed variations in consensual prediction maps among consensus approaches. Spatial correspondence among prediction maps was the highest when niche model accuracy was high and marginality and specialization were low. The difference in spatial predictions suggested that more attention should be paid to the range of spatial uncertainty before any decisions regarding specialist species can be made based on map outputs. The niche properties and single-model predictive performance provide promising insights that may further understanding of uncertainties in SDM. PMID:25786217
Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin
Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation.
Shahriyari, L.; Mahdipour-Shirayeh, A.
Studying the stem cell (SC) niche architecture is a crucial step for investigating the process of oncogenesis and obtaining an effective stem cell therapy for various cancers. Recently, it has been observed that there are two groups of SCs in the SC niche collaborating with each other to maintain tissue homeostasis: border stem cells (BSCs), which are responsible in controlling the number of non-stem cells as well as stem cells, and central stem cells (CeSCs), which regulate the SC niche. Here, we develop a bi-compartmental stochastic model for the SC niche to study the spread of mutants within the niche. The analytic calculations and numeric simulations, which are in perfect agreement, reveal that in order to delay the spread of mutants in the SC niche, a small but non-zero number of SC proliferations must occur in the CeSC compartment. Moreover, the migration of BSCs to CeSCs delays the spread of mutants. Furthermore, the fixation probability of mutants in the SC niche is independent of types of SC division as long as all SCs do not divide fully asymmetrically. Additionally, the progeny of CeSCs have a much higher chance than the progeny of BSCs to take over the entire niche.
diCenzo, George C.; Checcucci, Alice; Bazzicalupo, Marco; Mengoni, Alessio; Viti, Carlo; Dziewit, Lukasz; Finan, Turlough M.; Galardini, Marco; Fondi, Marco
The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes. PMID:27447951
Lloyd-Smith, James O.
A recurring theme in the epidemiological literature on disease eradication is that each pathogen occupies an ecological niche, and eradication of one pathogen leaves a vacant niche that favours the emergence of new pathogens to replace it. However, eminent figures have rejected this view unequivocally, stating that there is no basis to fear pathogen replacement and even that pathogen niches do not exist. After exploring the roots of this controversy, I propose resolutions to disputed issues by drawing on broader ecological theory, and advance a new consensus based on robust mechanistic principles. I argue that pathogen eradication (and cessation of vaccination) leads to a ‘vacated niche’, which could be re-invaded by the original pathogen if introduced. Consequences for other pathogens will vary, with the crucial mechanisms being competitive release, whereby the decline of one species allows its competitors to perform better, and evolutionary adaptation. Hence, eradication can cause a quantitative rise in the incidence of another infection, but whether this leads to emergence as an endemic pathogen depends on additional factors. I focus on the case study of human monkeypox and its rise following smallpox eradication, but also survey how these ideas apply to other pathogens and discuss implications for eradication policy. PMID:23798698
Wang, Zhicong; Li, Zhongjie; Li, Dunhai
Cyanobacterial blooms occur frequently in lakes due to eutrophication. Although a number of models have been proposed to forecast algal blooms, a good and applicable method is still lacking. This study explored a simple and effective mathematical-ecological model to evaluate the growth status and predict the population dynamics of Microcystis blooms. In this study, phytoplankton were collected and identified from 8 sampling sites in Chaohu Lake every month from July to October, 2010. The niche breadth and niche overlap of common species were calculated using standard equations, and the potential relative growth rates of Microcystis were calculated as a weighted-value of niche overlap. In July, the potential relative growth rate was 2.79 (a.u., arbitrary units) but then rapidly declined in the following months to -3.99 a.u. in September. A significant correlation ( R =0.998, P <0.01) was found in the model between the net-increase in biomass of Microcystis in the field and the predicted values calculated by the niche model, we concluded that the niche model is suitable for forecasting the dynamics of Microcystis blooms. Redundancy analysis indicated that decreases in water temperature, dissolved oxygen and total dissolved phosphorus might be major factors underlying bloom decline. Based on the theory of community succession being caused by resource competition, the growth and decline of blooms can be predicted from a community structure. This may provide a basis for early warning and control of algal blooms.
Puzachenko, Iu G; Zheltukhin, A S; Sandlerskiĭ, R B
A potential of discriminant analysis is demonstrated in a case study of the common marten (Martes martes L., 1758) ecological niche within the Central Forest Reserve and its buffer zone. The analysis is aimed at identifying how the probability to encounter a marten's footprint along a walking route depends on the relief and other parameters of the environment discerned by remote sensing. The analyses that were done individually for each of the eleven months from a three-year observation period have revealed the pattern of the species spatial distribution and a measure of its association with the environment to be dependent, to a large extent, on the weather conditions. In general, associations with the environment do increase under unfavorable conditions. The methods are suggested that integrate outcomes of the monthly analyses into a general map of habitat types. The technique presented has wide application opportunities in studying the ecology of populations and solving problems of practical ecology.
Clowers, Katie J; Will, Jessica L; Gasch, Audrey P
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of S. cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak × vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases, the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche.
Clowers, Katie J.; Will, Jessica L.; Gasch, Audrey P.
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of Saccharomyces cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak x vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak, and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche. PMID:26518477
Wiens, John J; Ackerly, David D; Allen, Andrew P; Anacker, Brian L; Buckley, Lauren B; Cornell, Howard V; Damschen, Ellen I; Jonathan Davies, T; Grytnes, John-Arvid; Harrison, Susan P; Hawkins, Bradford A; Holt, Robert D; McCain, Christy M; Stephens, Patrick R
The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within-species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?).
Druon, Jean-Noël; Fromentin, Jean-Marc; Hanke, Alex R.; Arrizabalaga, Haritz; Damalas, Dimitrios; Tičina, Vjekoslav; Quílez-Badia, Gemma; Ramirez, Karina; Arregui, Igor; Tserpes, George; Reglero, Patricia; Deflorio, Michele; Oray, Isik; Saadet Karakulak, F.; Megalofonou, Persefoni; Ceyhan, Tevfik; Grubišić, Leon; MacKenzie, Brian R.; Lamkin, John; Afonso, Pedro; Addis, Piero
An ecological niche modelling (ENM) approach was used to predict the potential feeding and spawning habitats of small (5-25 kg, only feeding) and large (>25 kg) Atlantic bluefin tuna (ABFT), Thunnus thynnus, in the Mediterranean Sea, the North Atlantic and the Gulf of Mexico. The ENM was built bridging knowledge on ecological traits of ABFT (e.g. temperature tolerance, mobility, feeding and spawning strategy) with patterns of selected environmental variables (chlorophyll-a fronts and concentration, sea surface current and temperature, sea surface height anomaly) that were identified using an extensive set of precisely geo-located presence data. The results highlight a wider temperature tolerance for larger fish allowing them to feed in the northern - high chlorophyll levels - latitudes up to the Norwegian Sea in the eastern Atlantic and to the Gulf of Saint Lawrence in the western basin. Permanent suitable feeding habitat for small ABFT was predicted to be mostly located in temperate latitudes in the North Atlantic and in the Mediterranean Sea, as well as in subtropical waters off north-west Africa, while summer potential habitat in the Gulf of Mexico was found to be unsuitable for both small and large ABFTs. Potential spawning grounds were found to occur in the Gulf of Mexico from March-April in the south-east to April-May in the north, while favourable conditions evolve in the Mediterranean Sea from mid-May in the eastern to mid-July in the western basin. Other secondary potential spawning grounds not supported by observations were predicted in the Azores area and off Morocco to Senegal during July and August when extrapolating the model settings from the Gulf of Mexico into the North Atlantic. The presence of large ABFT off Florida and the Bahamas in spring was not explained by the model as is, however the environmental variables other than the sea surface height anomaly appeared to be favourable for spawning in part of this area. Defining key spatial and
Hong, Jin-Kyung; Cho, Jae-Chang
To find environmental variables (EVs) shaping the ecological niche of the archaeal phylum Thaumarchaeota in terrestrial environments, we determined the abundance of Thaumarchaeota in various soil samples using real-time PCR targeting thaumarchaeotal 16S rRNA gene sequences. We employed our previously developed primer, THAUM-494, which had greater coverage for Thaumarchaeota and lower tolerance to nonthaumarchaeotal taxa than previous Thaumarchaeota-directed primers. The relative abundance estimates (RVs) of Thaumarchaeota (RTHAUM), Archaea (RARCH), and Bacteria (RBACT) were subjected to a series of statistical analyses. Redundancy analysis (RDA) showed a significant (p < 0.05) canonical relationship between RVs and EVs. Negative causal relationships between RTHAUM and nutrient level-related EVs were observed in an RDA biplot. These negative relationships were further confirmed by correlation and regression analyses. Total nitrogen content (TN) appeared to be the EV that affected RTHAUM most strongly, and total carbon content (TC), which reflected the content of organic matter (OM), appeared to be the EV that affected it least. However, in the path analysis, a path model indicated that TN might be a mediator EV that could be controlled directly by the OM. Additionally, another path model implied that water content (WC) might also indirectly affect RTHAUM by controlling ammonium nitrogen (NH4+-N) level through ammonification. Thus, although most directly affected by NH4+-N, RTHAUM could be ultimately determined by OM content, suggesting that Thaumarchaeota could prefer low-OM or low-WC conditions, because either of these EVs could subsequently result in low levels of NH4+-N in soil.
Title, Pascal O; Burns, Kevin J
By employing a recently inferred phylogeny and museum occurrence records, we examine the relationship of ecological niche evolution to diversification in the largest family of songbirds, the tanagers (Thraupidae). We test whether differences in species numbers in the major clades of tanagers can be explained by differences in rate of climatic niche evolution. We develop a methodological pipeline to process and filter occurrence records. We find that, of the ecological variables examined, clade richness is higher in clades with higher climatic niche rate, and that this rate is also greater for clades that occupy a greater extent of climatic space. Additionally, we find that more speciose clades contain species with narrower niche breadths, suggesting that clades in which species are more successful at diversifying across climatic gradients have greater potential for speciation or are more buffered from the risk of extinction.
Gabriele-Rivet, Vanessa; Arsenault, Julie; Badcock, Jacqueline; Cheng, Angela; Edsall, Jim; Goltz, Jim; Kennedy, Joe; Lindsay, L. Robbin; Pelcat, Yann; Ogden, Nicholas H.
Tick-borne diseases are a growing public health concern as their incidence and range have increased in recent decades. Lyme disease is an emerging infectious disease in Canada due to northward expansion of the geographic range of Ixodes scapularis, the principal tick vector for the Lyme disease agent Borrelia burgdorferi, into central and eastern Canada. In this study the geographical distributions of Ixodid ticks, including I. scapularis, and environmental factors associated with their occurrence were investigated in New Brunswick, Canada, where few I. scapularis populations have been found to date. Density of host-seeking ticks was evaluated by drag sampling of woodland habitats in a total of 159 sites. Ixodes scapularis ticks (n = 5) were found on four sites, Ixodes muris (n = 1) on one site and Haemaphysalis leporispalustris (n = 243) on 41 sites. One of four adult I. scapularis ticks collected was PCR-positive for B. burgdorferi. No environmental variables were significantly associated with the presence of I. scapularis although comparisons with surveillance data in neighbouring provinces (Québec and Nova Scotia) suggested that temperature conditions may be too cold for I. scapularis (< 2800 annual degree days above 0°C [DD > 0°C]) across much of New Brunswick. In contrast, the presence of H. leporispalustris, which is a competent vector of tularaemia, was significantly (P < 0.05) associated with specific ranges of mean DD > 0°C, mean annual precipitation, percentage of clay in site soil, elevation and season in a multivariable logistic regression model. With the exception of some localized areas, temperature conditions and deer density may be too low for the establishment of I. scapularis and Lyme disease risk areas in New Brunswick, while environmental conditions were suitable for H. leporispalustris at many sites. These findings indicate differing ecological niches for two tick species of public health significance. PMID:26131550
Smith, Benjamin C.; Zolnik, Christine P.; Usyk, Mykhaylo; Chen, Zigui; Kaiser, Katherine; Nucci-Sack, Anne; Peake, Ken; Diaz, Angela; Viswanathan, Shankar; Strickler, Howard D.; Schlecht, Nicolas F.; Burk, Robert D.
Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes, oral samples with Streptococcus and Prevotella, and cervical samples with Lactobacillus. The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual. PMID:27698612
Aguilar, María; Fiore-Donno, Anna-Maria; Lado, Carlos; Cavalier-Smith, Thomas
It is often discussed whether the biogeography of free-living protists is better explained by the 'everything is everywhere'(EiE) hypothesis, which postulates that only ecology drives their distribution, or by the alternative hypothesis of 'moderate endemicity' in which geographic barriers can limit their dispersal. To formally test this, it would be necessary not only to find organisms restricted to a geographical area but also to check for their presence in any other place with a similar ecology. We propose the use of environmental niche models to generate and test null EiE distributions. Here we have analysed the distribution of 18S rDNA variants (ribotypes) of the myxomycete Badhamia melanospora (belonging to the protozoan phylum Amoebozoa) using 125 specimens from 91 localities. Two geographically structured groups of ribotypes congruent with slight morphological differences in the spores can be distinguished. One group comprises all populations from Argentina and Chile, and the other is formed by populations from North America together with human-introduced populations from other parts of the world. Environmental climatic niche models constructed separately for the two groups have significant differences, but show several overlapping areas. However, only specimens from one group were found in an intensively surveyed area in South America where both niche models overlap. It can be concluded that everything is not everywhere for B. melanospora. This taxon constitutes a complex formed by at least two cryptic species that probably diverged allopatrically in North and South America.
Aguilar, María; Fiore-Donno, Anna-Maria; Lado, Carlos; Cavalier-Smith, Thomas
It is often discussed whether the biogeography of free-living protists is better explained by the ‘everything is everywhere'(EiE) hypothesis, which postulates that only ecology drives their distribution, or by the alternative hypothesis of ‘moderate endemicity' in which geographic barriers can limit their dispersal. To formally test this, it would be necessary not only to find organisms restricted to a geographical area but also to check for their presence in any other place with a similar ecology. We propose the use of environmental niche models to generate and test null EiE distributions. Here we have analysed the distribution of 18S rDNA variants (ribotypes) of the myxomycete Badhamia melanospora (belonging to the protozoan phylum Amoebozoa) using 125 specimens from 91 localities. Two geographically structured groups of ribotypes congruent with slight morphological differences in the spores can be distinguished. One group comprises all populations from Argentina and Chile, and the other is formed by populations from North America together with human-introduced populations from other parts of the world. Environmental climatic niche models constructed separately for the two groups have significant differences, but show several overlapping areas. However, only specimens from one group were found in an intensively surveyed area in South America where both niche models overlap. It can be concluded that everything is not everywhere for B. melanospora. This taxon constitutes a complex formed by at least two cryptic species that probably diverged allopatrically in North and South America. PMID:24132078
Baack, Eric J; Stanton, Maureen L
Chromosome doubling plays an important role in generating new species of flowering plants. However, reproductive incompatibilities between newly formed tetraploid plants and their diploid progenitors are expected to create a significant barrier to the persistence and establishment of neopolyploid populations. Ecological differentiation can reduce this barrier via prezygotic isolation arising from spatial separation. Alternatively, superior viability or fecundity of neotetraploid plants might compensate for the reproductive cost of incompatible pollen from diploid neighbors. The performance of plants of both cytotypes can be assessed in their respective habitats through reciprocal transplants, although such experiments have not been used previously in the study of tetraploid speciation. We used a series of seed and seedling transplant experiments to assess ecological differentiation and competitive ability during early establishment phases for tetraploid and diploid forms of the snow buttercup (Ranunculus adoneus). At two sites, seeds from diploids and tetraploids had similar germination probabilities. Tetraploid snow buttercup seedlings had a significant growth advantage in a controlled environment chamber experiment. However, in the field diploid and tetraploid buttercup seedlings did not differ consistently in survival or growth, nor did the two cytotypes show reciprocal advantages in performance, as expected if ecological differentiation has occurred. At the seed and seedling stages, neither niche differentiation nor tetraploid competitive superiority appears sufficient to explain neotetraploid success in the presence of their diploid progenitors.
Christensen, Mette K.; Lund, Ole
Scholarly communities are dependent on and often measured by their ability to attract and develop doctoral students. Recent literature suggests that most scholarly communities entail ecological niches in which the doctoral students learn the codes and practices of research. In this article, we explore the microclimate in an ecological niche of…
Asumda, Faizal Z
Adult stem cells are critical for organ-specific regeneration and self-renewal with advancing age. The prospect of being able to reverse tissue-specific post-injury sequelae by harvesting, culturing and transplanting a patient's own stem and progenitor cells is exciting. Mesenchymal stem cells have emerged as a reliable stem cell source for this treatment modality and are currently being tested in numerous ongoing clinical trials. Unfortunately, the fervor over mesenchymal stem cells is mitigated by several lines of evidence suggesting that their efficacy is limited by natural aging. This article discusses the mechanisms and manifestations of age-associated deficiencies in mesenchymal stem cell efficacy. A consideration of recent experimental findings suggests that the ecological niche might be responsible for mesenchymal stem cell aging.
Adult stem cells are critical for organ-specific regeneration and self-renewal with advancing age. The prospect of being able to reverse tissue-specific post-injury sequelae by harvesting, culturing and transplanting a patient’s own stem and progenitor cells is exciting. Mesenchymal stem cells have emerged as a reliable stem cell source for this treatment modality and are currently being tested in numerous ongoing clinical trials. Unfortunately, the fervor over mesenchymal stem cells is mitigated by several lines of evidence suggesting that their efficacy is limited by natural aging. This article discusses the mechanisms and manifestations of age-associated deficiencies in mesenchymal stem cell efficacy. A consideration of recent experimental findings suggests that the ecological niche might be responsible for mesenchymal stem cell aging. PMID:23673056
Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M
Niche shifts of non-native plants can occur when they colonize novel climatic conditions. However, the mechanistic basis for niche shifts during invasion is poorly understood and has rarely been captured within species distribution models. We quantified the consequence of between-population variation in phenology for invasion of common ragweed (Ambrosia artemisiifolia L.) across Europe. Ragweed is of serious concern because of its harmful effects as a crop weed and because of its impact on public health as a major aeroallergen. We developed a forward mechanistic species distribution model based on responses of ragweed development rates to temperature and photoperiod. The model was parameterized and validated from the literature and by re-analyzing data from a reciprocal common garden experiment in which native and invasive populations were grown within and beyond the current invaded range. It could therefore accommodate between-population variation in the physiological requirements for flowering, and predict the potentially-invaded ranges of individual populations. Northern-origin populations that were established outside the generally-accepted climate envelope of the species had lower thermal requirements for bud development, suggesting local adaptation of phenology had occurred during the invasion. The model predicts that this will extend the potentially-invaded range northwards and increase the average suitability across Europe by 90% in the current climate and 20% in the future climate. Therefore, trait variation observed at the population scale can trigger a climatic niche shift at the biogeographic scale. For ragweed, earlier flowering phenology in established northern populations could allow the species to spread beyond its current invasive range, substantially increasing its risk to agriculture and public health. Mechanistic species distribution models offer the possibility to represent niche shifts by varying the traits and niche responses of individual
Michel, Alix; Clermont, Olivier; Denamur, Erick; Tenaillon, Olivier
To determine bacteriophage PhiX174's ecological niche, 783 Escherichia coli isolates were screened for susceptibility. Sensitive strains are diverse regarding their phylogenies and core lipopolysaccharides (LPS), but all have rough phenotypes. Further analysis of E. coli K-12 LPS mutants revealed that PhiX174 can use a wide diversity of LPS structures to initiate its infectious process. PMID:20833781
Pigot, Alex L.; Trisos, Christopher H.; Tobias, Joseph A.
Variation in species richness across environmental gradients may be associated with an expanded volume or increased packing of ecological niche space. However, the relative importance of these alternative scenarios remains unknown, largely because standardized information on functional traits and their ecological relevance is lacking for major diversity gradients. Here, we combine data on morphological and ecological traits for 523 species of passerine birds distributed across an Andes-to-Amazon elevation gradient. We show that morphological traits capture substantial variation in species dietary (75%) and foraging niches (60%) when multiple independent trait dimensions are considered. Having established these relationships, we show that the 14-fold increase in species richness towards the lowlands is associated with both an increased volume and density of functional trait space. However, we find that increases in volume contribute little to changes in richness, with most (78%) lowland species occurring within the range of trait space occupied at high elevations. Taken together, our results suggest that high species richness is mainly associated with a denser occupation of functional trait space, implying an increased specialization or overlap of ecological niches, and supporting the view that niche packing is the dominant trend underlying gradients of increasing biodiversity towards the lowland tropics. PMID:26740616
Yu, Hai-yang; Zhang, Fei; Wang, Juan; Zhou, Mei
The theory of land economic ecological niche was used to analyze the regional landscape pattern in this article, with an aim to provide a new method for the characterization and representation of landscape pattern. The Jinghe County region, which is ecologically fragile, was selected as an example for the study, and the Landsat images of 1990, 1998, 2011 and 2013 were selected as remote sensing data. The land economic ecological niche of land use types calculated by ecostate-ecorole theory, combined with landscape ecology theory, was discussed in application of land economic ecological niche in county landscape pattern analysis. The results showed that, during the study period, the correlations between land economic ecological niche of farmland, construction land, and grassland with the parameters, including landscape patch number (NP), aggregated index (AI), fragmented index (FN) and fractal dimension (FD), were significant. Regional landscape was driven by the changes of land economic ecological niche, and the trend of economic development could be represented by land economic ecological niche change in Jinghe County. Land economic ecological niche was closely related with the land use types which could yield direct economic benefits, which could well explain the landscape pattern characteristics in Jinghe County when combined with the landscape indices.
Warren, Christopher P.; Pascual, Mercedes; Lafferty, Kevin D.; Kuris, Armand M.
Although parasites represent an important component of ecosystems, few field and theoretical studies have addressed the structure of parasites in food webs. We evaluate the structure of parasitic links in an extensive salt marsh food web, with a new model distinguishing parasitic links from non-parasitic links among free-living species. The proposed model is an extension of the niche model for food web structure, motivated by the potential role of size (and related metabolic rates) in structuring food webs. The proposed extension captures several properties observed in the data, including patterns of clustering and nestedness, better than does a random model. By relaxing specific assumptions, we demonstrate that two essential elements of the proposed model are the similarity of a parasite's hosts and the increasing degree of parasite specialization, along a one-dimensional niche axis. Thus, inverting one of the basic rules of the original model, the one determining consumers' generality appears critical. Our results support the role of size as one of the organizing principles underlying niche space and food web topology. They also strengthen the evidence for the non-random structure of parasitic links in food webs and open the door to addressing questions concerning the consequences and origins of this structure.
Wei, Hui; Liu, Wen; Zhang, Jiaen; Qin, Zhong
Acid rain is one of the severest environmental issues globally. Relative to other global changes (e.g., warming, elevated atmospheric [CO2], and nitrogen deposition), however, acid rain has received less attention than its due. Soil fauna play important roles in multiple ecological processes, but how soil fauna community responds to acid rain remains less studied. This microcosm experiment was conducted using latosol with simulated acid rain (SAR) manipulations to observe potential changes in soil fauna community under acid rain stress. Four pH levels, i.e., pH 2.5, 3.5, 4.5, and 5.5, and a neutral control of pH 7.0 were set according to the current pH condition and acidification trend of precipitation in southern China. As expected, we observed that the SAR treatments induced changes in soil fauna community composition and their ecological niches in the tested soil; the treatment effects tended to increase as acidity increased. This could be attributable to the environmental stresses (such as acidity, porosity and oxygen supply) induced by the SAR treatments. In addition to direct acidity effect, we propose that potential changes in permeability and movability of water and oxygen in soils induced by acid rain could also give rise to the observed shifts in soil fauna community composition. These are most likely indirect pathways of acid rain to affect belowground community. Moreover, we found that nematodes, the dominating soil fauna group in this study, moved downwards to mitigate the stress of acid rain. This is probably detrimental to soil fauna in the long term, due to the relatively severer soil conditions in the deep than surface soil layer. Our results suggest that acid rain could change soil fauna community and the vertical distribution of soil fauna groups, consequently changing the underground ecosystem functions such as organic matter decomposition and greenhouse gas emissions.
Liu, Ran; Xu, Chuan; Zhang, Qiangqiang; Wang, Shiyi; Fang, Weiguo
The fungal kingdom potentially has the most complex chitin synthase (CHS) gene family, but evolution of the fungal CHS gene family and its diversification to fulfill multiple functions remain to be elucidated. Here, we identified the full complement of CHSs from 231 fungal species. Using the largest dataset to date, we characterized the evolution of the fungal CHS gene family using phylogenetic and domain structure analysis. Gene duplication, domain recombination and accretion are major mechanisms underlying the diversification of the fungal CHS gene family, producing at least 7 CHS classes. Contraction of the CHS gene family is morphology-specific, with significant loss in unicellular fungi, whereas family expansion is lineage-specific with obvious expansion in early-diverging fungi. ClassV and ClassVII CHSs with the same domain structure were produced by the recruitment of domains PF00063 and PF08766 and subsequent duplications. Comparative analysis of their functions in multiple fungal species shows that the emergence of ClassV and ClassVII CHSs is important for the morphogenesis of filamentous fungi, development of pathogenicity in pathogenic fungi, and heat stress tolerance in Pezizomycotina fungi. This work reveals the evolution of the fungal CHS gene family, and its correlation with fungal morphogenesis and adaptation to ecological niches. PMID:28300148
Boivin, Nicole L.; Zeder, Melinda A.; Fuller, Dorian Q.; Crowther, Alison; Larson, Greger; Erlandson, Jon M.; Denham, Tim; Petraglia, Michael D.
The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences. PMID:27274046
Kurchenko, I M; Yurieva, E M; Voychuk, S I
Radial growth rate of (K(r)) 153 strains 6 species of micromycetes from different ecological niches was studied on 7 agar media: three standard (malt extract agar, potato-dextrose agar, Czapek's agar), and on agar media with plant polymers (carboxymethylcellulose, xylan, soluble starch and apple pectin). Endophytic and plant pathogenic strains (biotrophs) of all studied species did not differ significantly in their ability to grow on nutrient media of different composition--average values of K(r) for these two groups were the same (0,200 and 0,199 mm/h, respectively). Soil micromycetes (saprophytes) characterized by the lowest average growth rate (0,169 mm/h) and significantly differed from the endophytic and plant pathogenic ones. Average of the radial growth rates of studied microscopic fungi were higher on standard nutrient media than with plant polymers ones. Growth parameters of endophytes and plant pathogens of all studied species on various agar media differed from the soil strains. High growth rate of endophytic and plant pathogenic strains of Fusarium poae, Alternaria alternata and Ceratocystis sp. provides them the rapid colonization of plants. Penicillium funiculosum strains equally can exist as saprophytes in soil and as endophytic plant symbionts. A wide range of K(r) variation of endophytic dark pigmented Mycelia sterilia indicates the presence in this group of different species of micromycetes, which have no sporulation.
Gidoin, Cindy; Roques, Lionel; Boivin, Thomas
Theories of species coexistence and invasion ecology are fundamentally connected and provide a common theoretical framework for studying the mechanisms underlying successful invasions and their ecological impacts. Temporal fluctuations in resource availability and differences in life-history traits between invasive and resident species are considered as likely drivers of the dynamics of invaded communities. Current critical issues in invasion ecology thus relate to the extent to which such mechanisms influence coexistence between invasive and resident species and to the ability of resident species to persist in an invasive-dominated ecosystem. We tested how a fluctuating resource, and species trait differences may explain and help predict long-term impacts of biological invasions in forest specialist insect communities. We used a simple invasion system comprising closely related invasive and resident seed-specialized wasps (Hymenoptera: Torymidae) competing for a well-known fluctuating resource and displaying divergent diapause, reproductive and phenological traits. Based on extensive long-term field observations (1977-2010), we developed a combination of mechanistic and statistical models aiming to (i) obtain a realistic description of the population dynamics of these interacting species over time, and (ii) clarify the respective contributions of fluctuation-dependent and fluctuation-independent mechanisms to long-term impact of invasion on the population dynamics of the resident wasp species. We showed that a fluctuation-dependent mechanism was unable to promote coexistence of the resident and invasive species. Earlier phenology of the invasive species was the main driver of invasion success, enabling the invader to exploit an empty niche. Phenology also had the greatest power to explain the long-term negative impact of the invasive on the resident species, through resource pre-emption. This study provides strong support for the critical role of species
Hanafi-Bojd, A A; Rassi, Y; Yaghoobi-Ershadi, M R; Haghdoost, A A; Akhavan, A A; Charrahy, Z; Karimi, A
Visceral leishmaniasis (VL) is an important vector-borne disease in Iran. Till now, Leishmania infantum has been detected from five species of sand flies in the country including Phlebotomus kandelakii, Phlebotomus major s.l., Phlebotomus perfiliewi, Phlebotomus alexandri and Phlebotomus tobbi. Also, Phlebotomus keshishiani was found to be infected with Leishmania parasites. This study aimed at predicting the probable niches and distribution of vectors of visceral leishmaniasis in Iran. Data on spatial distribution studies of sand flies were obtained from Iranian database on sand flies. Sample points were included in data from faunistic studies on sand flies conducted during 1995-2013. MaxEnt software was used to predict the appropriate ecological niches for given species, using climatic and topographical data. Distribution maps were prepared and classified in ArcGIS to find main ecological niches of the vectors and hot spots for VL transmission in Iran. Phlebotomus kandelakii, Ph. major s.l. and Ph. alexandri seem to have played a more important role in VL transmission in Iran, so this study focuses on them. Representations of MaxEnt model for probability of distribution of the studied sand flies showed high contribution of climatological and topographical variables to predict the potential distribution of three vector species. Isothermality was found to be an environmental variable with the highest gain when used in isolation for Ph. kandelakii and Ph. major s.l., while for Ph. alexandri, the most effective variable was precipitation of the coldest quarter. The results of this study present the first prediction on distribution of sand fly vectors of VL in Iran. The predicted distributions were matched with the disease-endemic areas in the country, while it was found that there were some unaffected areas with the potential transmission. More comprehensive studies are recommended on the ecology and vector competence of VL vectors in the country.
Kondo, Yasuhisa; Sano, Katsuhiro; Kadowaki, Seiji; Naganuma, Masaki; Omori, Takayuki; Yoneda, Minoru; Nishiaki, Yoshihiro
Eco-cultural niche modelling (ECNM) is an application of ecological niche modelling (ENM) to estimate the human niche in response to environmental settings. The niche probability is calculated for each spatial pixel, based on (1) the location of known archaeological sites as occurrence data and (2) environmental factors such palaeoclimate (temperature and precipitation), palaeovegetation (biome) and palaeotopography (elevation, slope and aspect). Some ENM software packages, including MaxEnt (maximum entropy model), output the percentage of contribution for each environmental factor, and therefore it is possible to identify and evaluate environmental constraints to the geographic expansion of human populations. Based on this thought, the authors applied ECNM to Palaeolithic stone tool industries in Europe and Siberia at 50-46 kya, the time period during which the first anatomically modern humans (AMHs) are presumed to have appeared in those regions, under the assumption that stone tool groups may reflect different human groups in terms of subsistence strategy. The preliminary results suggested that the population using Emiran and related industries (Bohunician and Bachokirian) were likely to construct their niches in the geographic zones where the long-term variability of the coldest month temperature was larger than in those occupied by the populations using the Late Mousterian, Szeletian and Châtelperronean stone tool industries.
De Angelis, Antonella; Ricotta, Carlo; Conedera, Marco; Pezzatti, Gianni Boris
Fire regimes are strongly related to weather conditions that directly and indirectly influence fire ignition and propagation. Identifying the most important meteorological fire drivers is thus fundamental for daily fire risk forecasting. In this context, several fire weather indices have been developed focussing mainly on fire-related local weather conditions and fuel characteristics. The specificity of the conditions for which fire danger indices are developed makes its direct transfer and applicability problematic in different areas or with other fuel types. In this paper we used the low-to-intermediate fire-prone region of Canton Ticino as a case study to develop a new daily fire danger index by implementing a niche modelling approach (Maxent). In order to identify the most suitable weather conditions for fires, different combinations of input variables were tested (meteorological variables, existing fire danger indices or a combination of both). Our findings demonstrate that such combinations of input variables increase the predictive power of the resulting index and surprisingly even using meteorological variables only allows similar or better performances than using the complex Canadian Fire Weather Index (FWI). Furthermore, the niche modelling approach based on Maxent resulted in slightly improved model performance and in a reduced number of selected variables with respect to the classical logistic approach. Factors influencing final model robustness were the number of fire events considered and the specificity of the meteorological conditions leading to fire ignition.
De Angelis, Antonella; Ricotta, Carlo; Conedera, Marco; Pezzatti, Gianni Boris
Fire regimes are strongly related to weather conditions that directly and indirectly influence fire ignition and propagation. Identifying the most important meteorological fire drivers is thus fundamental for daily fire risk forecasting. In this context, several fire weather indices have been developed focussing mainly on fire-related local weather conditions and fuel characteristics. The specificity of the conditions for which fire danger indices are developed makes its direct transfer and applicability problematic in different areas or with other fuel types. In this paper we used the low-to-intermediate fire-prone region of Canton Ticino as a case study to develop a new daily fire danger index by implementing a niche modelling approach (Maxent). In order to identify the most suitable weather conditions for fires, different combinations of input variables were tested (meteorological variables, existing fire danger indices or a combination of both). Our findings demonstrate that such combinations of input variables increase the predictive power of the resulting index and surprisingly even using meteorological variables only allows similar or better performances than using the complex Canadian Fire Weather Index (FWI). Furthermore, the niche modelling approach based on Maxent resulted in slightly improved model performance and in a reduced number of selected variables with respect to the classical logistic approach. Factors influencing final model robustness were the number of fire events considered and the specificity of the meteorological conditions leading to fire ignition. PMID:25679957
Perrin, Laura; Probert, Ian; Langer, Gerald; Aloisi, Giovanni
Coccolithophores are unicellular calcifying marine algae that play an important role in the oceanic carbon cycle via their cellular processes of photosynthesis (a CO2 sink) and calcification (a CO2 source). In contrast to the well-studied, surface-water coccolithophore blooms visible from satellites, the lower photic zone is a poorly known but potentially important ecological niche for coccolithophores in terms of primary production and carbon export to the deep ocean. In this study, the physiological responses of an Emiliania huxleyi strain to conditions simulating the deep niche in the oligotrophic gyres along the BIOSOPE transect in the South Pacific Gyre were investigated. We carried out batch culture experiments with an E. huxleyi strain isolated from the BIOSOPE transect, reproducing the in situ conditions of light and nutrient (nitrate and phosphate) limitation. By simulating coccolithophore growth using an internal stores (Droop) model, we were able to constrain fundamental physiological parameters for this E. huxleyi strain. We show that simple batch experiments, in conjunction with physiological modelling, can provide reliable estimates of fundamental physiological parameters for E. huxleyi that are usually obtained experimentally in more time-consuming and costly chemostat experiments. The combination of culture experiments, physiological modelling and in situ data from the BIOSOPE cruise show that E. huxleyi growth in the deep BIOSOPE niche is limited by availability of light and nitrate. This study contributes more widely to the understanding of E. huxleyi physiology and behaviour in a low-light and oligotrophic environment of the ocean.
Ushiki, Norisuke; Jinno, Masaru; Fujitani, Hirotsugu; Suenaga, Toshikazu; Terada, Akihiko; Tsuneda, Satoshi
Nitrite oxidation is an aerobic process of the nitrogen cycle in natural ecosystems, and is performed by nitrite-oxidizing bacteria (NOB). Also, nitrite oxidation is a rate-limiting step of nitrogen removal in wastewater treatment plants (WWTPs). Although Nitrospira is known as dominant NOB in WWTPs, information on their physiological properties and kinetic parameters is limited. Here, we report the kinetic parameters and inhibition of nitrite oxidation by free ammonia in pure cultures of Nitrospira sp. strain ND1 and Nitrospira japonica strain NJ1, which were previously isolated from activated sludge in a WWTP. The maximum nitrite uptake rate ( [Formula: see text] ) and the half-saturation constant for nitrite uptake ( [Formula: see text] ) of strains ND1 and NJ1 were 45 ± 7 and 31 ± 5 (μmol NO2(-)/mg protein/h), and 6 ± 1 and 10 ± 2 (μM NO2(-)), respectively. The [Formula: see text] and [Formula: see text] of two strains indicated that they adapt to low-nitrite-concentration environments like activated sludge. The half-saturation constants for oxygen uptake ( [Formula: see text] ) of the two strains were 4.0±2.5 and 2.6±1.1 (μM O2), respectively. The [Formula: see text] values of the two strains were lower than those of other NOB, suggesting that Nitrospira in activated sludge could oxidize nitrite in the hypoxic environments often found in the interiors of biofilms and flocs. The inhibition thresholds of the two strains by free ammonia were 0.85 and 4.3 (mg-NH3 l(-1)), respectively. Comparing the physiological properties of the two strains, we suggest that tolerance for free ammonia determines competition and partitioning into ecological niches among Nitrospira populations.
Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagye, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hildén, Kristiina; Kües, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subramanian, Venkataramanan; Wösten, Han A. B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S. M.; Cullen, Dan; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis
Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics. PMID:23045686
Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G; Ohm, Robin A; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L; Bailey, Andrew M; Billette, Christophe; Coutinho, Pedro M; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hildén, Kristiina; Kües, Ursula; Labutti, Kurt M; Lapidus, Alla; Lindquist, Erika A; Lucas, Susan M; Murat, Claude; Riley, Robert W; Salamov, Asaf A; Schmutz, Jeremy; Subramanian, Venkataramanan; Wösten, Han A B; Xu, Jianping; Eastwood, Daniel C; Foster, Gary D; Sonnenberg, Anton S M; Cullen, Dan; de Vries, Ronald P; Lundell, Taina; Hibbett, David S; Henrissat, Bernard; Burton, Kerry S; Kerrigan, Richard W; Challen, Michael P; Grigoriev, Igor V; Martin, Francis
Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.
Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hilden, Kristiina; Kues, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subramanian, Venkataramanan; Wosten, Han A. B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S. M.; Cullen, Dan; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis
Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the button mushroom forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.
Zimkus, Breda M; Lawson, Lucinda P; Barej, Michael F; Barratt, Christopher D; Channing, Alan; Dash, Katrina M; Dehling, J Maximilian; Du Preez, Louis; Gehring, Philip-Sebastian; Greenbaum, Eli; Gvoždík, Václav; Harvey, James; Kielgast, Jos; Kusamba, Chifundera; Nagy, Zoltán T; Pabijan, Maciej; Penner, Johannes; Rödel, Mark-Oliver; Vences, Miguel; Lötters, Stefan
The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates of similarity in bioclimatic niche were calculated from species-distribution models (maxent) and multivariate statistics (Principal Component Analysis, Discriminant Function Analysis). Ancestral-area reconstructions were performed on the phylogeny using probabilistic approaches implemented in BioGeoBEARS. We detected high levels of genetic differentiation yielding ten distinct lineages or operational taxonomic units, and Central Africa was found to be a diversity hotspot for these frogs. Most speciation events took place throughout the Miocene, including "out-of-Africa" overseas dispersal events to Madagascar in the East and to São Tomé in the West. Bioclimatic niche was remarkably well conserved, with most species tolerating similar temperature and rainfall conditions common to the Central African region. The P. mascareniensis complex provides insights into how bioclimatic niche shaped the current biogeographic patterns with niche conservatism being exhibited by the Central African
van Riet, W. F.; Cooks, J.
In this article a model is proposed that could be used as a basis for ecological planning of natural resources. The role of people as part of the ecosystem is emphasized, and the various factors that should be considered in such planning are discussed. An understanding of ecological planning is dependent on the study of human activities in, and the nature of, natural ecosystems. It also depends on the fact that people are a part of nature, and as a result nature is of value to humans. Realizing the importance of this principle is a prerequisite to studying nature and also for an understanding of the various steps in the ecological planning approach. Realization of these values is often through a series of activities that may result in a negative environmental impact. Nature is described as an interacting group of natural features and processes. In this study both the features and processes are described as natural resources. The use of these natural resources obviously affects them, and if this use is to continue over a long period, both the activity and the resource must be understood if they are to be maintained in a productive state. In order to limit impact and maintain value, a planning aid called zoning is used to assist in the understanding of the processes involved.
Pertierra, Luis R; Aragón, Pedro; Shaw, Justine D; Bergstrom, Dana M; Terauds, Aleks; Olalla-Tárraga, Miguel Ángel
The two non-native grasses that have established long-term populations in Antarctica (Poa pratensis and Poa annua) were studied from a global multidimensional thermal niche perspective to address the biological invasion risk to Antarctica. These two species exhibit contrasting introduction histories and reproductive strategies and represent two referential case studies of biological invasion processes. We used a multistep process with a range of species distribution modelling techniques (ecological niche factor analysis, multidimensional envelopes, distance/entropy algorithms) together with a suite of thermoclimatic variables, to characterize the potential ranges of these species. Their native bioclimatic thermal envelopes in Eurasia, together with the different naturalized populations across continents, were compared next. The potential niche of P. pratensis was wider at the cold extremes; however, P. annua life history attributes enable it to be a more successful colonizer. We observe that particularly cold summers are a key aspect of the unique Antarctic environment. In consequence, ruderals such as P. annua can quickly expand under such harsh conditions, whereas the more stress-tolerant P. pratensis endures and persist through steady growth. Compiled data on human pressure at the Antarctic Peninsula allowed us to provide site-specific biosecurity risk indicators. We conclude that several areas across the region are vulnerable to invasions from these and other similar species. This can only be visualized in species distribution models (SDMs) when accounting for founder populations that reveal nonanalogous conditions. Results reinforce the need for strict management practices to minimize introductions. Furthermore, our novel set of temperature-based bioclimatic GIS layers for ice-free terrestrial Antarctica provide a mechanism for regional and global species distribution models to be built for other potentially invasive species.
Lipatov, Mikhail; Brown, Melissa J; Feldman, Marcus W
With introduction of social niche effects into a model of cultural change, the frequency of a practice cannot predict the frequency of its underlying belief. The combination of a general model with empirical data from a specific case illustrates the importance of collaboration between modellers and field researchers, and identifies the type of quantitative data necessary for analysing case studies. Demographic data from colonial-period household registers in Taiwan document a shift in marriage form within 40 years, from a mixture of uxorilocal marriages and virilocal marriages to the latter's dominance. Ethnographic data indicate marriage-related beliefs, costs, ethnic effects and colonial policies as well as the importance of horizontal cultural transmission. We present a formal model for the effects of moral beliefs about marriage and a population economic index on the decline of uxorilocal marriage. We integrate empirical marriage rates and an estimated economic index to produce five projections of the historical frequencies of one belief. These projections demonstrate how economic development may affect a cultural niche. They also indicate the need for future research on the relationship between wealth and cultural variability, the motivational force of cultural versus social factors, and the process of cultural niche construction.
Deane, David C; Nicol, Jason M; Gehrig, Susan L; Harding, Claire; Aldridge, Kane T; Goodman, Abigail M; Brookes, Justin D
Human use of water resources threatens environmental water supplies. If resource managers are to develop policies that avoid unacceptable ecological impacts, some means to predict ecosystem response to changes in water availability is necessary. This is difficult to achieve at spatial-scales relevant for water resource management because of the high natural variability in ecosystem hydrology and ecology. Water plant functional groups classify species with similar hydrological niche preferences together, allowing a qualitative means to generalise community responses to changes in hydrology. We tested the potential for functional groups in making quantitative prediction of water-plant-functional-group distributions across diverse wetland types over a large geographical extent. We sampled wetlands covering a broad range of hydrogeomorphic and salinity conditions in South Australia, collecting both hydrological and floristic data from 697 quadrats across 28 wetland hydrological gradients. We built hydrological-niche models for eight water plant functional groups using a range of candidate models combining different surface inundation metrics. We then tested the predictive performance of top-ranked individual and averaged models for each functional group. Cross validation showed models achieved acceptable predictive performance, with correct classification rates in the range 0.68 - 0.95. Model predictions can be made at any spatial scale that hydrological data are available and could be implemented in a geographical information system. We show the response of water plant functional groups to inundation is consistent enough across diverse wetland types to quantify the probability of hydrological impacts over regional spatial scales. This article is protected by copyright. All rights reserved.
Kirkpatrick, C. James
By definition, biomaterials are developed for clinical application. In the field of regenerative medicine their principal function is to play a significant, and, if possible, an instructive role in tissue healing. In the last analysis the latter involves targeting the ‘regenerative niche’. The present paper will address the problem of simulating this niche in the laboratory and adopts a life science approach involving the harnessing of heterotypic cellular communication to achieve this, that is, the ability of cells of different types to mutually influence cellular functions. Thus, co-culture systems using human cells are the methodological focus and will concern four exemplary fields of regeneration, namely, bone, soft tissue, lower respiratory tract and airway regeneration. The working hypothesis underlying this approach is that in vitro models of higher complexity will be more clinically relevant than simple monolayer cultures of transformed cell lines in testing innovative strategies with biomaterials for regeneration. PMID:26816650
König, Annekatrin; Shcherbata, Halyna R
The germaria of the fruit fly Drosophila melanogaster present an excellent model to study germline stem cell-niche interactions. Two to three adult stem cells are surrounded by a number of somatic cells that form the niche. Here we describe how Drosophilae germaria can be dissected and specifically immuno-stained to allow for identification and analysis of both the adult stem cells and their somatic niche cells.
Murrow, Lyndsay M; Weber, Robert J; Gartner, Zev J
For many tissues, single resident stem cells grown in vitro under appropriate three-dimensional conditions can produce outgrowths known as organoids. These tissues recapitulate much of the cell composition and architecture of the in vivo organ from which they derive, including the formation of a stem cell niche. This has facilitated the systematic experimental manipulation and single-cell, high-throughput imaging of stem cells within their respective niches. Furthermore, emerging technologies now make it possible to engineer organoids from purified cellular and extracellular components to directly model and test stem cell-niche interactions. In this Review, we discuss how organoids have been used to identify and characterize stem cell-niche interactions and uncover new niche components, focusing on three adult-derived organoid systems. We also describe new approaches to reconstitute organoids from purified cellular components, and discuss how this technology can help to address fundamental questions about the adult stem cell niche.
Naito, Yuichi I; Chikaraishi, Yoshito; Drucker, Dorothée G; Ohkouchi, Naohiko; Semal, Patrick; Wißing, Christoph; Bocherens, Hervé
This study provides a refined view on the diet and ecological niche of Neanderthals. The traditional view is that Neanderthals obtained most of their dietary protein from terrestrial animals, especially from large herbivores that roamed the open landscapes. Evidence based on the conventional carbon and nitrogen isotopic composition of bulk collagen has supported this view, although recent findings based on plant remains in the tooth calculus, microwear analyses, and small game and marine animal remains from archaeological sites have raised some questions regarding this assumption. However, the lack of a protein source other than meat in the Neanderthal diet may be due to methodological difficulties in defining the isotopic composition of plants. Based on the nitrogen isotopic composition of glutamic acid and phenylalanine in collagen for Neanderthals from Spy Cave (Belgium), we show that i) there was an inter-individual dietary heterogeneity even within one archaeological site that has not been evident in bulk collagen isotopic compositions, ii) they occupied an ecological niche different from those of hyenas, and iii) they could rely on plants for up to ∼20% of their protein source. These results are consistent with the evidence found of plant consumption by the Spy Neanderthals, suggesting a broader subsistence strategy than previously considered.
Ramírez-Albores, Jorge E; Bustamante, Ramiro O; Badano, Ernesto I
Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile) nor the origin of individuals (naturally established or man-planted), the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle), a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model). The second model only included occurrence records of naturally established mature individuals (adult niche model), while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model). When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with data of
Ramírez-Albores, Jorge E.; Bustamante, Ramiro O.
Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile) nor the origin of individuals (naturally established or man-planted), the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle), a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model). The second model only included occurrence records of naturally established mature individuals (adult niche model), while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model). When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with data of
Runemark, Anna; Sagonas, Kostas; Svensson, Erik I
Although rapid evolution of body size on islands has long been known, the ecological mechanisms behind this island phenomenon remain poorly understood. Diet is an important selective pressure for morphological divergence. Here we investigate if selection for novel diets has contributed to the multiple independent cases of island gigantism in the Skyros wall lizard (Podarcis gaigeae) and if diet, predation, or both factors best explain island gigantism. We combined data on body size, shape, bite force, and realized and available diets to address this. Several lines of evidence suggest that diet has contributed to the island gigantism. The larger islet lizards have relatively wider heads and higher bite performance in relation to mainland lizards than would be expected from size differences alone. The proportions of consumed and available hard prey are higher on islets than mainland localities, and lizard body size is significantly correlated with the proportion of hard prey. Furthermore, the main axis of divergence in head shape is significantly correlated with dietary divergence. Finally, a model with only diet and one including diet and predation regime explain body size divergence equally well. Our results suggest that diet is an important ecological factor behind insular body size divergence, but could be consistent with an additional role for predation.
Escobar, Luis E; Lira-Noriega, Andrés; Medina-Vogel, Gonzalo; Townsend Peterson, A
Emerging infectious diseases can present serious threats to wildlife, even to the point of causing extinction. Whitenose fungus (Pseudogymnoascus destructans) is causing an epizootic in bats that is expanding rapidly, both geographically and taxonomically. Little is known of the ecology and distributional potential of this intercontinental pathogen. We address this gap via ecological niche models that characterise coarse resolution niche differences between fungus populations on different continents, identifying areas potentially vulnerable to infection in South America. Here we explore a novel approach to identifying areas of potential distribution across novel geographic regions that avoids perilious extrapolation into novel environments. European and North American fungus populations show differential use of environmental space, but rather than niche differentiation, we find that changes are best attributed to climatic differences between the two continents. Suitable areas for spread of the pathogen were identified across southern South America; however caution should be taken to avoid underestimating the potential for spread of this pathogen in South America.
Navarro, Joan; Cardador, Laura; Brown, Ruth; Phillips, Richard A.
According to niche theory, mechanisms exist that allow co-existence of organisms that would otherwise compete for the same prey and other resources. How seabirds cope with potential competition during the non-breeding period is poorly documented, particularly for small species. Here we investigate for the first time the potential role of spatial, environmental (habitat) and trophic (isotopic) segregation as niche-partitioning mechanisms during the non-breeding season for four species of highly abundant, zooplanktivorous seabird that breed sympatrically in the Southern Ocean. Spatial segregation was found to be the main partitioning mechanism; even for the two sibling species of diving petrel, which spent the non-breeding period in overlapping areas, there was evidence from distribution and stable isotope ratios for differences in habitat use and diving depth. PMID:26165162
Hogerwerf, Lenny; Wallace, Rob G.; Ottaviani, Daniela; Slingenbergh, Jan; Prosser, Diann; Bergmann, Luc; Gilbert, Marius
The highly pathogenic avian influenza (HPAI) H5N1 virus has spread across Eurasia and into Africa. Its persistence in a number of countries continues to disrupt poultry production, impairs smallholder livelihoods, and raises the risk a genotype adapted to human-to-human transmission may emerge. While previous studies identified domestic duck reservoirs as a primary risk factor associated with HPAI H5N1 persistence in poultry in Southeast Asia, little is known of such factors in countries with different agro-ecological conditions, and no study has investigated the impact of such conditions on HPAI H5N1 epidemiology at the global scale. This study explores the patterns of HPAI H5N1 persistence worldwide, and for China, Indonesia, and India includes individual provinces that have reported HPAI H5N1 presence during the 2004–2008 period. Multivariate analysis of a set of 14 agricultural, environmental, climatic, and socio-economic factors demonstrates in quantitative terms that a combination of six variables discriminates the areas with human cases and persistence: agricultural population density, duck density, duck by chicken density, chicken density, the product of agricultural population density and chicken output/input ratio, and purchasing power per capita. The analysis identifies five agro-ecological clusters, or niches, representing varying degrees of disease persistence. The agro-ecological distances of all study areas to the medoid of the niche with the greatest number of human cases are used to map HPAI H5N1 risk globally. The results indicate that few countries remain where HPAI H5N1 would likely persist should it be introduced.
Coletta, John; Bradley, James
Presents a method which organizes concepts and relates different phenomena to a single model of ecology. Describes how this model is used to explain the overall significance of biological and ecological cycles and its usefulness in helping students to understand the various dangers to and remedies available for an ecosystem. (CS)
Yackulic, Charles B.; Nichols, James D.; Reid, Janice; Der, Ricky
Ecologists frequently try to predict the future geographic distributions of species. Most studies assume that the current distribution of a species reflects its environmental requirements (i.e., the species' niche). However, the current distributions of many species are unlikely to be at equilibrium with the current distribution of environmental conditions, both because of ongoing invasions and because the distribution of suitable environmental conditions is always changing. This mismatch between the equilibrium assumptions inherent in many analyses and the disequilibrium conditions in the real world leads to inaccurate predictions of species' geographic distributions and suggests the need for theory and analytical tools that avoid equilibrium assumptions. Here, we develop a general theory of environmental associations during periods of transient dynamics. We show that time-invariant relationships between environmental conditions and rates of local colonization and extinction can produce substantial temporal variation in occupancy–environment relationships. We then estimate occupancy–environment relationships during three avian invasions. Changes in occupancy–environment relationships over time differ among species but are predicted by dynamic occupancy models. Since estimates of the occupancy–environment relationships themselves are frequently poor predictors of future occupancy patterns, research should increasingly focus on characterizing how rates of local colonization and extinction vary with environmental conditions.
Gardiner, Jayne M.; Atema, Jelle; Hueter, Robert E.; Motta, Philip J.
The underwater sensory world and the sensory systems of aquatic animals have become better understood in recent decades, but typically have been studied one sense at a time. A comprehensive analysis of multisensory interactions during complex behavioral tasks has remained a subject of discussion without experimental evidence. We set out to generate a general model of multisensory information extraction by aquatic animals. For our model we chose to analyze the hierarchical, integrative, and sometimes alternate use of various sensory systems during the feeding sequence in three species of sharks that differ in sensory anatomy and behavioral ecology. By blocking senses in different combinations, we show that when some of their normal sensory cues were unavailable, sharks were often still capable of successfully detecting, tracking and capturing prey by switching to alternate sensory modalities. While there were significant species differences, odor was generally the first signal detected, leading to upstream swimming and wake tracking. Closer to the prey, as more sensory cues became available, the preferred sensory modalities varied among species, with vision, hydrodynamic imaging, electroreception, and touch being important for orienting to, striking at, and capturing the prey. Experimental deprivation of senses showed how sharks exploit the many signals that comprise their sensory world, each sense coming into play as they provide more accurate information during the behavioral sequence of hunting. The results may be applicable to aquatic hunting in general and, with appropriate modification, to other types of animal behavior. PMID:24695492
Larsen, Peter E.; Collart, Frank R.; Dai, Yang; Blanchard, Jeffrey L.
The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.
Kaiser, Kristine; Pollinger, John
The amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been implicated in amphibian declines around the globe. Although it has been found in most countries in Central America, its presence has never been assessed in Belize. We set out to determine the range, prevalence, and diversity of Bd using quantitative PCR (qPCR) and sequencing of a portion of the 5.8 s and ITS1-2 regions. Swabs were collected from 524 amphibians of at least 26 species in the protected areas of the Maya Mountains of Belize. We sequenced a subset of 72 samples that had tested positive for Bd by qPCR at least once; 30 samples were verified as Bd. Eight unique Bd haplotypes were identified in the Maya Mountains, five of which were previously undescribed. We identified unique ecological niches for the two most broadly distributed haplotypes. Combined with data showing differing virulence shown in different strains in other studies, the 5.8 s - ITS1-2 region diversity found in this study suggests that there may be substantial differences among populations or haplotypes. Future work should focus on whether specific haplotypes for other genomic regions and possibly pathogenicity can be associated with haplotypes at this locus, as well as the integration of molecular tools with other ecological tools to elucidate the ecology and pathogenicity of Bd.
Cavender-Bares, Jeannine; Pahlich, Annette
The genus Quercus (the oaks) is notorious for interspecific hybrization, generating questions about the mechanisms that permit coexistence of closely related species. Two sister oak species, Quercus virginiana and Q. geminata, occur in sympatry in Florida and throughout the southeastern United States. In 11 sites from northern and southeastern regions of Florida, we used a leaf-based morphological index to identify individuals to species. Eleven nuclear microsatellite markers significantly differentiated between the species with a high correspondence between molecular and morphological typing of specimens. Nevertheless, Bayesian clustering analysis indicates interspecific gene flow, and six of 109 individuals had mixed ancestry. The identity of several individuals also was mismatched using molecular markers and morphological characters. In a common environment, the two species performed differently in terms of photosynthetic performance and growth, corresponding to their divergent ecological niches with respect to soil moisture and other edaphic properties. Our data support earlier hypotheses that divergence in flowering time causes assortative mating, allowing these ecologically distinct sister species to occur in sympatry. Limited gene flow that permits ecological differentiation helps to explain the overdispersion of oak species in local communities.
The positive relationship between habitat heterogeneity and species richness is a cornerstone of ecology. Recently, it was suggested that this relationship should be unimodal rather than linear due to a tradeoff between environmental heterogeneity and population sizes. Increased environmental heterogeneity will decrease effective habitat sizes, which in turn will increase the rate of local species extinctions. The occurrence of the unimodal richness-heterogeneity relationship at the habitat scale was confirmed in both empirical and theoretical studies. However, it is unclear whether it can occur at broader spatial scales, for meta-communities in diverse and patchy landscapes. Here, I used a spatially explicit meta-community model to quantify the roles of two species-level characteristics, niche width and immigration rates, on the type of the richness-heterogeneity relationship at the landscape scale. I found that both positive and unimodal richness-heterogeneity relationships can occur in meta-communities in patchy landscapes. The type of the relationship was affected by the interactions between inter-patch immigration rates and species' niche widths. Unimodal relationships were prominent in meta-communities comprising species with wide niches but low inter-patch immigration rates. In contrast, meta-communities consisting of species with narrow niches and high immigration rates exhibited positive relationships. Meta-communities comprising generalist species are therefore likely to exhibit unimodal richness-heterogeneity relationships as long as low immigration rates prevent rescue effects and patches are small. The richness-heterogeneity relationship at the landscape scale is dictated by species' niche widths and inter-patch immigration rates. These immigration rates, in turn, depend on the interaction between species dispersal capabilities and habitat connectivity, highlighting the roles of both species traits and landscape structure in generating the richness
Rödder, Dennis; Lötters, Stefan
The use of species distribution models (SDMs) to predict potential distributions of species is steadily increasing. A necessary assumption when projecting models throughout space or time is that climatic niches are conservative, but recent findings of niche shifts during biological invasion of particular plant and animal species have indicated that this assumption is not categorically valid. One reason for observed shifts may relate to variable selection for modelling. In this study, we assess differences in climatic niches in the native and invasive ranges of the Greenhouse frog ( Eleutherodactylus planirostris). We analyze which variables are more ‘conserved’ in comparison to more ‘relaxed’ variables (i.e. subject to niche shift) and how they influence transferability of SDMs developed with Maxent on the basis of ten bioclimatic layers best describing the climatic requirements of the target species. We focus on degrees of niche similarity and conservatism using Schoener's index and Hellinger distance. Significance of results are tested with null models. Results indicate that the degrees of niche similarity and conservatism vary greatly among the predictive variables. Some shifts can be attributed to active habitat selection, whereas others apparently reflect variation in the availability of climate conditions or biotic interactions between the frogs' native and invasive ranges. Patterns suggesting active habitat selection also vary among variables. Our findings evoke considerable implications on the transferability of SDMs over space and time, which is strongly affected by the choice and number of predictors. The incorporation of ‘relaxed’ predictors not or only indirectly correlated with biologically meaningful predictors may lead to erroneous predictions when projecting SDMs. We recommend thorough assessments of invasive species' ecology for the identification biologically meaningful predictors facilitating transferability.
Anacker, Brian L; Strauss, Sharon Y
A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under 'budding' speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister-non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities.
Anacker, Brian L.; Strauss, Sharon Y.
A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under ‘budding’ speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister–non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities
Ricci, Jessica N; Coleman, Maureen L; Welander, Paula V; Sessions, Alex L; Summons, Roger E; Spear, John R; Newman, Dianne K
Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (P-value<10−6); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche. PMID:24152713
Soberón, Jorge; Nakamura, Miguel
Estimating actual and potential areas of distribution of species via ecological niche modeling has become a very active field of research, yet important conceptual issues in this field remain confused. We argue that conceptual clarity is enhanced by adopting restricted definitions of "niche" that enable operational definitions of basic concepts like fundamental, potential, and realized niches and potential and actual distributional areas. We apply these definitions to the question of niche conservatism, addressing what it is that is conserved and showing with a quantitative example how niche change can be measured. In this example, we display the extremely irregular structure of niche space, arguing that it is an important factor in understanding niche evolution. Many cases of apparently successful models of distributions ignore biotic factors: we suggest explanations to account for this paradox. Finally, relating the probability of observing a species to ecological factors, we address the issue of what objects are actually calculated by different niche modeling algorithms and stress the fact that methods that use only presence data calculate very different quantities than methods that use absence data. We conclude that the results of niche modeling exercises can be interpreted much better if the ecological and mathematical assumptions of the modeling process are made explicit.
Kozak, Kenneth H; Wiens, John J
A major goal of evolutionary biology and ecology is to understand why species richness varies among clades. Previous studies have suggested that variation in richness among clades might be related to variation in rates of morphological evolution among clades (e.g., body size and shape). Other studies have suggested that richness patterns might be related to variation in rates of climatic-niche evolution. However, few studies, if any, have tested the relative importance of these variables in explaining patterns of richness among clades. Here, we test their relative importance among major clades of Plethodontidae, the most species-rich family of salamanders. Earlier studies have suggested that climatic-niche evolution explains patterns of diversification among plethodontid clades, whereas rates of morphological evolution do not. A subsequent study stated that rates of morphological evolution instead explained patterns of species richness among plethodontid clades (along with "ecological limits" on richness of clades, leading to saturation of clades with species, given limited resources). However, they did not consider climatic-niche evolution. Using phylogenetic multiple regression, we show that rates of climatic-niche evolution explain most variation in richness among plethodontid clades, whereas rates of morphological evolution do not. We find little evidence that ecological limits explain patterns of richness among plethodontid clades. We also test whether rates of morphological and climatic-niche evolution are correlated, and find that they are not. Overall, our results help explain richness patterns in a major amphibian group and provide possibly the first test of the relative importance of climatic niches and morphological evolution in explaining diversity patterns.
Alba, T. W.; Goertz, G.; Williams, A. J.; Cole, J. K.; Murugapiran, S. K.; Dodsworth, J. A.; Hedlund, B. P.
';Aigarchaeota' (formerly known as pSL4 and Hot Water Crenarchaeotic Group I (HWCGI)) is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultivation-independent microbial surveys and a single composite genome from Candidatus ';Caldiarchaeum subterraneum', an inhabitant of a subterranean gold mine in Japan. Sequences reported in various publications are found exclusively in geothermal settings, but a comprehensive assessment has not yet been performed. We mined public databases for 16S rRNA gene sequences related to known ';Aigarchaeota' and used a combination of approaches to rigorously define the phylogenetic boundaries of the phylum. The analyses supported the proposed relationship between ';Aigarchaeota', Thaumarchaeota, Crenarchaeota, and Korarchaeota in the so-called 'TACK superphylum' and identified ~200 16S rRNA genes and gene fragments belonging to ';Aigarchaeota', including those recovered from terrestrial geothermal systems on several continents (North America, Asia, Africa, Europe, and Oceania) and marine geothermal and subsurface samples in both the Atlantic and Pacific. ';Aigarchaeota' belonged to at least three family- to order-level groups and at least seven genus-level groups. All genus-level groups were recovered from geographically distant locations, suggesting a global distribution within amenable habitats. ';Aigarchaeota'-specific primers for the polymerase chain reaction (PCR) amplification of 16S rRNA genes were designed using SP-Designer and reviewed using the Ribosomal Database Project Probe Match tool. The primers will be used to determine the presence and abundance of ';Aigarchaeota' in a wide variety of samples from terrestrial geothermal systems in the western U.S. and Asia. These phylogenetic data, along with a large geochemical database, will be analyzed using multivariate statistics to develop biogeographic and habitat niche models for ';Aigarchaeota'. This study offers the first coherent view of the
Perkins, Nicholas R.; Hill, Nicole A.; Foster, Scott D.; Barrett, Neville S.
Poleward range shifts of species as a result of global climate change are being increasingly documented. As species extend into new ranges their ecological impacts and the niches that they occupy may be unpredictable. We use benthic imagery obtained from the broad-scale deployment of an Autonomous Underwater Vehicle (AUV) to quantify the depth distribution of barrens habitat formed by a recent range extension of the sea urchin species, Centrostephanus rodgersii, a known ecosystem engineer. AUV transects covering similar depths from both the historical range of New South Wales, Australia, and from the range extension area of the east coast of Tasmania were examined for the presence of barrens. We find that C. rodgersii occupies a different realised niche in its extended range, with barrens habitat occurring significantly deeper in Tasmanian waters (16-58 m) compared to NSW waters (7-27 m). The expansion of barrens habitat has devastating impacts on biodiversity, with flow-on effects to ecosystem services and local fisheries, and in Tasmania this threat extends to deeper, invertebrate-dominated habitats. This finding has important management implications, in particular the need to incorporate deeper reef systems into planning, with increased barrens expected under future climate change predictions. One conservation management approach is the use of no-take Marine Protected Areas (MPAs) to prevent barren establishment in representative habitats by rebuilding viable populations of urchin predators. We also examine the correlation between MPA status and the occurrence of barrens within a small, no-take Tasmanian reserve and adjacent control sites. We find that there is suggestive, but inconclusive, evidence for fewer barrens in the MPA (p = 0.07). Our study highlights the utility of a novel technology for conducting large-scale benthic surveys and monitoring the impacts of range extending species.
Lazar, Cassandre Sara; Baker, Brett J; Seitz, Kiley; Hyde, Andrew S; Dick, Gregory J; Hinrichs, Kai-Uwe; Teske, Andreas P
Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.
Cale, Jr, W. G.; Shugart, H. H.
Definitions of model realism and model validation are developed. Ecological and mathematical arguments are then presented to show that model equations which explicitly treat ecosystem processes can be systematically improved such that greater realism is attained and the condition of validity is approached. Several examples are presented.
Hosner, Peter A; Sánchez-González, Luis A; Peterson, A Townsend; Moyle, Robert G
Avian diversification in oceanic archipelagos is largely attributed to isolation across marine barriers. During glacial maxima, lowered sea levels resulted in repeated land connections between islands joined by shallow seas. Consequently, such islands are not expected to show endemism. However, if climate fluctuations simultaneously caused shifts in suitable environmental conditions, limiting populations to refugia, then occurrence on and dispersal across periodic land bridges are not tenable. To assess the degree to which paleoclimate barriers, rather than marine barriers, drove avian diversification in the Philippine Archipelago, we produced ecological niche models for current-day, glacial maxima, and interglacial climate scenarios to infer potential Pleistocene distributions and paleoclimate barriers. We then tested marine and paleoclimate barriers for correspondence to geographic patterns of population divergence, inferred from DNA sequences from eight codistributed bird species. In all species, deep-water channels corresponded to zones of genetic differentiation, but six species exhibited deeper divergence associated with a periodic land bridge in the southern Philippines. Ecological niche models for these species identified a common paleoclimate barrier that coincided with deep genetic structure among populations. Although dry land connections joined southern Philippine islands during low sea level stands, unfavorable environmental conditions limited populations within landmasses, resulting in long-term isolation and genetic differentiation. These results highlight the complex nature of diversification in archipelagos: marine barriers, changes in connectivity due to sea level change, and climate-induced refugia acted in concert to produce great species diversity and endemism in the Philippines.
Shaner, Pei-Jen L; Tsao, Tzu-Hsuan; Lin, Rong-Chien; Liang, Wei; Yeh, Chia-Fen; Yang, Xiao-Jun; Lei, Fu-Min; Zhou, Fang; Yang, Can-Chao; Hung, Le Manh; Hsu, Yu-Cheng; Li, Shou-Hsien
Niche evolution underpins the generation and maintenance of biological diversity, but niche conservatism, in which niches remain little changed over time in closely related taxa, and the role of ecology in niche evolution are continually debated. To test whether climate niches are conserved in two closely related passerines in East Asia - the vinous-throated (Paradoxornis webbianus) and ashy-throated (P. alphonsianus) parrotbills - we established their potential allopatric and sympatric regions using ecological niche models and compared differences in their climate niches using niche overlap indices in background tests and multivariate statistical analyses. We also used polymorphism data on 44 nuclear genes to infer their divergence demography. We found that these two parrotbills occupy different climate niches, in both their allopatric and potential sympatric regions. Because the potential sympatric region is the area predicted to be suitable for both parrotbills based on the ecological niche models, it can serve as a natural common garden. Therefore, their observed niche differences in this potential sympatry were not simply rendered by phenotypic plasticity and probably had a genetic basis. Our genetic analyses revealed that the two parrotbills are not evolutionarily independent for the most recent part of their divergence history. The two parrotbills diverged c. 856,000 years ago and have had substantial gene flow since a presumed secondary contact c. 290,000 years ago. This study provides an empirical case demonstrating that climate niches may not be homogenized in nascent species in spite of substantial, ongoing gene flow, which in turn suggests a role for ecology in promoting and maintaining diversification among incipient species.
Ellis, Crystal N; Traverse, Charles C; Mayo-Smith, Leslie; Buskirk, Sean W; Cooper, Vaughn S
Colonization of vacant environments may catalyze adaptive diversification and be followed by competition within the nascent community. How these interactions ultimately stabilize and affect productivity are central problems in evolutionary ecology. Diversity can emerge by character displacement, in which selection favors phenotypes that exploit an alternative resource and reduce competition, or by facilitation, in which organisms change the environment and enable different genotypes or species to become established. We previously developed a model of long-term experimental evolution in which bacteria attach to a plastic bead, form a biofilm, and disperse to a new bead. Here, we focus on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity. Adaptive mutants initially competed for space, but later competition declined, consistent with character displacement and the predicted effects of the evolved mutations. The community reached a stable equilibrium as each ecotype evolved to inhabit distinct, complementary regions of the biofilm. Interactions among ecotypes ultimately became facilitative and enhanced mixed productivity. Observing the succession of genotypes within niches illuminated changing selective forces within the community, including a fundamental role for genotypes producing small colony variants that underpin chronic infections caused by B. cenocepacia.
Bergman, Aviv; Gligorijevic, Bojana
Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.
Gutiérrez, Mariano; Ramirez, Argiro; Bertrand, Sophie; Móron, Octavio; Bertrand, Arnaud
The world’s largest mono-specific fishery, the Peruvian anchovy or anchoveta ( Engraulis ringens) fishery, has been the subject of many studies since the 1960s. Details of its relationship with other species have mainly focused on alternations with sardine, Sardinops sagax, and little effort has so far been paid to interactions with other species sharing the same ecosystem. This is the case for Pleuroncodes monodon, the crustacean squat lobster or ’munida’, which has become highly abundant along the Peruvian coast since the mid-1990s. Munida is now an important prey for seabirds, mammals and coastal predatory fish. Knowledge of patterns of distribution and ecological niche of munida is scarce however off Peru. Here we describe and compare spatial patterns of distribution of anchoveta and munida and their ecological niches based on data from 26 acoustic surveys performed along the Peruvian coast between 1998 and 2006. The results indicate that munida and anchoveta share ecological niches but that munida is restricted to the coldest part of the productive cold coastal waters whereas anchoveta do not present any temperature preference over a large range (14-23 °C). The recent increase in munida abundance off Peru is concomitant with colder conditions; with their onset munida extended its range from central Chile northwards. Off Peru the very shallow oxycline keeps munida from its usual bottom habitat and has forced it to adopt pelagic behaviour.
Soto, W.; Gutierrez, J.; Remmenga, M. D.; Nishiguchi, M. K.
Vibrio fischeri is a bioluminescent bacterial symbiont of sepiolid squids (Cephalopoda: Sepiolidae) and monocentrid fishes (Actinopterygii: Monocentridae). V. fischeri exhibit competitive dominance within the allopatrically distributed squid genus Euprymna, which have led to the evolution of V. fischeri host specialists. In contrast, the host genus Sepiola contains sympatric species that is thought to have given rise to V. fischeri that have evolved as host generalists. Given that these ecological lifestyles may have a direct effect upon the growth spectrum and survival limits in contrasting environments, optimal growth ranges were obtained for numerous V. fischeri isolates from both free-living and host environments. Upper and lower limits of growth were observed in sodium chloride concentrations ranging from 0.0% to 9.0%. Sepiola symbiotic isolates possessed the least variation in growth throughout the entire salinity gradient, whereas isolates from Euprymna were the least uniform at <2.0% NaCl. V. fischeri fish symbionts (CG101 and MJ101) and all free-living strains were the most dissimilar at >5.0% NaCl. Growth kinetics of symbiotic V. fischeri strains were also measured under a range of salinity and temperature combinations. Symbiotic V. fischeri ES114 and ET101 exhibited a synergistic effect for salinity and temperature, where significant differences in growth rates due to salinity existed only at low temperatures. Thus, abiotic factors such as temperature and salinity have differential effects between free-living and symbiotic strains of V. fischeri, which may alter colonization efficiency prior to infection. PMID:18587609
Zhu, Geng-Ping; Ye, Zhen; Du, Juan; Zhang, Dan-Li; Zhen, Ya-hui; Zheng, Chen-guang; Zhao, Li; Li, Min; Bu, Wen-Jun
Invasive species’ Pleistocene history contains much information on its present population structure, dispersability and adaptability. In this study, the Pleistocene history of a global invasive pest (Brown Marmorated Stink Bug BMSB, Halyomorpha halys) was unveiled using the coupled approach of phylogeography and ecological niche modelling. Rangewide molecular data suggests that the Taiwan and other native populations had diverged in mid-Pleistocene. In mainland China, the native BMSB did not experience population contraction and divergence during last glacial, but persisted in interconnected populations. Combined Bayesian Skyline Plot (BSP) and niche modelling revealed a rapid expansion occurred during the transition of Last Inter Glacial (LIG) to Last Glacial Maximum (LGM). High genetic diversity and multi-reticular haplotypes network exist in the original sources populations of BMSB invasion in northern China. They were speculated to be colonized from the central China, with many derived haplotypes evolved to adapt the novel environment. The ENM future prediction suggest that BMSB may expand northward to higher latitudes in the US and Europe, because of its high invasive ability, together with the available suitable climate space there. PMID:26996353
Heneghan, Mary N.; Burns, Claire; Costa, Ana M. S. B.; Burton, Kerry S.; Challen, Michael P.
Summary Agaricus bisporus is a secondary decomposer fungus and an excellent model for the adaptation, persistence and growth of fungi in humic‐rich environments such as soils of temperate woodland and pastures. The A. bisporus serine proteinase SPR1 is induced by humic acids and is highly expressed during growth on compost. Three Spr1 gene silencing cassettes were constructed around sense, antisense and non‐translatable‐stop strategies (pGRsensehph, pGRantihph and pGRstophph). Transformation of A. bisporus with these cassettes generated cultures showing a reduction in extracellular proteinase activity as demonstrated by the reduction, or abolition, of a clearing zone on plate‐based bioassays. These lines were then assessed by detailed enzyme assay, RT‐qPCR and fruiting. Serine proteinase activity in liquid cultures was reduced in 83% of transformants. RT‐qPCR showed reduced Spr1 mRNA levels in all transformants analysed, and these correlated with reduced enzyme activity. When fruiting was induced, highly‐silenced transformant AS5 failed to colonize the compost, whilst for those that did colonize the compost, 60% gave a reduction in mushroom yield. Transcriptional, biochemical and developmental observations, demonstrate that SPR1 has an important role in nutrient acquisition in compost and that SPR1 is a key enzyme in the adaptation of Agaricus to the humic‐rich ecological niche formed during biomass degradation. PMID:27113919
Glazer, B. T.; Chan, C. S. Y.; Mcallister, S.; Leavitt, A.; Emerson, D.
Microbial mats are formed by microorganisms working in coordinated symbiosis, often benefitting the community by controlling the local geochemical or physical environment. Thus, the ecology of the mat depends on the individual roles of microbes organized into niches within a larger architecture. Chemolithotrophic Fe-oxidizing bacteria (FeOB) form distinctive Fe oxyhydroxide biominerals which constitute the building blocks of the mat. However, the majority of our progress has been in understanding the overall community structure. Understanding the physical mat structure on the microbial scale is important to unraveling FeOB evolution, the biogeochemistry and ecology of Fe-rich habitats, and ultimately interpreting FeOB biosignatures in the rock record. Mats in freshwater and marine environments contain strikingly similar biomineral morphologies, yet they are formed by phylogenetically distinct microorganisms. This suggests that the overall architecture and underlying genetics of freshwater and marine mats has evolved to serve particular roles specific to Fe oxidation. Thus, we conducted a comparative study of Fe seep freshwater mats and marine hydrothermal mats. We have developed a new approach to sampling Fe mats in order to preserve the delicate structure for analysis by confocal and scanning electron microscopy. Our analyses of these intact mats show that freshwater and marine mats are similarly initiated by a single type of structure-former. These ecosystem engineers form either a hollow sheath or a twisted stalk biomineral during mat formation, with a highly directional structure. These microbes appear to be the vanguard organisms that anchor the community within oxygen/Fe(II) gradients, further allowing for community succession in the mat interior as evidenced by other mineralized morphologies. Patterns in biomineral thickness and directionality were indicative of redox gradients and temporal changes in the geochemical environment. These observations show that
Hom, Erik F Y; Murray, Andrew W
Mutualistic symbioses shape the evolution of species and ecosystems and catalyze the emergence of biological complexity, yet how such symbioses first form is unclear. We show that an obligate mutualism between the yeast Saccharomyces cerevisiae and the alga Chlamydomonas reinhardtii--two model eukaryotes with very different life histories--can arise spontaneously in an environment requiring reciprocal carbon and nitrogen exchange. This capacity for mutualism is phylogenetically broad, extending to other Chlamydomonas and fungal species. Furthermore, we witnessed the spontaneous association of Chlamydomonas algal cells physically interacting with filamentous fungi. These observations demonstrate that under specific conditions, environmental change induces free-living species to become obligate mutualists and establishes a set of experimentally tractable, phylogenetically related, synthetic systems for studying the evolution of symbiosis.
Iriki, Atsushi; Taoka, Miki
Hominin evolution has involved a continuous process of addition of new kinds of cognitive capacity, including those relating to manufacture and use of tools and to the establishment of linguistic faculties. The dramatic expansion of the brain that accompanied additions of new functional areas would have supported such continuous evolution. Extended brain functions would have driven rapid and drastic changes in the hominin ecological niche, which in turn demanded further brain resources to adapt to it. In this way, humans have constructed a novel niche in each of the ecological, cognitive and neural domains, whose interactions accelerated their individual evolution through a process of triadic niche construction. Human higher cognitive activity can therefore be viewed holistically as one component in a terrestrial ecosystem. The brain's functional characteristics seem to play a key role in this triadic interaction. We advance a speculative argument about the origins of its neurobiological mechanisms, as an extension (with wider scope) of the evolutionary principles of adaptive function in the animal nervous system. The brain mechanisms that subserve tool use may bridge the gap between gesture and language--the site of such integration seems to be the parietal and extending opercular cortices.
Jager, Yetta; King, Anthony Wayne
Applied ecological models that are used to understand and manage natural systems often rely on spatial data as input. Spatial uncertainty in these data can propagate into model predictions. Uncertainty analysis, sensitivity analysis, error analysis, error budget analysis, spatial decision analysis, and hypothesis testing using neutral models are all techniques designed to explore the relationship between variation in model inputs and variation in model predictions. Although similar methods can be used to answer them, these approaches address different questions. These approaches differ in (a) whether the focus is forward or backward (forward to evaluate the magnitude of variation in model predictions propagated or backward to rank input parameters by their influence); (b) whether the question involves model robustness to large variations in spatial pattern or to small deviations from a reference map; and (c) whether processes that generate input uncertainty (for example, cartographic error) are of interest. In this commentary, we propose a taxonomy of approaches, all of which clarify the relationship between spatial uncertainty and the predictions of ecological models. We describe existing techniques and indicate a few areas where research is needed.
Larsen, Peter E.; Collart, Frank R.; Dai, Yang; ...
The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter ofmore » plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.« less
Cao, Shu-yan; Xie, Gao-di
Ecological footprint (EF) is an important index of ecological carrying capacity. The original EF model is excellent in simplicity, aggregation, comparability, and lifelikeness in presenting results, but short in predictability, configuration, and applicability. To overcome these shortcomings, many researches were conducted to modify and promote the EF model, and developed it from static with single time scale to diversified ones, which included: 1) time series EF model, 2) input-output analysis based EF model, 3) integrated assessment incorporated EF model, 4) land disturbance degree based EF model, and 5) life cycle analysis based EF model, or component EF model. The function of EF as a measurement of ecological carrying capacity was significantly improved, but its accuracy and integrality still need to be advanced.
St Leger, R J; Joshi, L; Roberts, D W
-Phe-Val-Arg-NA. V. albo-atrum and V. dahliae also produced low levels of neutral (pI ca 7) and basic (pI ca 9.5) subtilisin-like proteases active against a chymotrypsin substrate (Succinyl-Ala2-Pro-Phe-NA) and insect cuticle. In contrast, subtilisins comprised the major protease component secreted by V. lecanii and V. fungicola. Both V. lecanii and V. albo-atrum produced the highest levels of subtilisin and trypsin-like activities during growth on collagen or insect cuticle. Results are discussed in terms of the adaptation of fungi to the requirements of their ecological niches.
Rivera, Paula C; Di Cola, Valeria; Martínez, Juan J; Gardenal, Cristina N; Chiaraviglio, Margarita
Until recently, the genus Epicrates (Boidae) presented only one continental species, Epicrates cenchria, distributed in Central and South America, but after a taxonomic revision using morphologic characters five species were recognized: E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi. We analyzed two independent data sets, environmental niche models and phylogeny based on molecular information, to explore species delimitation in the continental species of this genus. Our results indicated that the environmental requirements of the species are different; therefore there are not evidences of ecological interchangeability among them. There is a clear correlation between species distributions and the major biogeographic regions of Central and South America. Their overall distribution reveals that allopatry or parapatry is the general pattern. These evidences suggest that habitat isolation prevents or limits gene exchange among them. The phylogenetic reconstruction showed that the continental Epicrates are monophyletic, being E. alvarezi the sister species for the remaining two clades: E. crassus-E. assisi, and E. maurus-E. cenchria. The clade grouping the continental Epicrates is the sister taxon of the genus Eunectes and not of the Caribbean Epicrates clade, indicating that the genus is paraphyletic. There is a non-consistent pattern in niche evolution among continental Epicrates. On the contrary, a high variation and abrupt shifts in environmental variables are shown when ancestral character states were reconstructed on the sequence-based tree. The degree of genetic and ecological divergence among continental Epicrates and the phylogenetic analyses support the elevation to full species of E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi.
Munoz, Ana Isabel; Tello, J Ignacio
We propose a mathematical model to describe tumor cells movement towards a metastasis location into the bone marrow considering the influence of chemotaxis inhibition due to the action of a drug. The model considers the evolution of the signaling molecules CXCL-12 secreted by osteoblasts (bone cells responsible of the mineralization of the bone) and PTHrP (secreted by tumor cells) which activates osteoblast growth. The model consists of a coupled system of second order PDEs describing the evolution of CXCL-12 and PTHrP, an ODE of logistic type to model the Osteoblasts density and an extra equation for each cancer cell. We also simulate the system to illustrate the qualitative behavior of the solutions. The numerical method of resolution is also presented in detail.
Soininen, Janne; Alard, Didier; Rosebery, Juliette
Species cooccurrence patterns give significant insights into the processes shaping communities. While biotic interactions have been widely studied using cooccurrence analyses in animals and larger plants, studies about cooccurrences among micro-organisms are still relatively rare. We examined stream diatom cooccurrences in France through a national database of samples. In order to test the relative influence of environmental, biotic and spatial constraints on species’ incidence distribution, cooccurrence and nestedness patterns of real communities were compared with the patterns generated from a set of standard and environmentally constrained null models. Real communities showed a higher level of segregation than the most conservative standard null models, but a general aggregation of cooccurrences when compared to environmentally constrained null models. We did not find any evidence of limiting similarity between cooccurring species. Aggregations of species cooccurrences were associated with the high levels of nestedness. Altogether, these results suggested that biotic interactions were not structuring cooccurrences of diatom species at our study scale. Instead, the patterns were more likely to be related with colonization patterns, mass effect, and local temporal dynamics of diatom biofilms. We further highlight that the association of standard and environmentally constrained null models may give realistic insight into the cooccurrence patterns of microbial communities. PMID:27128737
Jeanblanc, Christine; Goodrich, Angelina Daisy; Colletti, Evan; Mokhtari, Saloomeh; Porada, Christopher D; Zanjani, Esmail D; Almeida-Porada, Graça
The fetal sheep model has served as a biologically relevant and translational model to study in utero haematopoietic stem cell transplantation (IUHSCT), yet little is known about the ontogeny of the bone marrow (BM) niches in this model. Because the BMmicroenvironment plays a critical role in the outcome of haematopoietic engraftment, we have established the correlation between the fetal-sheep and fetal-human BM niche ontogeny, so that studies addressing the role of niche development at the time of IUHSCT could be accurately performed. Immunofluorescence confocal microscopic analysis of sheep fetal bone from gestational days (gd) 25-68 showed that the BM microenvironment commences development with formation of the vascular niche between 25 and 36 gd in sheep; correlating with the events at 10-11 gestational weeks (gw) in humans. Subsequently, between 45 and 51 gd in sheep (c. 14 gw in humans), the osteoblastic/endosteal niche started developing, the presence of CD34(+) CD45(+) cells were promptly detected, and their number increased with gestational age. IUHSCT, performed in sheep at 45 and 65 gd, showed significant haematopoietic engraftment only at the later time point, indicating that a fully functional BM microenvironment improved engraftment. These studies show that sheep niche ontogeny closely parallels human, validating this model for investigating niche influence/manipulation in IUHSCT engraftment.
Poncet, Valérie; Munoz, François; Munzinger, Jérôme; Pillon, Yohan; Gomez, Céline; Couderc, Marie; Tranchant-Dubreuil, Christine; Hamon, Serge; de Kochko, Alexandre
Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range-wide genetic diversity based on nuclear microsatellite data and detected four well-differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum (LGM, c. 21,000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra- and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon.
The liver is recognized as the target organ of metastases of almost all prominent malignancies. Its unique biology renders this organ particularly susceptible to circulating disseminated tumour cells (DTCs), and it can be assumed that very early metastasis occurs in the liver. The premetastatic niche concept may explain very early metastasis, as it defines priming of a future target organ of metastasis by factors that may already be secreted from premalignant lesions. This review shows that comprehensive knowledge on mechanisms of premetastatic niche formation in the liver is based on pre-clinical models only and still rather rare, mostly due to the scarcity of mouse liver metastasis models displaying a tumour cell-free period in the liver or lack of liver-tropic syngeneic tumour cells to probe for the niche. Attentive re-assessment of previous studies and reviews was undertaken revealing only two clearly identified tumour-derived secreted factors (TDSFs), both inducing infiltration of the liver by bone marrow-derived cells and increased liver metastasis, namely tissue inhibitor of metalloproteinases-1 (TIMP-1) and macrophage-inducing factor (MIF). Future directions of this research area will comprise elucidation of the impact of TDSFs on regulation and activity of myeloid-derived suppressor cells and/or the specific architecture and homeostasis of the liver, as well as development of prognostic TDSF detection in patients at risk of liver metastasis.
Acevedo, Pelayo; Alzaga, Vanesa; Cassinello, Jorge; Gortázar, Christian
In the present work, we derive a habitat suitability model of the broom hare and the Pyrenean grey partridge in the Cantabrian Mountains by using the Ecological Niche Factor Analysis. Both species are endemic to the northern of Iberian mountains, and because of the vulnerability of the hare to endangerment or extinction and because of the great interest in the partridge, this habitat requires specific conservation measures. Literature on these animals' biology and ecology is practically nonexistent. Habitat suitability analyses show that the hare and partridge occupy very similar ecological niches, characterized by a high percentage of broom and heather scrublands, high altitude and slope, and limited human accessibility. We have identified differences in habitat selection between the Pyrenean grey partridge and other subspecies of partridge present in central-northern Europe. Our results indicate a probable metapopulation structure for both the hare and partridge; however, according to our predictive maps, there is a high connectivity between suitable habitats. Current decline of traditional rural activities, such as mountain livestock, are affecting the mosaic landscape. This, in turn, enhances biodiversity in the area and, particularly, the viability of these valuable animal populations.
Preston, Daniel L; Jacobs, Abigail Z; Orlofske, Sarah A; Johnson, Pieter T J
Most food webs use taxonomic or trophic species as building blocks, thereby collapsing variability in feeding linkages that occurs during the growth and development of individuals. This issue is particularly relevant to integrating parasites into food webs because parasites often undergo extreme ontogenetic niche shifts. Here, we used three versions of a freshwater pond food web with varying levels of node resolution (from taxonomic species to life stages) to examine how complex life cycles and parasites alter web properties, the perceived trophic position of organisms, and the fit of a probabilistic niche model. Consistent with prior studies, parasites increased most measures of web complexity in the taxonomic species web; however, when nodes were disaggregated into life stages, the effects of parasites on several network properties (e.g., connectance and nestedness) were reversed, due in part to the lower trophic generality of parasite life stages relative to free-living life stages. Disaggregation also reduced the trophic level of organisms with either complex or direct life cycles and was particularly useful when including predation on parasites, which can inflate trophic positions when life stages are collapsed. Contrary to predictions, disaggregation decreased network intervality and did not enhance the fit of a probabilistic niche model to the food webs with parasites. Although the most useful level of biological organization in food webs will vary with the questions of interest, our results suggest that disaggregating species-level nodes may refine our perception of how parasites and other complex life cycle organisms influence ecological networks.
Latombe, Guillaume; McGeoch, Melodie A.
Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral–niche community dynamics. The neutral–niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology. PMID:26702047
Hu, Junhua; Broennimann, Olivier; Guisan, Antoine; Wang, Bin; Huang, Yan; Jiang, Jianping
The role of ecological niche in lineage diversification has been the subject of long-standing interest of ecologists and evolutionary biologists. Gynandropaa frogs diversified into three independent clades endemic to the southeastern Qinghai-Tibetan Plateau. Here, we address the question whether these clades kept the same niche after separation, and what it tells us about possible diversification processes. We applied predictions in geographical (G)-space and tests of niche conservatism in environmental (E)-space. Niche models in G-space indicate separate regions with high suitability for the different clades, with some potential areas of sympatry. While the pair of central and eastern clades displayed the largest niche overlap for most variables, and strict niche equivalency was rejected for all clade-pairs, we found no strong evidence for niche divergence, but rather the signature of niche conservatism compared to null models in E-space. These results suggest a common ancestral ecological niche, and as such give good support to divergence through allopatric speciation, but alternative explanations are also possible. Our findings illustrate how testing for niche conservatism in lineage diversification can provide insights into underlying speciation processes, and how this information may guide further research and conservation practices, as illustrated here for amphibians on the Qinghai-Tibetan Plateau.
Hu, Junhua; Broennimann, Olivier; Guisan, Antoine; Wang, Bin; Huang, Yan; Jiang, Jianping
The role of ecological niche in lineage diversification has been the subject of long-standing interest of ecologists and evolutionary biologists. Gynandropaa frogs diversified into three independent clades endemic to the southeastern Qinghai-Tibetan Plateau. Here, we address the question whether these clades kept the same niche after separation, and what it tells us about possible diversification processes. We applied predictions in geographical (G)-space and tests of niche conservatism in environmental (E)-space. Niche models in G-space indicate separate regions with high suitability for the different clades, with some potential areas of sympatry. While the pair of central and eastern clades displayed the largest niche overlap for most variables, and strict niche equivalency was rejected for all clade-pairs, we found no strong evidence for niche divergence, but rather the signature of niche conservatism compared to null models in E-space. These results suggest a common ancestral ecological niche, and as such give good support to divergence through allopatric speciation, but alternative explanations are also possible. Our findings illustrate how testing for niche conservatism in lineage diversification can provide insights into underlying speciation processes, and how this information may guide further research and conservation practices, as illustrated here for amphibians on the Qinghai-Tibetan Plateau. PMID:27601098
Wogan, Guinevere O. U.
A primary assumption of environmental niche models (ENMs) is that models are both accurate and transferable across geography or time; however, recent work has shown that models may be accurate but not highly transferable. While some of this is due to modeling technique, individual species ecologies may also underlie this phenomenon. Life history traits certainly influence the accuracy of predictive ENMs, but their impact on model transferability is less understood. This study investigated how life history traits influence the predictive accuracy and transferability of ENMs using historically calibrated models for birds. In this study I used historical occurrence and climate data (1950-1990s) to build models for a sample of birds, and then projected them forward to the ‘future’ (1960-1990s). The models were then validated against models generated from occurrence data at that ‘future’ time. Internal and external validation metrics, as well as metrics assessing transferability, and Generalized Linear Models were used to identify life history traits that were significant predictors of accuracy and transferability. This study found that the predictive ability of ENMs differs with regard to life history characteristics such as range, migration, and habitat, and that the rarity versus commonness of a species affects the predicted stability and overlap and hence the transferability of projected models. Projected ENMs with both high accuracy and transferability scores, still sometimes suffered from over- or under- predicted species ranges. Life history traits certainly influenced the accuracy of predictive ENMs for birds, but while aspects of geographic range impact model transferability, the mechanisms underlying this are less understood. PMID:26959979
Maynard, Daniel S.; Leonard, Kenneth E.; Drake, John M.; Hall, David W.; Crowther, Thomas W.; Bradford, Mark A.
Linking competitive outcomes to environmental conditions is necessary for understanding species' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified, and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts. PMID:26136444
Agostini, Ilaria; Holzmann, Ingrid; Di Bitetti, Mario S
According to the principle of competitive exclusion, niche differentiation allows the stable coexistence of closely related species. We analyzed dietary profile and diversity, and dietary overlap between syntopic brown howlers (BR; Alouatta guariba clamitans) and black and gold howlers (BLG; A. caraya) in the Atlantic Forest of NE Argentina, with the objective of evaluating the degree of trophic niche overlap and potential interspecific competition for food. During 12 months, we collected data on feeding behavior of two groups of each howler species using the scan sampling method, together with data on food availability. Both at the group- and species-level, we analyzed feeding behavior in terms of monthly percentages of time spent feeding on each food type and specific food item, dietary diversity (Shannon index H'), and we estimated dietary overlap using the percentage index and the Morisita-Horn index (C(H)). Across months, both howlers showed species-specific preferences for certain food items, and BLG had a more diverse diet (mean+/-SE, H'=2.77+/-0.08) than BR (H'=2.39+/-0.09). However, diets of both species overlapped extensively (percentage index=45.64+/-2.97%; C(H)=0.6+/-0.05) and diets of conspecific groups did not overlap more than diets of groups of different species. Given their high degree of trophic overlap, syntopic BR and BLG meet one of the conditions necessary for interspecific food competition to occur. Although at present we lack direct evidence for interspecific competition in these howler species, we conclude that high levels of niche overlap may have an important role in maintaining the essentially parapatric distribution of howler species throughout the Neotropics.
Smirnov, D G; Vekhnik, V P
A complex analysis of the food range of 15 bat species inhabiting floodplain ecosystems of the Samara Bend has been performed. It is shown that, in bats, an important component of the structuring of their communities is the division of food resources. The guild structure and position of species in the trophic space are described. Seven food guilds consisting of nonspecialized and specialized species are distinguished. It is noted that most species are characterized by a wide overlapping of their trophic niches, which may be a consequence of their weak competition in an environment that is rich in food resources.
Miller, Scott R; Wood, A Michelle; Blankenship, Robert E; Kim, Maria; Ferriera, Steven
Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA.
Materna, Arne C; Friedman, Jonathan; Bauer, Claudia; David, Christina; Chen, Sara; Huang, Ivy B; Gillens, April; Clarke, Sean A; Polz, Martin F; Alm, Eric J
Hutchinson's fundamental niche, defined by the physical and biological environments in which an organism can thrive in the absence of inter-species interactions, is an important theoretical concept in ecology. However, little is known about the overlap between the fundamental niche and the set of conditions species inhabit in nature, and about natural variation in fundamental niche shape and its change as species adapt to their environment. Here, we develop a custom-made dual gradient apparatus to map a cross-section of the fundamental niche for several marine bacterial species within the genus Vibrio based on their temperature and salinity tolerance, and compare tolerance limits to the environment where these species commonly occur. We interpret these niche shapes in light of a conceptual model comprising five basic niche shapes. We find that the fundamental niche encompasses a much wider set of conditions than those strains typically inhabit, especially for salinity. Moreover, though the conditions that strains typically inhabit agree well with the strains' temperature tolerance, they are negatively correlated with the strains' salinity tolerance. Such relationships can arise when the physiological response to different stressors is coupled, and we present evidence for such a coupling between temperature and salinity tolerance. Finally, comparison with well-documented ecological range in V. vulnificus suggests that biotic interactions limit the occurrence of this species at low-temperature-high-salinity conditions. Our findings highlight the complex interplay between the ecological, physiological and evolutionary determinants of niche morphology, and caution against making inferences based on a single ecological factor.
11 Hierarchy Theory The predictability of ecological systems is inherently limited and is dependent on the scales (May 1986; Levin 1989; Vasconcelos ...and associates (1987) advocate a hierarchical paradigm to better understand the patterns in landscape ecology. Vasconcelos , Zeigler, and associates...modeling system is hierarchical and includes individuals, patch, and the whole landscape (Perestrello de Vasconcelos , Zeigler, et al. 1993). These are but
The image of a ball rolling along a series of hills and valleys is an effective heuristic by which to communicate stability concepts in ecology. However, the dynamics of this landscape model have little to do with ecological systems. Other landscape representations, however, are ...
García-Caballero, Melissa; van de Velde, Maureen; Blacher, Silvia; Lambert, Vincent; Balsat, Cédric; Erpicum, Charlotte; Durré, Tania; Kridelka, Frédéric; Noel, Agnès
Lymphangiogenesis, the formation of new lymphatic vessels, occurs in primary tumors and in draining lymph nodes leading to pre-metastatic niche formation. Reliable in vivo models are becoming instrumental for investigating alterations occurring in lymph nodes before tumor cell arrival. In this study, we demonstrate that B16F10 melanoma cell encapsulation in a biomaterial, and implantation in the mouse ear, prevents their rapid lymphatic spread observed when cells are directly injected in the ear. Vascular remodeling in lymph nodes was detected two weeks after sponge implantation, while their colonization by tumor cells occurred two weeks later. In this model, a huge lymphangiogenic response was induced in primary tumors and in pre-metastatic and metastatic lymph nodes. In control lymph nodes, lymphatic vessels were confined to the cortex. In contrast, an enlargement and expansion of lymphatic vessels towards paracortical and medullar areas occurred in pre-metastatic lymph nodes. We designed an original computerized-assisted quantification method to examine the lymphatic vessel structure and the spatial distribution. This new reliable and accurate model is suitable for in vivo studies of lymphangiogenesis, holds promise for unraveling the mechanisms underlying lymphatic metastases and pre-metastatic niche formation in lymph nodes, and will provide new tools for drug testing.
García-Caballero, Melissa; Van de Velde, Maureen; Blacher, Silvia; Lambert, Vincent; Balsat, Cédric; Erpicum, Charlotte; Durré, Tania; Kridelka, Frédéric; Noel, Agnès
Lymphangiogenesis, the formation of new lymphatic vessels, occurs in primary tumors and in draining lymph nodes leading to pre-metastatic niche formation. Reliable in vivo models are becoming instrumental for investigating alterations occurring in lymph nodes before tumor cell arrival. In this study, we demonstrate that B16F10 melanoma cell encapsulation in a biomaterial, and implantation in the mouse ear, prevents their rapid lymphatic spread observed when cells are directly injected in the ear. Vascular remodeling in lymph nodes was detected two weeks after sponge implantation, while their colonization by tumor cells occurred two weeks later. In this model, a huge lymphangiogenic response was induced in primary tumors and in pre-metastatic and metastatic lymph nodes. In control lymph nodes, lymphatic vessels were confined to the cortex. In contrast, an enlargement and expansion of lymphatic vessels towards paracortical and medullar areas occurred in pre-metastatic lymph nodes. We designed an original computerized-assisted quantification method to examine the lymphatic vessel structure and the spatial distribution. This new reliable and accurate model is suitable for in vivo studies of lymphangiogenesis, holds promise for unraveling the mechanisms underlying lymphatic metastases and pre-metastatic niche formation in lymph nodes, and will provide new tools for drug testing. PMID:28128294
Morin, Xavier; Lechowicz, Martin J
Pioneering efforts to predict shifts in species distribution under climate change used simple models based on the correlation between contemporary environmental factors and distributions. These models make predictions at coarse spatial scales and assume the constancy of present correlations between environment and distribution. Adaptive management of climate change impacts requires models that can make more robust predictions at finer spatio-temporal scales by accounting for processes that actually affect species distribution on heterogeneous landscapes. Mechanistic models of the distribution of both species and vegetation types have begun to emerge to meet these needs. We review these developments and highlight how recent advances in our understanding of relationships among the niche concept, species diversity and community assembly point the way towards more effective models for the impacts of global change on species distribution and community diversity.
Ortiz-Medrano, Alejandra; Scantlebury, Daniel Patrick; Vázquez-Lobo, Alejandra; Mastretta-Yanes, Alicia; Piñero, Daniel
The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.
Parker, Jackson; Patterson, Jerry L.
The authors suggest that the aura of authority traditionally placed on educational research and evaluation has been based on an outdated understanding of the scientific enterprise. They outline an alternative view of science which is more ecological and provides more scope and power for evaluating educational programs. They propose a new framework…
Strona, Giovanni; Lafferty, Kevin D.
Parasite Niche Modeler (PaNic) is a free online software tool that suggests potential hosts for fish parasites. For a particular parasite species from the major helminth groups (Acanthocephala, Cestoda, Monogenea, Nematoda, Trematoda), PaNic takes data from known hosts (maximum body length, growth rate, life span, age at first maturity, trophic level, phylogeny, and biogeography) and hypothesizes similar fish species that might serve as hosts to that parasite. Users can give varying weights to host attributes and create custom models. In addition to suggesting plausible hosts (with varying degrees of confidence), the models indicate known host species that appear to be outliers in comparison to other known hosts. These unique features make PaNic an innovative tool for addressing both theoretical and applied questions in fish parasitology. PaNic can be accessed at
Lewis, Emily Elizabeth Louise; Wheadon, Helen; Lewis, Natasha; Yang, Jingli; Mullin, Margaret; Hursthouse, Andrew; Stirling, David; Dalby, Matthew John; Berry, Catherine Cecilia
The bone marrow niche represents a specialized environment that regulates mesenchymal stem cell quiescence and self-renewal, yet fosters stem cell migration and differentiation upon demand. An in vitro model that embodies these features would open up the ability to perform detailed study of stem cell behavior. In this paper we present a simple bone marrow-like niche model, which comprises of nanomagnetically levitated stem cells cultured as multicellular spheroids within a type I collagen gel. The stem cells maintained are nestin positive and remain quiescent until regenerative demand is placed upon them. In response to coculture wounding, they migrate and appropriately differentiate upon engraftment. This tissue engineered regeneration-responsive bone marrow-like niche model will allow for greater understanding of stem cell response to injury and also facilitate as a testing platform for drug candidates in a multiwell plate format.
Duran, Andressa; Pie, Marcio R
Climatic niches have increasingly become a nexus in our understanding of a variety of ecological and evolutionary phenomena, from species distributions to latitudinal diversity gradients. Despite the increasing availability of comprehensive datasets on species ranges, phylogenetic histories, and georeferenced environmental conditions, studies on the evolution of climate niches have only begun to understand how niches evolve over evolutionary timescales. Here, using primates as a model system, we integrate recently developed phylogenetic comparative methods, species distribution patterns, and climatic data to explore primate climatic niche evolution, both among clades and over time. In general, we found that simple, constant-rate models provide a poor representation of how climatic niches evolve. For instance, there have been shifts in the rate of climatic niche evolution in several independent clades, particularly in response to the increasingly cooler climates of the past 10 My. Interestingly, rate accelerations greatly outnumbered rate decelerations. These results highlight the importance of considering more realistic evolutionary models that allow for the detection of heterogeneity in the tempo and mode of climatic niche evolution, as well as to infer possible constraining factors for species distributions in geographical space.
Goddard, Matthew R.; Greig, Duncan
Different species are usually thought to have specific adaptations, which allow them to occupy different ecological niches. But recent neutral ecology theory suggests that species diversity can simply be the result of random sampling, due to finite population sizes and limited dispersal. Neutral models predict that species are not necessarily adapted to specific niches, but are functionally equivalent across a range of habitats. Here, we evaluate the ecology of Saccharomyces cerevisiae, one of the most important microbial species in human history. The artificial collection, concentration and fermentation of large volumes of fruit for alcohol production produce an environment in which S. cerevisiae thrives, and therefore it is assumed that fruit is the ecological niche that S. cerevisiae inhabits and has adapted to. We find very little direct evidence that S. cerevisiae is adapted to fruit, or indeed to any other specific niche. We propose instead a neutral nomad model for S. cerevisiae, which we believe should be used as the starting hypothesis in attempting to unravel the ecology of this important microbe. PMID:25725024
Prajsnar, Tomasz K; Hamilton, Ruth; Garcia-Lara, Jorge; McVicker, Gareth; Williams, Alexander; Boots, Michael; Foster, Simon J; Renshaw, Stephen A
The innate immune system is the primary defence against the versatile pathogen, Staphylococcus aureus. How this organism is able to avoid immune killing and cause infections is poorly understood. Using an established larval zebrafish infection model, we have shown that overwhelming infection is due to subversion of phagocytes by staphylococci, allowing bacteria to evade killing and found foci of disease. Larval zebrafish coinfected with two S. aureus strains carrying different fluorescent reporter gene fusions (but otherwise isogenic) had bacterial lesions, at the time of host death, containing predominantly one strain. Quantitative data using two marked strains revealed that the strain ratios, during overwhelming infection, were often skewed towards the extremes, with one strain predominating. Infection with passaged bacterial clones revealed the phenomenon not to bedue to adventitious mutations acquired by the pathogen. After infection of the host, all bacteria are internalized by phagocytes and the skewing of population ratios is absolutely dependent on the presence of phagocytes. Mathematical modelling of pathogen population dynamics revealed the data patterns are consistent with the hypothesis that a small number of infected phagocytes serve as an intracellular reservoir for S. aureus, which upon release leads to disseminated infection. Strategies to specifically alter neutrophil/macrophage numbers were used to map the potential subpopulation of phagocytes acting as a pathogen reservoir, revealing neutrophils as the likely 'niche'. Subsequently in a murine sepsis model, S. aureus abscesses in kidneys were also found to be predominantly clonal, therefore likely founded by an individual cell, suggesting a potential mechanism analogous to the zebrafish model with few protected niches. These findings add credence to the argument that S. aureus control regimes should recognize both the intracellular as well as extracellular facets of the S. aureus life
Proctor, Michael C. F.
Background and Aims Hymenophyllaceae (filmy ferns) are typically plants of shady, constantly moist habitats. They attain greatest species diversity and biomass in humid tropical montane forests and temperate hyperoceanic climates. This paper presents ecophysiological data bearing on their worldwide ecological niche space and its limits. Methods Chlorophyll fluorescence was used to monitor recovery in desiccation experiments, and for measurements of 95 % saturating irradiance [photosynthetic photon flux density (PPFD95 %)] of photosynthetic electron flow and other parameters, in the New Zealand Hymenophyllum sanguinolentum, and three species each of Hymenophyllum and Trichomanes from forests in Trinidad and Venezuela. Key Results Hymenophyllum sanguinolentum was comparable in desiccation tolerance and light responses with the European species. The more common species in the two tropical forests showed PPFD95 % >100 µmol m−2 s−1, and withstood moderate desiccation (–40 MPa) for several days. The four most shade-adapted species had PPFD95 % ≤51 µmol m−2 s−1, and were sensitive to even mild and brief desiccation (–22 MPa for 3 d). Conclusions Light and desiccation responses of filmy ferns can be seen as an integrated package. At low light and windspeed in humid forests, net radiation and saturation deficit are low, and diffusion resistance high. Water loss is slow and can be supported by modest conduction from the sub-stratum. With higher irradiance, selection pressure for desiccation tolerance increases progressively. With low light and high humidity, the filmy fern pattern of adaptation is probably optimal, and the vascular plant leaf with mesophyll and stomata offers no advantage in light capture, water economy or CO2 uptake. Trade-offs between light adaptation and desiccation tolerance, and between stem conduction and water absorption through the leaf surface, underlie adaptive radiation and niche differentiation of species within the family
Benavides, Ana B; Ulcuango, Mario; Yépez, Lucía; Tenea, Gabriela N
Lactic acid bacteria are known for their biotechnological potential. In various regions of Ecuador numerous indigenous biological resources are largely undocumented. In this study, we evaluated the potential probiotic characteristics and antagonistic in vitro properties of some lactic acid bacteria from native niches of the subtropical rain forests of Ecuador. These isolates were identified according to their morphological properties, standard API50CH fermentation profile and RAPD-DNA polymorphism pattern. The selected isolates were further evaluated for their probiotic potential. The isolates grew at 15°C and 45°C, survived at a pH ranging from 2.5 to 4.5 in the presence of 0.3% bile (>90%) and grew under sodium chloride conditions. All selected isolates were sensitive to ampicillin, amoxicillin and cefuroxime and some showed resistance to gentamicin, kanamycin and tetracycline. Moreover, the agar well diffusion assay showed that the supernatant of each strain at pH 3.0 and pH 4.0, but not at pH 7.0 exhibited increased antimicrobial activity (inhibition zone >15mm) against two foodborne pathogens, Escherichia coli and Salmonella spp. To our knowledge, this is the first report describing the antagonistic activity against two foodborne pathogens and the probiotic in vitro potential of lactic acid bacteria isolated from native biota of Ecuador.
Morin, Xavier; Thuiller, Wilfried
Obtaining reliable predictions of species range shifts under climate change is a crucial challenge for ecologists and stakeholders. At the continental scale, niche-based models have been widely used in the last 10 years to predict the potential impacts of climate change on species distributions all over the world, although these models do not include any mechanistic relationships. In contrast, species-specific, process-based predictions remain scarce at the continental scale. This is regrettable because to secure relevant and accurate predictions it is always desirable to compare predictions derived from different kinds of models applied independently to the same set of species and using the same raw data. Here we compare predictions of range shifts under climate change scenarios for 2100 derived from niche-based models with those of a process-based model for 15 North American boreal and temperate tree species. A general pattern emerged from our comparisons: niche-based models tend to predict a stronger level of extinction and a greater proportion of colonization than the process-based model. This result likely arises because niche-based models do not take phenotypic plasticity and local adaptation into account. Nevertheless, as the two kinds of models rely on different assumptions, their complementarity is revealed by common findings. Both modeling approaches highlight a major potential limitation on species tracking their climatic niche because of migration constraints and identify similar zones where species extirpation is likely. Such convergent predictions from models built on very different principles provide a useful way to offset uncertainties at the continental scale. This study shows that the use in concert of both approaches with their own caveats and advantages is crucial to obtain more robust results and that comparisons among models are needed in the near future to gain accuracy regarding predictions of range shifts under climate change.
Describes a general systems evolutionary model and demonstrates how a previously established ecological model is a function of its past development based on the evolution of the rock, nutrient, and water cycles. Discusses the applications of the model in environmental education. (MDH)
Estay, Sergio A.; Labra, Fabio A.; Sepulveda, Roger D.; Bacigalupe, Leonardo D.
Pine sawyer beetle species of the genus Monochamus are vectors of the nematode pest Bursaphelenchus xylophilus. The introduction of these species into new habitats is a constant threat for those regions where the forestry industry depends on conifers, and especially on species of Pinus. To obtain information about the potential risk of establishment of these insects in Chile, we performed climate-based niche modeling using data for five North American and four Eurasian Monochamus species using a Maxent approach. The most important variables that account for current distribution of these species are total annual precipitation and annual and seasonal average temperatures, with some differences between North American and Eurasian species. Projections of potential geographic distribution in Chile show that all species could occupy at least 37% of the area between 30° and 53°S, where industrial plantations of P. radiata are concentrated. Our results indicated that Chile seems more suitable for Eurasian than for North American species. PMID:25019408
Miyashita, Hideyuki; Niwano, Hiroko; Yoshida, Satoru; Hatou, Shin; Inagaki, Emi; Tsubota, Kazuo; Shimmura, Shigeto
Cultures of epithelial cells are limited by the proliferative capacity of primary cells and cell senescence. Herein we show that primary human epithelial cell sheets cultured without dermal equivalents maintained homeostasis in vitro for at least 1 year. Transparency of these sheets enabled live observation of pigmented melanocytes and Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) labeled epithelial cells during wound healing. Cell turn over and KRT15 expression pattern stabilized within 3 months, when KRT15 bright clusters often associated with niche-like melanocytes became apparent. EdU labels were retained in a subset of epithelial cells and melanocytes after 6 months chasing, suggesting their slow cell cycling property. FUCCI-labeling demonstrated robust cell migration and proliferation following wounding. Transparency and long-term (1 year) homeostasis of this model will be a powerful tool for the study of wound healing and cell linage tracing. PMID:28233843
Estay, Sergio A; Labra, Fabio A; Sepulveda, Roger D; Bacigalupe, Leonardo D
Pine sawyer beetle species of the genus Monochamus are vectors of the nematode pest Bursaphelenchus xylophilus. The introduction of these species into new habitats is a constant threat for those regions where the forestry industry depends on conifers, and especially on species of Pinus. To obtain information about the potential risk of establishment of these insects in Chile, we performed climate-based niche modeling using data for five North American and four Eurasian Monochamus species using a Maxent approach. The most important variables that account for current distribution of these species are total annual precipitation and annual and seasonal average temperatures, with some differences between North American and Eurasian species. Projections of potential geographic distribution in Chile show that all species could occupy at least 37% of the area between 30° and 53°S, where industrial plantations of P. radiata are concentrated. Our results indicated that Chile seems more suitable for Eurasian than for North American species.
Estrada-Peña, A; Estrada-Sánchez, A; Estrada-Sánchez, D
Interest is increasing in inferring the climate niche of health-threatening arthropods and projecting such inferences onto a territory. This approach is intended to predict the range of tick distribution and to elucidate tick responses to climate scenarios, using so-called correlative models. However, some methodological gaps might prevent achieving an adequate background for hypothesis testing. We explore, describe, and illustrate these procedural inaccuracies with examples focused on the tick Ixodes ricinus and examine how these factors might affect modelling outcomes. Our aim was to develop a backdrop of rules for developing reliable models for these parasites. The use of partial sets of tick occurrences might produce unreliable associations with climate because the algorithms cannot capture the complete niche with which the tick is associated. Reliability measures of the model cannot detect these inaccuracies, and undesirable estimations of the niche will prevail in the chain of further calculations. The use of inadequate environmental variables (covariates) may lead to inflation of the results of the model through two statistical processes, autocorrelation and colinearity. We demonstrate the high colinearity existing in climate products derived from interpolation of climate recording stations. Our explicit advice is to focus on the training of climate models with satellite-derived information of climate, from which colinearity of the time series has been removed through a harmonic regression. We also emphasize the high uncertainty if inference about the climate niche is expanded into different time slices, like projected climate scenarios.
Lall, Chandan; Kumar, K. Vinod; Raj, R. Vimal; Vedhagiri, K.; Vijayachari, P.
Leptospirosis is an emerging disease around the globe. South Andaman Island is an endemic region for leptospirosis. We herein compared the prevalence of leptospires in urban and rural areas of South Andaman Island. The PCR detection and isolation of Leptospira revealed that pathogenic leptospires were prevalent in sewage water and household drainage water in urban areas and in paddy fields, vegetable field water, and stream water in rural areas. These results demonstrate that intermediates are ubiquitously present in the environment and may be responsible for asymptomatic infections, and also provide an insight into disease ecology. PMID:26936796
Jakubikova, Jana; Cholujova, Danka; Hideshima, Teru; Gronesova, Paulina; Soltysova, Andrea; Harada, Takeshi; Joo, Jungnam; Kong, Sun-Young; Szalat, Raphael E; Richardson, Paul G; Munshi, Nikhil C; Dorfman, David M; Anderson, Kenneth C
Specific niches within the tumor bone marrow (BM) microenvironment afford a sanctuary for multiple myeloma (MM) clones due to stromal cell-tumor cell interactions, which confer survival advantage and drug resistance. Defining the sequelae of tumor cell interactions within the MM niches on an individualized basis may provide the rationale for personalized therapies. To mimic the MM niche, we here describe a new 3D co-culture ex-vivo model in which primary MM patient BM cells are co-cultured with mesenchymal stem cells (MSC) in a hydrogel 3D system. In the 3D model, MSC with conserved phenotype (CD73+CD90+CD105+) formed compact clusters with active fibrous connections, and retained lineage differentiation capacity. Extracellular matrix molecules, integrins, and niche related molecules including N-cadherin and CXCL12 are expressed in 3D MSC model. Furthermore, activation of osteogenesis (MMP13, SPP1, ADAMTS4, and MGP genes) and osteoblastogenic differentiation was confirmed in 3D MSC model. Co-culture of patient-derived BM mononuclear cells with either autologous or allogeneic MSC in 3D model increased proliferation of MM cells, CXCR4 expression, and SP cells. We carried out immune profiling to show that distribution of immune cell subsets was similar in 3D and 2D MSC model systems. Importantly, resistance to novel agents (IMiDs, bortezomib, carfilzomib) and conventional agents (doxorubicin, dexamethasone, melphalan) was observed in 3D MSC system, reflective of clinical resistance. This 3D MSC model may therefore allow for studies of MM pathogenesis and drug resistance within the BM niche. Importantly, ongoing prospective trials are evaluating its utility to inform personalized targeted and immune therapy in MM.
Jakubikova, Jana; Cholujova, Danka; Hideshima, Teru; Gronesova, Paulina; Soltysova, Andrea; Harada, Takeshi; Joo, Jungnam; Kong, Sun-Young; Szalat, Raphael E.; Richardson, Paul G.; Munshi, Nikhil C.; Dorfman, David M.; Anderson, Kenneth C.
Specific niches within the tumor bone marrow (BM) microenvironment afford a sanctuary for multiple myeloma (MM) clones due to stromal cell-tumor cell interactions, which confer survival advantage and drug resistance. Defining the sequelae of tumor cell interactions within the MM niches on an individualized basis may provide the rationale for personalized therapies. To mimic the MM niche, we here describe a new 3D co-culture ex-vivo model in which primary MM patient BM cells are co-cultured with mesenchymal stem cells (MSC) in a hydrogel 3D system. In the 3D model, MSC with conserved phenotype (CD73+CD90+CD105+) formed compact clusters with active fibrous connections, and retained lineage differentiation capacity. Extracellular matrix molecules, integrins, and niche related molecules including N-cadherin and CXCL12 are expressed in 3D MSC model. Furthermore, activation of osteogenesis (MMP13, SPP1, ADAMTS4, and MGP genes) and osteoblastogenic differentiation was confirmed in 3D MSC model. Co-culture of patient-derived BM mononuclear cells with either autologous or allogeneic MSC in 3D model increased proliferation of MM cells, CXCR4 expression, and SP cells. We carried out immune profiling to show that distribution of immune cell subsets was similar in 3D and 2D MSC model systems. Importantly, resistance to novel agents (IMiDs, bortezomib, carfilzomib) and conventional agents (doxorubicin, dexamethasone, melphalan) was observed in 3D MSC system, reflective of clinical resistance. This 3D MSC model may therefore allow for studies of MM pathogenesis and drug resistance within the BM niche. Importantly, ongoing prospective trials are evaluating its utility to inform personalized targeted and immune therapy in MM. PMID:27764795
Munson, Bruce H.
Presents a summary of the research literature on students' ecological conceptions and the implications of misconceptions. Topics include food webs, ecological adaptation, carrying capacity, ecosystem, and niche. (Contains 35 references.) (MKR)
Fisher-Reid, M Caitlin; Kozak, Kenneth H; Wiens, John J
The rate of climatic-niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic-niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic-niche evolution and climatic-niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic-niche evolution and climatic-niche breadths. Contrary to some expectations, we find no general relationship between climatic-niche breadth and the rate of climatic-niche evolution. Climatic-niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic-niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution.
Zhu, Gengping; Liu, Guoqing; Bu, Wenjun; Lis, Jerzy A.
Parastrachiidae is a small stinkbug family containing only one genus and two species, Parastrachia japonensis (Scott) (Hemiptera: Heteroptera: Pentatomoidea) and Parastrachia nagaensis Distant. The geographic distribution of the genus has been poorly studied. Niche conservatism refers to that idea that closely related species are more ecologically similar than would be expected, whereas niche divergence predicts they occupy distinct niche spaces. The existence of only two species within one genus suggests niche conservatism or differentiation might exist among them. Herein, the distribution of the genus was mapped, potential distributions were predicted using ecological niche modeling, and climate spaces occupied by the two species were identified and compared. Our outlined map supports the general spreading route proposed by Schaefer et al. The potential distributions suggest that the genus’ range could extend beyond its presently known distribution, and further investigation into this area could aid in their conservation, particularly P. nagaensis. The niche space inferred by ecological niche modeling suggests the two species do not occupy identical habitat, but the differences between their models could simply be due to the differential availability of habitat in the different regions that they occupy. PMID:24738857
Ai, Dexiecuo; Desjardins-Proulx, Philippe; Chu, Chengjin; Wang, Gang
Repeatability of community composition has been a critical aspect for community structure, which is closely associated with community stability, predictability, conservation biology and ecological restoration. It has been shown that both immigration and local dispersal limitation can affect the community composition in both neutral and niche model. Hence, we use a spatially explicit individual-based model to investigate the potential influence of immigration rate and strength of local dispersal limitation on repeatability in both neutral and niche models. Similarity measures are used to quantify repeatability. We examine the repeatability of community composition among replicate communities (which means the same community repeats many times), and between niche and neutral replicate communities. We find the correlation between repeatability and immigration rate is positive in the neutral model and an inverted unimodal in the niche model. The correlation between repeatability and local dispersal distance is positive in the niche model and negative in the neutral model. High repeatability between niche communities and neutral communities is observed with high immigration rates or when high local dispersal distance appears in the niche model or low local dispersal distance in the neutral model. Our results show that repeatability of community composition is not only dependent on the types of community models (niche vs. neutrality) but also strongly determined by immigration rates and local dispersal limitation.
Mammola, Stefano; Piano, Elena; Isaia, Marco
The geometry of the Hutchinson's hypervolume derives from multiple selective pressures defined, on one hand, by the physiological tolerance of the species, and on the other, by intra- and interspecific competition. The quantification of these evolutionary forces is essential for the understanding of the coexistence of predators in light of competitive exclusion dynamics. We address this topic by investigating the ecological niche of two medium-sized troglophile spiders (Meta menardi and Pimoa graphitica). Over one year, we surveyed several populations in four subterranean sites in the Western Italian Alps, monitoring monthly their spatial and temporal dynamics and the associated physical and ecological variables. We assessed competition between the two species by means of multi regression techniques and by evaluating the intersection between their multidimensional hypervolumes. We detected a remarkable overlap between the microclimatic and trophic niche of M. menardi and P. graphitica, however, the former -being larger in size- resulted the best competitor in proximity of the cave entrance, causing the latter to readjust its spatial niche towards the inner part, where prey availability is scarcer ("step back effect"). In parallel to the slight variations in the subterranean microclimatic condition, the niche of the two species was also found to be seasonal dependent, varying over the year. With this work, we aim at providing new insights about the relationships among predators, demonstrating that energy-poor environments such as caves maintain the potential for diversification of predators via niche differentiation and serve as useful models for theoretical ecological studies.
da Costa, Paulo Martins; Loureiro, Luís; Matos, Augusto J F
The use of antimicrobial agents has been claimed to be the driving force for the emergence and spread of microbial resistance. However, several studies have reported the presence of multidrug-resistant bacteria in populations exposed to low levels of antimicrobial drugs or even never exposed. For many pathogens, especially those organisms for which asymptomatic colonization typically precedes infection (e.g., Enterococcus spp. and Escherichia coli), the selective effects of antimicrobial use can only be understood if we considerer all biological and environmental pathways which enable these bacteria, and the genes they carry, to spread between different biomes. This ecological framework provides an essential perspective for formulating antimicrobial use policies, precisely because it encompasses the root causes of these problems rather than merely their consequences.
da Costa, Paulo Martins; Loureiro, Luís; Matos, Augusto J. F.
The use of antimicrobial agents has been claimed to be the driving force for the emergence and spread of microbial resistance. However, several studies have reported the presence of multidrug-resistant bacteria in populations exposed to low levels of antimicrobial drugs or even never exposed. For many pathogens, especially those organisms for which asymptomatic colonization typically precedes infection (e.g., Enterococcus spp. and Escherichia coli), the selective effects of antimicrobial use can only be understood if we considerer all biological and environmental pathways which enable these bacteria, and the genes they carry, to spread between different biomes. This ecological framework provides an essential perspective for formulating antimicrobial use policies, precisely because it encompasses the root causes of these problems rather than merely their consequences. PMID:23343983
Watson, Charles M.; Burggren, Warren W.
Three congeneric lizards from the southeastern United States (Plestiodon fasciatus, P. inexpectatus, and P. laticeps) exhibit a unique nested distribution. All three skink species inhabit the US Southeast, but two extend northward to central Ohio (P. fasciatus and P. laticeps) and P. fasciatus extends well into Canada. Distinct interspecific differences in microhabitat selection and behavior are associated with the cooler temperatures of the more Northern ranges. We hypothesized that interspecific differences in metabolic temperature sensitivity locally segregates them across their total range. Resting oxygen consumption was measured at 20°, 25° and 30°C. Plestiodon fasciatus, from the coolest habitats, exhibited greatly elevated oxygen consumption compared to the other species at high ecologically-relevant temperatures (0.10, 0.17 and 0.83 ml O2. g-1. h-1 at 20°, 25° and 30°C, respectively). Yet, P. inexpectatus, from the warmest habitats, exhibited sharply decreased oxygen consumption compared to the other species at lower ecologically-relevant temperatures (0.09, 0.27 and 0.42 ml O2. g-1. h-1 at 20°, 25° and 30°C, respectively). Plestiodon laticeps, from both open and closed microhabitats and intermediate latitudinal range, exhibited oxygen consumptions significantly lower than the other two species (0.057, 0.104 and 0.172 ml O2. g-1. h-1 at 20°, 25° and 30°C, respectively). Overall, Plestiodon showed metabolic temperature sensitivities (Q10s) in the range of 2–3 over the middle of each species’ normal temperature range. However, especially P. fasciatus and P. inexpectatus showed highly elevated Q10s (9 to 25) at the extreme ends of their temperature range. While morphologically similar, these skinks are metabolically distinct across the genus’ habitat, likely having contributed to their current distribution. PMID:27760215
Ghylin, Trevor W; Garcia, Sarahi L; Moya, Francisco; Oyserman, Ben O; Schwientek, Patrick; Forest, Katrina T; Mutschler, James; Dwulit-Smith, Jeffrey; Chan, Leong-Keat; Martinez-Garcia, Manuel; Sczyrba, Alexander; Stepanauskas, Ramunas; Grossart, Hans-Peter; Woyke, Tanja; Warnecke, Falk; Malmstrom, Rex; Bertilsson, Stefan; McMahon, Katherine D
Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits. PMID:25093637
Ghylin, Trevor W; Garcia, Sarahi L; Moya, Francisco; Oyserman, Ben O; Schwientek, Patrick; Forest, Katrina T; Mutschler, James; Dwulit-Smith, Jeffrey; Chan, Leong-Keat; Martinez-Garcia, Manuel; Sczyrba, Alexander; Stepanauskas, Ramunas; Grossart, Hans-Peter; Woyke, Tanja; Warnecke, Falk; Malmstrom, Rex; Bertilsson, Stefan; McMahon, Katherine D
Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.
ICT integration of teacher preparation programmes was undertaken by the Australian Teaching Teachers for the Future (TTF) project in all 39 Australian teacher education institutions and highlighted the need for guidelines to inform systemic ICT integration approaches. A Social Ecological Model (SEM) was used to positively inform integration…
Moo-Llanes, David; Ibarra-Cerdeña, Carlos N.; Rebollar-Téllez, Eduardo A.; Ibáñez-Bernal, Sergio; González, Camila; Ramsey, Janine M.
Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i) potential change in niche breadth, ii) direction and magnitude of niche centroid shifts, iii) shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3), for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%), while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases. PMID:24069478
Kolář, Filip; Fuxová, Gabriela; Záveská, Eliška; Nagano, Atsushi J; Hyklová, Lucie; Lučanová, Magdalena; Kudoh, Hiroshi; Marhold, Karol
Quaternary climatic oscillations profoundly impacted temperate biodiversity. For many diverse yet undersampled areas, however, the consequences of this impact are still poorly known. In Europe, particular uncertainty surrounds the role of Balkans, a major hotspot of European diversity, in postglacial recolonization of more northerly areas, and the Carpathians, a debatable candidate for a northern 'cryptic' glacial refugium. Using genome-wide SNPs and microsatellites, we examined how the interplay of historical processes and niche shifts structured genetic diversity of diploid Arabidopsis arenosa, a little-known member of the plant model genus that occupies a wide niche range from sea level to alpine peaks across eastern temperate Europe. While the northern Balkans hosted one isolated endemic lineage, most of the genetic diversity was concentrated further north in the Pannonian Basin and the Carpathians, where it likely survived the last glaciation in northern refugia. Finally, a distinct postglacial environment in northern Europe was colonized by populations of admixed origin from the two Carpathian lineages. Niche differentiation along altitude-related bioclimatic gradients was the main trend in the phylogeny of A. arenosa. The most prominent niche shifts, however, characterized genetically only slightly divergent populations that expanded into narrowly defined alpine and northern coastal postglacial environments. Our study highlights the role of eastern central European mountains not only as refugia for unique temperate diversity but also sources for postglacial expansion into novel high-altitude and high-latitude niches. Knowledge of distinct genetic substructure of diploid A. arenosa also opens new opportunities for follow-up studies of this emerging model of evolutionary biology.
Ferguson, Gayle C.; Bertels, Frederic; Rainey, Paul B.
Pseudomonas fluorescens is a model for the study of adaptive radiation. When propagated in a spatially structured environment, the bacterium rapidly diversifies into a range of niche specialist genotypes. Here we present a genetic dissection and phenotypic characterization of the fuzzy spreader (FS) morphotype—a type that arises repeatedly during the course of the P. fluorescens radiation and appears to colonize the bottom of static broth microcosms. The causal mutation is located within gene fuzY (pflu0478)—the fourth gene of the five-gene fuzVWXYZ operon. fuzY encodes a β-glycosyltransferase that is predicted to modify lipopolysaccharide (LPS) O antigens. The effect of the mutation is to cause cell flocculation. Analysis of 92 independent FS genotypes showed each to have arisen as the result of a loss-of-function mutation in fuzY, although different mutations have subtly different phenotypic and fitness effects. Mutations within fuzY were previously shown to suppress the phenotype of mat-forming wrinkly spreader (WS) types. This prompted a reinvestigation of FS niche preference. Time-lapse photography showed that FS colonizes the meniscus of broth microcosms, forming cellular rafts that, being too flimsy to form a mat, collapse to the vial bottom and then repeatably reform only to collapse. This led to a reassessment of the ecology of the P. fluorescens radiation. Finally, we show that ecological interactions between the three dominant emergent types (smooth, WS, and FS), combined with the interdependence of FS and WS on fuzY, can, at least in part, underpin an evolutionary arms race with bacteriophage SBW25Φ2, to which mutation in fuzY confers resistance. PMID:24077305
Terribile, L C; Diniz-Filho, J A F; De Marco jr, P
The use of ecological niche models (ENM) to generate potential geographic distributions of species has rapidly increased in ecology, conservation and evolutionary biology. Many methods are available and the most used are Maximum Entropy Method (MAXENT) and the Genetic Algorithm for Rule Set Production (GARP). Recent studies have shown that MAXENT perform better than GARP. Here we used the statistics methods of ROC - AUC (area under the Receiver Operating Characteristics curve) and bootstrap to evaluate the performance of GARP and MAXENT in generate potential distribution models for 39 species of New World coral snakes. We found that values of AUC for GARP ranged from 0.923 to 0.999, whereas those for MAXENT ranged from 0.877 to 0.999. On the whole, the differences in AUC were very small, but for 10 species GARP outperformed MAXENT. Means and standard deviations for 100 bootstrapped samples with sample sizes ranging from 3 to 30 species did not show any trends towards deviations from a zero difference in AUC values of GARP minus AUC values of MAXENT. Ours results suggest that further studies are still necessary to establish under which circumstances the statistical performance of the methods vary. However, it is also important to consider the possibility that this empirical inductive reasoning may fail in the end, because we almost certainly could not establish all potential scenarios generating variation in the relative performance of models.
Lee-Yaw, J A; Irwin, D E
The relative importance of ecological vs. non-ecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages--such as the distinct genetic groups that make up the ranges of many northern species--represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long-toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long-toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non-ecological factors to play a more important role in the maintenance of northern taxa.
Cummings, David O.; Buhl, Jerome; Lee, Raymond W.; Simpson, Stephen J.; Holmes, Sebastian P.
Distributions of stable isotopes have been used to infer an organism's trophic niche width, the ‘isotopic niche’, and examine resource partitioning. Spatial variation in the isotopic composition of prey may however confound the interpretation of isotopic signatures especially when foragers exploit resources across numerous locations. In this study the isotopic compositions from marine assemblages are modelled to determine the role of variation in the signature of prey items and the effect of dietary breadth and foraging strategies on predator signatures. Outputs from the models reveal that isotopic niche widths can be greater for populations of dietary specialists rather than for generalists, which contravenes what is generally accepted in the literature. When a range of different mixing models are applied to determine if the conversion from δ to p-space can be used to improve model accuracy, predator signature variation is increased rather than model precision. Furthermore the mixing models applied failed to correctly identify dietary specialists and/or to accurately estimate diet contributions that may identify resource partitioning. The results presented illustrate the need to collect sufficiently large sample sizes, in excess of what is collected under most current studies, across the complete distribution of a species and its prey, before attempts to use stable isotopes to make inferences about niche width can be made. PMID:22876280
To better understand the potential geographical distributions of nonindigenous species (NIS), we are evaluating the ability of niche models to predict the presence of existing native and NIS species within individual estuaries based on landscape characteristics. One model being ...
Heckbert, Scott; Baynes, Tim; Reeson, Andrew
Interconnected social and environmental systems are the domain of ecological economics, and models can be used to explore feedbacks and adaptations inherent in these systems. Agent-based modeling (ABM) represents autonomous entities, each with dynamic behavior and heterogeneous characteristics. Agents interact with each other and their environment, resulting in emergent outcomes at the macroscale that can be used to quantitatively analyze complex systems. ABM is contributing to research questions in ecological economics in the areas of natural resource management and land-use change, urban systems modeling, market dynamics, changes in consumer attitudes, innovation, and diffusion of technology and management practices, commons dilemmas and self-governance, and psychological aspects to human decision making and behavior change. Frontiers for ABM research in ecological economics involve advancing the empirical calibration and validation of models through mixed methods, including surveys, interviews, participatory modeling, and, notably, experimental economics to test specific decision-making hypotheses. Linking ABM with other modeling techniques at the level of emergent properties will further advance efforts to understand dynamics of social-environmental systems.
Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira
Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the F(ST)-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.
Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M.; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira
Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the FST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele. PMID:22768049
Yoo, Byunghee; Kavishwar, Amol; Wang, Ping; Ross, Alana; Pantazopoulos, Pamela; Dudley, Michael; Moore, Anna; Medarova, Zdravka
Treatment of stage IV metastatic breast cancer patients is limited to palliative options and represents an unmet clinical need. Here, we demonstrate that pharmacological inhibition of miRNA-10b - a master regulator of metastatic cell viability – leads to elimination of distant metastases in a mouse model of metastatic breast cancer. This was achieved using the miRNA-10b inhibitory nanodrug, MN-anti-miR10b, which consists of magnetic nanoparticles, conjugated to LNA-based miR-10b antagomirs. Intravenous injection of MN-anti-miR10b into mice bearing lung, bone, and brain metastases from breast cancer resulted in selective accumulation of the nanodrug in metastatic tumor cells. Weekly treatments of mice with MN-anti-miR-10b and low-dose doxorubicin resulted in complete regression of pre-existing distant metastases in 65% of the animals and a significant reduction in cancer mortality. These observations were supported by dramatic reduction in proliferation and increase in apoptosis in metastatic sites. On a molecular level, we observed a significant increase in the expression of HOXD10, which is a known target of miRNA-10b. These results represent first steps into the uncharted territory of therapy targeted to the metastatic niche. PMID:28322342
Wang, Lin; Kamocka, Malgorzata M; Zollman, Amy; Carlesso, Nadia
Increasing evidence indicates that normal hematopoiesis is regulated by distinct microenvironmental cues in the BM, which include specialized cellular niches modulating critical hematopoietic stem cell (HSC) functions(1)(,)(2). Indeed, a more detailed picture of the hematopoietic microenvironment is now emerging, in which the endosteal and the endothelial niches form functional units for the regulation of normal HSC and their progeny(3)(,)(4)(,)(5). New studies have revealed the importance of perivascular cells, adipocytes and neuronal cells in maintaining and regulating HSC function(6)(,)(7)(,)(8). Furthermore, there is evidence that cells from different lineages, i.e. myeloid and lymphoid cells, home and reside in specific niches within the BM microenvironment. However, a complete mapping of the BM microenvironment and its occupants is still in progress. Transgenic mouse strains expressing lineage specific fluorescent markers or mice genetically engineered to lack selected molecules in specific cells of the BM niche are now available. Knock-out and lineage tracking models, in combination with transplantation approaches, provide the opportunity to refine the knowledge on the role of specific "niche" cells for defined hematopoietic populations, such as HSC, B-cells, T-cells, myeloid cells and erythroid cells. This strategy can be further potentiated by merging the use of two-photon microscopy of the calvarium. By providing in vivo high resolution imaging and 3-D rendering of the BM calvarium, we can now determine precisely the location where specific hematopoietic subsets home in the BM and evaluate the kinetics of their expansion over time. Here, Lys-GFP transgenic mice (marking myeloid cells)(9) and RBPJ knock-out mice (lacking canonical Notch signaling)(10) are used in combination with IVFM to determine the engraftment of myeloid cells to a Notch defective BM microenvironment.
Porceddu, Marco; Mattana, Efisio; Pritchard, Hugh W.; Bacchetta, Gianluigi
Background and Aims Mediterranean mountain species face exacting ecological conditions of rainy, cold winters and arid, hot summers, which affect seed germination phenology. In this study, a soil heat sum model was used to predict field emergence of Rhamnus persicifolia, an endemic tree species living at the edge of mountain streams of central eastern Sardinia. Methods Seeds were incubated in the light at a range of temperatures (10–25 and 25/10 °C) after different periods (up to 3 months) of cold stratification at 5 °C. Base temperatures (Tb), and thermal times for 50 % germination (θ50) were calculated. Seeds were also buried in the soil in two natural populations (Rio Correboi and Rio Olai), both underneath and outside the tree canopy, and exhumed at regular intervals. Soil temperatures were recorded using data loggers and soil heat sum (°Cd) was calculated on the basis of the estimated Tb and soil temperatures. Key Results Cold stratification released physiological dormancy (PD), increasing final germination and widening the range of germination temperatures, indicative of a Type 2 non-deep PD. Tb was reduced from 10·5 °C for non-stratified seeds to 2·7 °C for seeds cold stratified for 3 months. The best thermal time model was obtained by fitting probit germination against log °Cd. θ50 was 2·6 log °Cd for untreated seeds and 2·17–2·19 log °Cd for stratified seeds. When θ50 values were integrated with soil heat sum estimates, field emergence was predicted from March to April and confirmed through field observations. Conclusions Tb and θ50 values facilitated model development of the thermal niche for in situ germination of R. persicifolia. These experimental approaches may be applied to model the natural regeneration patterns of other species growing on Mediterranean mountain waterways and of physiologically dormant species, with overwintering cold stratification requirement and spring germination. PMID:24201139
Peirson, Leslea J; Boydell, Katherine M; Ferguson, H Bruce; Ferris, Lorraine E
In June 2007 the American Journal of Community Psychology published a special issue focused on theories, methods and interventions for systems change which included calls from the editors and authors for theoretical advancement in this field. We propose a conceptual model of systems change that integrates familiar and fundamental community psychology principles (succession, interdependence, cycling of resources, adaptation) and accentuates a process orientation. To situate our framework we offer a definition of systems change and a brief review of the ecological perspective and principles. The Ecological Process Model of Systems Change is depicted, described and applied to a case example of policy driven systems level change in publicly funded social programs. We conclude by identifying salient implications for thinking and action which flow from the Model.
Larson, Elizabeth; Miller-Bishoff, Thomas
Using mixed methods, this study examined the relationship of caregivers of children with disabilities’ psychological well-being (PWB) and their orchestration of daily routines within their ecological niche. Thirty-nine U.S. caregivers completed in-depth interviews, PWB Scales, and Family Time and Routines Index (FTRI). We used a multi-step analysis. Interview data was coded and vignettes created without knowledge of PWB and FTRI ratings. Next, the relationship of quantitative measures was analyzed. Four groups were created using FTRI-extent and PWB means: (1) low routine-low PWB, (2) low routine-high PWB, (3) high routine-low PWB, and (4) high routine-high PWB. We examined qualitative differences in key features between groups. Findings: Total PWB and FTRI scores were not significantly correlated, PWB Purpose in Life and FTRI-extent scores were moderately positively correlated, and PWB Environmental Mastery and FTRI-extent correlation approached significance. Qualitative findings describe caregivers’ structuring of routines, intensity of oversight, support in routines, management of dinner, paid work, and needs for respite. The four groups differed in paid work, household support, degree the child could self-occupy, Environmental Mastery, and opportunities to recuperate. Caregivers with higher levels of well-being and more regular routines did paid work, had supportive spouses, had children who more often could follow routines, had higher Environmental Mastery, could orchestrate a family meal, and had breaks from care in either work or leisure. All Native American caregivers and Mexican American caregivers with spouses were in the high routine-high PWB group. Insight into this complex negotiation between family members within daily routines may provide practitioners a better understanding of how to work within family circles to foster therapeutic alliances, identify focused intervention targets, and promote positive family wide outcomes. PMID:24910625
Ouisse, Tiphaine; Bonte, Dries; Lebouvier, Marc; Hendrickx, Frederik; Renault, David
Comprehensive studies to identify species-specific drivers of survival to environmental stress, reproduction, growth, and recruitment are vital to gaining a better understanding of the main ecological factors shaping species habitat distribution and dispersal routes. The present study performed a field-based assessment of habitat distribution in the invasive carabid beetle Merizodus soledadinus for the Kerguelen archipelago. The results emphasised humid habitats as a key element of the insect's realised niche. In addition, insects faced food and water stress during dispersal events. We evaluated quantitatively how water availability and trophic resources governed the spatial distribution of this invasive predatory insect at Îles Kerguelen. Food and water stress survival durations [in 100%, 70%, and 30% relative humidity (RH) conditions] and changes in a set of primary metabolic compounds (metabolomics) were determined. Adult M. soledadinus supplied with water ad libitum were highly tolerant to prolonged starvation (LT50=51.7±6.2d). However, food-deprived insect survival decreased rapidly in moderate (70% RH, LT50=30.37±1.39h) and low (30% RH, LT50=13.03±0.48h) RH conditions. Consistently, body water content decreased rapidly in insects exposed to 70% and 30% RH. Metabolic variation evidenced the effects of food deprivation in control insects (exposed to 100% RH), which exhibited a progressive decline of most glycolytic sugars and tricarboxylic acid cycle intermediates. Most metabolite levels were elevated levels during the first few hours of exposure to 30% and 70% RH. Augmented alanine and lactate levels suggested a shift to anaerobic metabolism. Simultaneously, peaks in threonine and glycolytic sugars pointed to metabolic disruption and a progressive physiological breakdown in dehydrating individuals. Overall, the results of our study indicate that the geographic distribution of M. soledadinus populations is highly dependent on habitat RH and water
Nair, Anusree V; Pradeep, M A; Vijayan, K K
Bacillus and Pseudomonas are the dominant groups of bacteria known for their antagonistic potential against many plant and animal pathogens. Presently, exploration of these genera with antagonistic property for disease management of aquaculture system is gaining more importance to overcome the use of antibiotics and related resistance issues. Rapid screening and identification of these genera from diverse bacterial populations by conventional methods is laborious, cost-intensive, and time-consuming. To overcome these limiting factors, in the present study, a colony multiplex PCR (cmPCR) method was developed and evaluated for the rapid detection of Bacillus and Pseudomonas. The technique amplifies the partial 16S rRNA gene of Bacillus and Pseudomonas with a product size of ~1,100 and ~375 bp, respectively, using single forward (BSF2) and two reverse primers (PAGSR and BK1R). Reliability of the cmPCR method was confirmed by screening 472 isolates obtained from ten different eco-stations, of which 133 isolates belonged to Bacillus and 32 to Pseudomonas. The cmPCR method also helped to identify six different Pseudomonas spp. and 14 different Bacillus spp. from environmental samples. Of the total 472 isolates studied, 46 showed antagonistic activity, among which 63 % were Bacillus and 17.4 % were Pseudomonas. Thus, the newly developed molecular approach provides a quick, sensitive, and potential screening tool to detect novel, antagonistically important Bacillus and Pseudomonas genera for their use in aquaculture. Further, it can also act as a taxonomic tool to understand the distribution of these genera from wide ecological niches and their exploitation for diverse biotechnological applications.
Shapiro, Liza J; Young, Jesse W; VandeBerg, John L
Recently proposed ancestral locomotor and morphological 'stages' leading to the evolution of primates have emphasized small body size, and a transition from a clawed non-grasping stage, to a clawed, grasping stage with clawless opposable hallux, to a fully-nailed primate with grasping extremities. This evolutionary transition was presumably associated with frequent use of the small branch niche. To model elements of these evolutionary transitions, we investigate how body size, substrate size, substrate orientation and grasping morphology interact to influence quadrupedal kinematics within and between ontogenetic samples of two small-bodied marsupials, one arboreal (Petaurus breviceps) and the other mainly terrestrial (Monodelphis domestica). Longitudinal morphometric and kinematic data were collected from four juvenile P. breviceps (33-75 g) and two juvenile M. domestica (18-95 g) walking across poles of three diameters (2.5, 1.0, and 0.5 cm) and three orientations (horizontal, 30° incline, 30° decline). The two species responded similarly to some substrate conditions, but diverged in response to others. Kinematic divergence between the two species reflects Monodelphis' relatively shorter digits, reduced grasping ability and greater need for stabilizing mechanisms on narrow substrates. At a given relative body size or pole orientation, Monodelphis used higher limb duty factors, more limbs in support per stride, lower limb phases, and in some conditions, faster speeds compared with Petaurus. Interspecific differences were the least distinct on declined poles, highlighting the particular challenge of this substrate condition, even for arboreally adapted species. Small-bodied, arboreal primate ancestors would likely have employed the kinematic mechanisms common to our model taxa, but those with enhanced grasping adaptations would most likely not have required the increased level of stabilizing mechanisms exhibited by Monodelphis. Thus, using these two species
Yeung, Pan; Sin, Hoi Shun; Chan, Shing; Chan, Godfrey Chi Fung; Chan, Barbara Pui
There is a growing trend for researchers to use in vitro 3D models in cancer studies, as they can better recapitulate the complex in vivo situation. And the fact that the progression and development of tumor are closely associated to its stromal microenvironment has been increasingly recognized. The establishment of such tumor supportive niche is vital in understanding tumor progress and metastasis. The mesenchymal origin of many cells residing in the cancer niche provides the rationale to include MSCs in mimicking the niche in neuroblastoma. Here we co-encapsulate and co-culture NBCs and MSCs in a 3D in vitro model and investigate the morphology, growth kinetics and matrix remodeling in the reconstituted stromal environment. Results showed that the incorporation of MSCs in the model lead to accelerated growth of cancer cells as well as recapitulation of at least partially the tumor microenvironment in vivo. The current study therefore demonstrates the feasibility for the collagen microsphere to act as a 3D in vitro cancer model for various topics in cancer studies. PMID:26657086
Aichinger, Ernst; Kornet, Noortje; Friedrich, Thomas; Laux, Thomas
Multicellular organisms possess pluripotent stem cells to form new organs, replenish the daily loss of cells, or regenerate organs after injury. Stem cells are maintained in specific environments, the stem cell niches, that provide signals to block differentiation. In plants, stem cell niches are situated in the shoot, root, and vascular meristems-self-perpetuating units of organ formation. Plants' lifelong activity-which, as in the case of trees, can extend over more than a thousand years-requires that a robust regulatory network keep the balance between pluripotent stem cells and differentiating descendants. In this review, we focus on current models in plant stem cell research elaborated during the past two decades, mainly in the model plant Arabidopsis thaliana. We address the roles of mobile signals on transcriptional modules involved in balancing cell fates. In addition, we discuss shared features of and differences between the distinct stem cell niches of Arabidopsis.
Waterson, A. M.; Edgar, K. M.; Schmidt, D. N.; Valdes, P. J.
The application of transfer functions on fossil assemblages to reconstruct past environments is fundamentally based on the assumption of stable environmental niches in both space and time. We quantitatively test this assumption for six dominant planktic foraminiferal species (Globigerinoides ruber (pink), G. ruber (white), Trilobatus sacculifer, Truncorotalia truncatulinoides, Globigerina bulloides, and Neogloboquadrina pachyderma) by contrasting reconstructions of species realized and optimum distributions in the modern and during the Last Glacial Maximum (LGM) using an ecological niche model (ENM; MaxEnt) and ordination framework. Global ecological niche models calibrated in the modern ocean have high predictive performance when projected to the LGM for subpolar and polar species, indicating that the environmental niches of these taxa are largely stable at the global scale across this interval. In contrast, ENMs had much poorer predictive performance for the optimal niche of tropical-dwelling species, T. sacculifer and G. ruber (pink). This finding is supported by independent metrics of niche margin change, suggesting that niche stability in environmental space was greatest for (sub)polar species, with greatest expansion of the niche observed for tropical species. We find that globally calibrated ENMs showed good predictions of species occurrences globally, whereas models calibrated in either the Pacific or Atlantic Oceans only and then projected globally performed less well for T. sacculifer. Our results support the assumption of environmental niche stability over the last 21,000 years for most of our focal planktic foraminiferal species and, thus, the application of transfer function techniques for palaeoenvironmental reconstruction during this interval. However, the lower observed niche stability for (sub)tropical taxa T. sacculifer and G. ruber (pink) suggests that (sub)tropical temperatures could be underestimated in the glacial ocean with the strongest
The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.
DeAngelis, Donald L.; Yurek, Simeon
The use of spatially explicit models (SEMs) in ecology has grown enormously in the past two decades. One major advancement has been that fine-scale details of landscapes, and of spatially dependent biological processes, such as dispersal and invasion, can now be simulated with great precision, due to improvements in computer technology. Many areas of modeling have shifted toward a focus on capturing these fine-scale details, to improve mechanistic understanding of ecosystems. However, spatially implicit models (SIMs) have played a dominant role in ecology, and arguments have been made that SIMs, which account for the effects of space without specifying spatial positions, have an advantage of being simpler and more broadly applicable, perhaps contributing more to understanding. We address this debate by comparing SEMs and SIMs in examples from the past few decades of modeling research. We argue that, although SIMs have been the dominant approach in the incorporation of space in theoretical ecology, SEMs have unique advantages for addressing pragmatic questions concerning species populations or communities in specific places, because local conditions, such as spatial heterogeneities, organism behaviors, and other contingencies, produce dynamics and patterns that usually cannot be incorporated into simpler SIMs. SEMs are also able to describe mechanisms at the local scale that can create amplifying positive feedbacks at that scale, creating emergent patterns at larger scales, and therefore are important to basic ecological theory. We review the use of SEMs at the level of populations, interacting populations, food webs, and ecosystems and argue that SEMs are not only essential in pragmatic issues, but must play a role in the understanding of causal relationships on landscapes.
Sun, Zepeng; de Roos, André M
We formulate and analyze a stage-structured consumer-resource biomass model, in which consumers reproduce in a pulsed event at the beginning of a growing season and furthermore go through a niche shift during their life history. We show that the resulting semi-discrete model can exhibit two stable states that can be characterized as a development-controlled state and a reproduction-controlled state. Varying resource availabilities and varying the extent of the niche shift determines whether juveniles or adults are more limited by their resource(s) and can lead to switches between the alternative stable states. Furthermore, we quantify the persistence of the consumer population and the occurrence of the two alternative stable states as a function of resource availabilities and extent of the niche shift. All the results show that irrespective of the type of reproduction of the consumers (continuous or seasonal), the stage-structured model will exhibit alternative stable states as long as development of the juvenile stage and reproduction of the adult stage are both resource-dependent.
Mandle, Lisa; Warren, Dan L; Hoffmann, Matthias H; Peterson, A Townsend; Schmitt, Johanna; von Wettberg, Eric J
Determining the degree to which climate niches are conserved across plant species' native and introduced ranges is valuable to developing successful strategies to limit the introduction and spread of invasive plants, and also has important ecological and evolutionary implications. Here, we test whether climate niches differ between native and introduced populations of Impatiens walleriana, globally one of the most popular horticultural species. We use approaches based on both raw climate data associated with occurrence points and ecological niche models (ENMs) developed with Maxent. We include comparisons of climate niche breadth in both geographic and environmental spaces, taking into account differences in available habitats between the distributional areas. We find significant differences in climate envelopes between native and introduced populations when comparing raw climate variables, with introduced populations appearing to expand into wetter and cooler climates. However, analyses controlling for differences in available habitat in each region do not indicate expansion of climate niches. We therefore cannot reject the hypothesis that observed differences in climate envelopes reflect only the limited environments available within the species' native range in East Africa. Our results suggest that models built from only native range occurrence data will not provide an accurate prediction of the potential for invasiveness if applied to areas containing a greater range of environmental combinations, and that tests of niche expansion may overestimate shifts in climate niches if they do not control carefully for environmental differences between distributional areas.
Encarnación-Luévano, Alondra; Rojas-Soto, Octavio R; Sigala-Rodríguez, J Jesús
The importance of climatic conditions in shaping the geographic distribution of amphibian species is mainly associated to their high sensitivity to environmental conditions. How they cope with climate gradients through behavioral adaptations throughout their distribution is an important issue due to the ecological and evolutionary implications for population viability. Given their low dispersal abilities, the response to seasonal climate changes may not be migration, but behavioral and physiological adaptations. Here we tested whether shifts in climatic seasonality can predict the temporal variation of surface activity of the fossorial Lowland Burrowing Treefrog (Smilisca fodiens) across its geographical distribution. We employed Ecological Niche Modeling (ENM) to perform a monthly analysis of spatial variation of suitable climatic conditions (defined by the July conditions, the month of greatest activity), and then evaluated the geographical correspondence of monthly projections with the occurrence data per month. We found that the species activity, based on the species' occurrence data, corresponds with the latitudinal variation of suitable climatic conditions. Due to the behavioral response of this fossorial frog to seasonal climate variation, we suggest that precipitation and temperature have played a major role in the definition of geographical and temporal distribution patterns, as well as in shaping behavioral adaptations to local climatic conditions. This highlights the influence of macroclimate on shaping activity patterns and the important role of fossorials habits to meet the environmental requirements necessary for survival.
Gardner, R.H.; Turner, M.G.; Dale, V.H.; O'Neill, R.V.
The boundary zone between adjacent communities has long been recognized as a functionally important component of ecosystems. The diversity and abundance of species, the flow and accumulation of material and energy, and the propagation of disturbances may all be affected by landscape boundaries. However, the spatial arrangement of different habitats and their boundaries has received little direct study. The difficulty in studying landscape boundaries has been due, in part, to the variety of responses of organisms to ecotones. Therefore, definitive tests of relationships between ecological processes and the pattern of landscape boundaries will be greatly assisted by developing a standard against which comparisons can be made. Neutral models can define this standard by producing the expected'' Poisson distribution have been well established, but a general approach for relating ecological processes and landscape patterns must still be defined. The purpose of this chapter is to illustrate how neutral models that are developed from percolation theory can be used to address the problem How do ecological system boundaries influence biotic diversity and the flow of energy, information and materials '' 26 refs., 4 figs., 1 tab.
Chimenti, Isotta; Massai, Diana; Morbiducci, Umberto; Beltrami, Antonio Paolo; Pesce, Maurizio; Messina, Elisa
Improved protocols/devices for in vitro culture of 3D cell spheroids may provide essential cues for proper growth and differentiation of stem/progenitor cells (S/PCs) in their niche, allowing preservation of specific features, such as multi-lineage potential and paracrine activity. Several platforms have been employed to replicate these conditions and to generate S/PC spheroids for therapeutic applications. However, they incompletely reproduce the niche environment, with partial loss of its highly regulated network, with additional hurdles in the field of cardiac biology, due to debated resident S/PCs therapeutic potential and clinical translation. In this contribution, the essential niche conditions (metabolic, geometric, mechanical) that allow S/PCs maintenance/commitment will be discussed. In particular, we will focus on both existing bioreactor-based platforms for the culture of S/PC as spheroids, and on possible criteria for the scaling-up of niche-like spheroids, which could be envisaged as promising tools for personalized cardiac regenerative medicine, as well as for high-throughput drug screening.
Evans, Matthew R
The world is changing at an unprecedented rate. In such a situation, we need to understand the nature of the change and to make predictions about the way in which it might affect systems of interest; often we may also wish to understand what might be done to mitigate the predicted effects. In ecology, we usually make such predictions (or forecasts) by making use of mathematical models that describe the system and projecting them into the future, under changed conditions. Approaches emphasizing the desirability of simple models with analytical tractability and those that use assumed causal relationships derived statistically from data currently dominate ecological modelling. Although such models are excellent at describing the way in which a system has behaved, they are poor at predicting its future state, especially in novel conditions. In order to address questions about the impact of environmental change, and to understand what, if any, action might be taken to ameliorate it, ecologists need to develop the ability to project models into novel, future conditions. This will require the development of models based on understanding the processes that result in a system behaving the way it does, rather than relying on a description of the system, as a whole, remaining valid indefinitely.
Zhu, Hong-Ru; Liu, Lu; Zhou, Xiao-Nong; Yang, Guo-Jing
Background Schistosomiasis japonica is a parasitic disease that remains endemic in seven provinces in the People’s Republic of China (P.R. China). One of the most important measures in the process of schistosomiasis elimination in P.R. China is control of Oncomelania hupensis, the unique intermediate host snail of Schistosoma japonicum. Compared with plains/swamp and lake regions, the hilly/mountainous regions of schistosomiasis endemic areas are more complicated, which makes the snail survey difficult to conduct precisely and efficiently. There is a pressing call to identify the snail habitats of mountainous regions in an efficient and cost-effective manner. Methods Twelve out of 56 administrative villages distributed with O. hupensis in Eryuan, Yunnan Province, were randomly selected to set up the ecological model. Thirty out of the rest of 78 villages (villages selected for building model were excluded from the villages for validation) in Eryuan and 30 out of 89 villages in Midu, Yunnan Province were selected via a chessboard method for model validation, respectively. Nine-year-average Normalized Difference Vegetation Index (NDVI) and Land Surface Temperature (LST) as well as Digital Elevation Model (DEM) covering Eryuan and Midu were extracted from MODIS and ASTER satellite images, respectively. Slope, elevation and the distance from every village to its nearest stream were derived from DEM. Suitable survival environment conditions for snails were defined by comparing historical snail presence data and remote sensing derived images. According to the suitable conditions for snails, environment factors, i.e. NDVI, LST, elevation, slope and the distance from every village to its nearest stream, were integrated into an ecological niche model to predict O. hupensis potential habitats in Eryuan and Midu. The evaluation of the model was assessed by comparing the model prediction and field investigation. Then, the consistency rate of model validation was calculated
Seeholzer, Glenn F; Claramunt, Santiago; Brumfield, Robb T
Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic-niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic-niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic-niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic-niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined.
Montiglio, Pierre-Olivier; Ferrari, Caterina; Réale, Denis
Several personality traits are mainly expressed in a social context, and others, which are not restricted to a social context, can be affected by the social interactions with conspecifics. In this paper, we focus on the recently proposed hypothesis that social niche specialization (i.e. individuals in a population occupy different social roles) can explain the maintenance of individual differences in personality. We first present ecological and social niche specialization hypotheses. In particular, we show how niche specialization can be quantified and highlight the link between personality differences and social niche specialization. We then review some ecological factors (e.g. competition and environmental heterogeneity) and the social mechanisms (e.g. frequency-dependent, state-dependent and social awareness) that may be associated with the evolution of social niche specialization and personality differences. Finally, we present a conceptual model and methods to quantify the contribution of ecological factors and social mechanisms to the dynamics between personality and social roles. In doing so, we suggest a series of research objectives to help empirical advances in this research area. Throughout this paper, we highlight empirical studies of social niche specialization in mammals, where available.
Su, Jing; Zhang, Le; Zhang, Wen; Choi, Dong Song; Wen, Jianguo; Jiang, Beini; Chang, Chung-Che; Zhou, Xiaobo
Multiple myeloma, the second most common hematological cancer, is currently incurable due to refractory disease relapse and development of multiple drug resistance. We and others recently established the biophysical model that myeloma initiating (stem) cells (MICs) trigger the stiffening of their niches via SDF-1/CXCR4 paracrine; The stiffened niches then promote the colonogenesis of MICs and protect them from drug treatment. In this work we examined in silico the pharmaceutical potential of targeting MIC niche stiffness to facilitate cytotoxic chemotherapies. We first established a multi-scale agent-based model using the Markov Chain Monte Carlo approach to recapitulate the niche stiffness centric, pro-oncogenetic positive feedback loop between MICs and myeloma-associated bone marrow stromal cells (MBMSCs), and investigated the effects of such intercellular chemo-physical communications on myeloma development. Then we used AMD3100 (to interrupt the interactions between MICs and their stroma) and Bortezomib (a recently developed novel therapeutic agent) as representative drugs to examine if the biophysical properties of myeloma niches are drugable. Results showed that our model recaptured the key experimental observation that the MBMSCs were more sensitive to SDF-1 secreted by MICs, and provided stiffer niches for these initiating cells and promoted their proliferation and drug resistance. Drug synergism analysis suggested that AMD3100 treatment undermined the capability of MICs to modulate the bone marrow microenvironment, and thus re-sensitized myeloma to Bortezomib treatments. This work is also the first attempt to virtually visualize in 3D the dynamics of the bone marrow stiffness during myeloma development. In summary, we established a multi-scale model to facilitate the translation of the niche-stiffness centric myeloma model as well as experimental observations to possible clinical applications. We concluded that targeting the biophysical properties of stem
A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport modeling with the U.S. EPA's general water quality model, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...
Peers, Michael J L; Thornton, Daniel H; Murray, Dennis L
Determining the patterns, causes and consequences of character displacement is central to our understanding of competition in ecological communities. However, the majority of competition research has occurred over small spatial extents or focused on fine-scale differences in morphology or behaviour. The effects of competition on broad-scale distribution and niche characteristics of species remain poorly understood but critically important. Using range-wide species distribution models, we evaluated whether Canada lynx (Lynx canadensis) or bobcat (Lynx rufus) were displaced in regions of sympatry. Consistent with our prediction, we found that lynx niches were less similar to those of bobcat in areas of sympatry versus allopatry, with a stronger reliance on snow cover driving lynx niche divergence in the sympatric zone. By contrast, bobcat increased niche breadth in zones of sympatry, and bobcat niches were equally similar to those of lynx in zones of sympatry and allopatry. These findings suggest that competitively disadvantaged species avoid competition at large scales by restricting their niche to highly suitable conditions, while superior competitors expand the diversity of environments used. Our results indicate that competition can manifest within climatic niche space across species' ranges, highlighting the importance of biotic interactions occurring at large spatial scales on niche dynamics.
Prosdocimi, Erica M; Mapelli, Francesca; Gonella, Elena; Borin, Sara; Crotti, Elena
Among the animals of the Kingdom Animalia, insects are unparalleled for their widespread diffusion, diversity and number of occupied ecological niches. In recent years they have raised researcher interest not only because of their importance as human and agricultural pests, disease vectors and as useful breeding species (e.g. honeybee and silkworm), but also because of their suitability as animal models. It is now fully recognized that microorganisms form symbiotic relationships with insects, influencing their survival, fitness, development, mating habits and the immune system and other aspects of the biology and ecology of the insect host. Thus, any research aimed at deepening the knowledge of any given insect species (perhaps species of applied interest or species emerging as novel pests or vectors) must consider the characterization of the associated microbiome. The present review critically examines the microbiology and molecular ecology techniques that can be applied to the taxonomical and functional analysis of the microbiome of non-model insects. Our goal is to provide an overview of current approaches and methods addressing the ecology and functions of microorganisms and microbiomes associated with insects. Our focus is on operational details, aiming to provide a concise guide to currently available advanced techniques, in an effort to extend insect microbiome research beyond simple descriptions of microbial communities.
Fitzpatrick, Megan J; Mathewson, Paul D; Porter, Warren P
Mechanistic models provide a powerful, minimally invasive tool for gaining a deeper understanding of the ecology of animals across geographic space and time. In this paper, we modified and validated the accuracy of the mechanistic model Niche Mapper for simulating heat exchanges of animals with counter-current heat exchange mechanisms in their legs and animals that wade in water. We then used Niche Mapper to explore the effects of wading and counter-current heat exchange on the energy expenditures of Whooping Cranes, a long-legged wading bird. We validated model accuracy against the energy expenditure of two captive Whooping Cranes measured using the doubly-labeled water method and time energy budgets. Energy expenditure values modeled by Niche Mapper were similar to values measured by the doubly-labeled water method and values estimated from time-energy budgets. Future studies will be able to use Niche Mapper as a non-invasive tool to explore energy-based limits to the fundamental niche of Whooping Cranes and apply this knowledge to management decisions. Basic questions about the importance of counter-current exchange and wading to animal physiological tolerances can also now be explored with the model.
Fitzpatrick, Megan J.; Mathewson, Paul D.; Porter, Warren P.
Mechanistic models provide a powerful, minimally invasive tool for gaining a deeper understanding of the ecology of animals across geographic space and time. In this paper, we modified and validated the accuracy of the mechanistic model Niche Mapper for simulating heat exchanges of animals with counter-current heat exchange mechanisms in their legs and animals that wade in water. We then used Niche Mapper to explore the effects of wading and counter-current heat exchange on the energy expenditures of Whooping Cranes, a long-legged wading bird. We validated model accuracy against the energy expenditure of two captive Whooping Cranes measured using the doubly-labeled water method and time energy budgets. Energy expenditure values modeled by Niche Mapper were similar to values measured by the doubly-labeled water method and values estimated from time-energy budgets. Future studies will be able to use Niche Mapper as a non-invasive tool to explore energy-based limits to the fundamental niche of Whooping Cranes and apply this knowledge to management decisions. Basic questions about the importance of counter-current exchange and wading to animal physiological tolerances can also now be explored with the model. PMID:26308207
Heumann, Benjamin W; Walsh, Stephen J; Verdery, Ashton M; McDaniel, Phillip M; Rindfuss, Ronald R
Understanding the pattern-process relations of land use/land cover change is an important area of research that provides key insights into human-environment interactions. The suitability or likelihood of occurrence of land use such as agricultural crop types across a human-managed landscape is a central consideration. Recent advances in niche-based, geographic species distribution modeling (SDM) offer a novel approach to understanding land suitability and land use decisions. SDM links species presence-location data with geospatial information and uses machine learning algorithms to develop non-linear and discontinuous species-environment relationships. Here, we apply the MaxEnt (Maximum Entropy) model for land suitability modeling by adapting niche theory to a human-managed landscape. In this article, we use data from an agricultural district in Northeastern Thailand as a case study for examining the relationships between the natural, built, and social environments and the likelihood of crop choice for the commonly grown crops that occur in the Nang Rong District - cassava, heavy rice, and jasmine rice, as well as an emerging crop, fruit trees. Our results indicate that while the natural environment (e.g., elevation and soils) is often the dominant factor in crop likelihood, the likelihood is also influenced by household characteristics, such as household assets and conditions of the neighborhood or built environment. Furthermore, the shape of the land use-environment curves illustrates the non-continuous and non-linear nature of these relationships. This approach demonstrates a novel method of understanding non-linear relationships between land and people. The article concludes with a proposed method for integrating the niche-based rules of land use allocation into a dynamic land use model that can address both allocation and quantity of agricultural crops.
Heumann, Benjamin W.; Walsh, Stephen J.; Verdery, Ashton M.; McDaniel, Phillip M.; Rindfuss, Ronald R.
Understanding the pattern-process relations of land use/land cover change is an important area of research that provides key insights into human-environment interactions. The suitability or likelihood of occurrence of land use such as agricultural crop types across a human-managed landscape is a central consideration. Recent advances in niche-based, geographic species distribution modeling (SDM) offer a novel approach to understanding land suitability and land use decisions. SDM links species presence-location data with geospatial information and uses machine learning algorithms to develop non-linear and discontinuous species-environment relationships. Here, we apply the MaxEnt (Maximum Entropy) model for land suitability modeling by adapting niche theory to a human-managed landscape. In this article, we use data from an agricultural district in Northeastern Thailand as a case study for examining the relationships between the natural, built, and social environments and the likelihood of crop choice for the commonly grown crops that occur in the Nang Rong District – cassava, heavy rice, and jasmine rice, as well as an emerging crop, fruit trees. Our results indicate that while the natural environment (e.g., elevation and soils) is often the dominant factor in crop likelihood, the likelihood is also influenced by household characteristics, such as household assets and conditions of the neighborhood or built environment. Furthermore, the shape of the land use-environment curves illustrates the non-continuous and non-linear nature of these relationships. This approach demonstrates a novel method of understanding non-linear relationships between land and people. The article concludes with a proposed method for integrating the niche-based rules of land use allocation into a dynamic land use model that can address both allocation and quantity of agricultural crops. PMID:24187378
Martínez, Brezo; Arenas, Francisco; Trilla, Alba; Viejo, Rosa M; Carreño, Francisco
Species distribution models (SDM) are a useful tool for predicting species range shifts in response to global warming. However, they do not explore the mechanisms underlying biological processes, making it difficult to predict shifts outside the environmental gradient where the model was trained. In this study, we combine correlative SDMs and knowledge on physiological limits to provide more robust predictions. The thermal thresholds obtained in growth and survival experiments were used as proxies of the fundamental niches of two foundational marine macrophytes. The geographic projections of these species' distributions obtained using these thresholds and existing SDMs were similar in areas where the species are either absent-rare or frequent and where their potential and realized niches match, reaching consensus predictions. The cold-temperate foundational seaweed Himanthalia elongata was predicted to become extinct at its southern limit in northern Spain in response to global warming, whereas the occupancy of southern-lusitanic Bifurcaria bifurcata was expected to increase. Combined approaches such as this one may also highlight geographic areas where models disagree potentially due to biotic factors. Physiological thresholds alone tended to over-predict species prevalence, as they cannot identify absences in climatic conditions within the species' range of physiological tolerance or at the optima. Although SDMs tended to have higher sensitivity than threshold models, they may include regressions that do not reflect causal mechanisms, constraining their predictive power. We present a simple example of how combining correlative and mechanistic knowledge provides a rapid way to gain insight into a species' niche resulting in consistent predictions and highlighting potential sources of uncertainty in forecasted responses to climate change.
Wan, Ji-Zhong; Wang, Chun-Jing; Tan, Jing-Fang; Yu, Fei-Hai
Testing climatic niche divergence and modeling habitat suitability under conditions of climate change are important for developing strategies to limit the introduction and expansion of alien invasive weeds (AIWs) and providing important ecological and evolutionary insights. We assessed climatic niches in both native and invasive ranges as well as habitat suitability under climate change for eight representative Chinese AIWs from the American continent. We used climatic variables associated with occurrence records and developed ecological niche models with Maxent. Interestingly, the climatic niches of all eight AIWs diverged significantly between the native and invasive ranges (the American continent and China). Furthermore, the AIWs showed larger climatic niche breadths in the invasive ranges than in the native ranges. Our results suggest that climatic niche shifts between native and invasive ranges occurred. Thus, the occurrence records of both native and invasive regions must be considered when modeling and predicting the spatial distributions of AIWs under current and future climate scenarios. Owing to high habitat suitability, AIWs were more likely to expand into regions of low latitude, and future climate change was predicted to result in a shift in the AIWs in Qinghai and Tibet (regions of higher altitude) as well as Heilongjiang, Jilin, Liaoning, Inner Mongolia, and Gansu (regions of higher latitude). Our results suggest that we need measures to prevent and control AIW expansion at the country-wide level.
Pauliuk, Stefan; Arvesen, Anders; Stadler, Konstantin; Hertwich, Edgar G.
Technology-rich integrated assessment models (IAMs) address possible technology mixes and future costs of climate change mitigation by generating scenarios for the future industrial system. Industrial ecology (IE) focuses on the empirical analysis of this system. We conduct an in-depth review of five major IAMs from an IE perspective and reveal differences between the two fields regarding the modelling of linkages in the industrial system, focussing on AIM/CGE, GCAM, IMAGE, MESSAGE, and REMIND. IAMs ignore material cycles and recycling, incoherently describe the life-cycle impacts of technology, and miss linkages regarding buildings and infrastructure. Adding IE system linkages to IAMs adds new constraints and allows for studying new mitigation options, both of which may lead to more robust and policy-relevant mitigation scenarios.
Sweet cherries, Prunus avium (L.) L., grown in the western United States are exported to many countries around the world. Some of these countries have enforced strict quarantine rules and trade restrictions due to concerns about the potential establishment and subsequent spread of western cherry fru...
Winemiller, Kirk O; Fitzgerald, Daniel B; Bower, Luke M; Pianka, Eric R
Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche 'dimensions', or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait-value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification.
Gilbert, Benjamin; Lechowicz, Martin J.
A fundamental goal of ecology is to understand what controls the distribution and abundance of species. Both environmental niches and trade-offs among species in dispersal and competitive ability have traditionally been cited as determinants of plant community composition. More recently, neutral models have shown that communities of species with identical life-history characteristics and no adaptation to environmental niches can form spatial distribution patterns similar to those found in nature, so long as the species have a limited dispersal distance. If there is a strong correlation between geographic distance and change in environmental conditions, however, such spatial patterns can arise through either neutral or niche-based processes. To test these competing theories, we developed a sampling design that decoupled distance and environment in the understory plant communities of an old-growth, temperate forest. We found strong evidence of niche-structuring but almost no support for neutral predictions. Dispersal limitation acted in conjunction with environmental gradients to determine species' distributions, and both functional and phylogenetic constraints appear to contribute to the niche differentiation that structures community assembly. Our results indicate that testing a neutral hypothesis without accounting for environmental gradients will at best cause unexplained variation in plant distributions and may well provide misleading support for neutrality because of a correlation between geographic distance and environment. PMID:15128948
Yu, Vionnie W.C.; Lymperi, Stefania; Ferraro, Francesca; Scadden, David T.
The bone marrow niche is recognized as a central player in maintaining and regulating the behavior of hematopoietic stem and progenitor cells. Specific gain-of and loss-of function experiments perturbing a range of osteolineage cells or their secreted proteins had been shown to affect stem cell maintenance (Calvi et al, 2003 ; Stier et al., 2005 ; Zhang et al., 2003 ; Nilsson et al., 2005 ; Greenbaum et al., 2013 ) and engraftment (Adam et al., 2006, 2009 , ). We used specific in vivo cell deletion approaches to dissect the niche cell-parenchymal cell dependency in a complex bone marrow microenvironment. Endogenous deletion of osteocalcin-expressing (Ocn+) cells led to a loss of T immune cells (Yu et al., 2015 . Ocn+ cells express the Notch ligand DLL4 to communicate with T-competent progenitors, and thereby ensuring T precursor production and expression of chemotactic molecules on their cell surface for subsequent thymic seeding. In contrast, depletion of osterix-expressing (Osx+) osteoprogenitors led to reduced B immune cells. These distinct hematopoietic phenotypes suggest specific pairing of mesenchymal niche cells and parenchymal hematopoietic cells in the bone marrow to create unique functional units to support hematopoiesis. Here, we present the global gene expression profiles of these osteolineage subtypes utilizing a triple fluorescent transgenic mouse model (OsxCre+;Rosa-mCh+;Ocn:Topaz+) that labels Osx+ cells red, Ocn+ cells green, and Osx+ Ocn+ cells yellow. This system allows isolation of distinct osteolineage subsets within the same animal by flow cytometry. Array data that have been described in our study  are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042. Differences in gene expression may correlate with functional difference in supporting hematopoiesis. PMID:26484277
Brieland, J; McClain, M; LeGendre, M; Engleberg, C
The potential role of inhaled protozoa as a niche for intrapulmonary replication of Legionella pneumophila was investigated in vivo with mutant strains of L. pneumophila which have reduced virulence for the amoeba Hartmannella vermiformis. L. pneumophila AA488 and AA502 were derived from wild-type strain AA100 after transposon mutagenesis. These mutants have reduced virulence for H. vermiformis but are fully virulent for mononuclear phagocytic cells. A/J mice, which are susceptible to replicative L. pneumophila lung infections, were inoculated intratracheally with L. pneumophila AA100, AA488, or AA502 (10 bacteria per mouse) or were coinoculated with one of the L. pneumophila strains (10 bacteria per mouse) and uninfected H. vermiformis (10 amoebae per mouse). The effect of coinoculation with H. vermiformis on intrapulmonary growth of each L. pneumophila strain was subsequently assessed. In agreement with our previous studies, coinoculation with H. vermiformis significantly enhanced intrapulmonary growth of the parent L. pneumophila strain (AA100). In contrast, intrapulmonary growth of L. pneumophila AA488 or AA502 was not significantly enhanced by coinoculation of mice with H. vermiformis. These studies demonstrate that L. pneumophila virulence for amoebae is required for maximal intrapulmonary growth of the bacteria in mice coinoculated with H. vermiformis and support the hypothesis that inhaled amoebae may potentiate intrapulmonary growth of L. pneumophila by providing a niche for bacterial replication. PMID:9353084
Lafferty, Kevin D.; Dunne, Jennifer A.
Stochastic ecological network occupancy (SENO) models predict the probability that species will occur in a sample of an ecological network. In this review, we introduce SENO models as a means to fill a gap in the theoretical toolkit of ecologists. As input, SENO models use a topological interaction network and rates of colonization and extinction (including consumer effects) for each species. A SENO model then simulates the ecological network over time, resulting in a series of sub-networks that can be used to identify commonly encountered community modules. The proportion of time a species is present in a patch gives its expected probability of occurrence, whose sum across species gives expected species richness. To illustrate their utility, we provide simple examples of how SENO models can be used to investigate how topological complexity, species interactions, species traits, and spatial scale affect communities in space and time. They can categorize species as biodiversity facilitators, contributors, or inhibitors, making this approach promising for ecosystem-based management of invasive, threatened, or exploited species.
Fransz, H. G.; Mommaerts, J. P.; Radach, G.
North Sea ecosystem models published in accessible literature are partitioned into groups with respect to their emphasis on significance and detail of different trophic levels of the ecosystem. These subsets are treated separately in the three main chapters, which deal with relationships with physical dynamics, lower trophic level interactions and higher trophic level interactions. They are preceded by chapters that introduce the scope of the models, the history of modelling approaches, main purposes and specific aims, general aspects of internal structure, and modelling techniques applied. The main chapters compare the process descriptions characteristic of the subsets of models, and discuss aims and results with emphasis on significance and contribution of the processes considered. The chapter on plankton dynamics in relation to physical dynamics relates plankton responses in the mixed layer to changes in the physical environment. Attention is given to seasonal forcing functions, the coupling of horizontal and vertical plankton distributions, the flow of matter and the sensitivity of the plankton system. The chapter on lower trophic levels deals with primary production and its limiting factors, nutrient cycles, eutrophication, the microbial loop, and mineralization of organic matter in the pelagic and benthic compartments. The chapter on higher trophic levels highlights predator-prey interactions, the impact of grazing, and the significance of predation for system stability. A final chapter discusses what has been achieved so far with models of North Sea ecosystems and what must be aimed at in the future. It argues for lucidity and more methodology in simplification to the degree allowed by the questions to be solved, more attention for models as carriers of unifying concepts in marine ecological theory, technical solutions in handling different time and space scales for different processes and distributions, cooperation of different disciplines to find answers
Jager, H.I.; Ashwood, T.L.; Jackson, B.L.; King, A.W.
The authors evaluated the sensitivity of a habitat model and a source-sink population model to spatial uncertainty in landscapes with different statistical properties and for hypothetical species with different habitat requirements. Sequential indicator simulation generated alternative landscapes from a source map. Their results showed that spatial uncertainty was highest for landscapes in which suitable habitat was rare and spatially uncorrelated. Although, they were able to exert some control over the degree of spatial uncertainty by varying the sampling density drawn from the source map, intrinsic spatial properties (i.e., average frequency and degree of spatial autocorrelation) played a dominant role in determining variation among realized maps. To evaluate the ecological significance of landscape variation, they compared the variation in predictions from a simple habitat model to variation among landscapes for three species types. Spatial uncertainty in predictions of the amount of source habitat depended on both the spatial life history characteristics of the species and the statistical attributes of the synthetic landscapes. Species differences were greatest when the landscape contained a high proportion of suitable habitat. The predicted amount of source habitat was greater for edge-dependent (interior) species in landscapes with spatially uncorrelated(correlated) suitable habitat. A source-sink model demonstrated that, although variation among landscapes resulted in relatively little variation in overall population growth rate, this spatial uncertainty was sufficient in some situations, to produce qualitatively different predictions about population viability (i.e., population decline vs. increase).
Matthews, Thomas J; Whittaker, Robert J
Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research. PMID:25360266
Kendal, Jeremy; Tehrani, Jamshid J.; Odling-Smee, John
Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene–culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue. PMID:21320894
Davis, S.M.; Loftus, W.F.; Gaiser, E.E.; Huffman, A.E.
About 190,000 ha of higher-elevation marl prairies flank either side of Shark River Slough in the southern Everglades. Water levels typically drop below the ground surface each year in this landscape. Consequently, peat soil accretion is inhibited, and substrates consist either of calcitic marl produced by algal periphyton mats or exposed limestone bedrock. The southern marl prairies support complex mosaics of wet prairie, sawgrass sawgrass (Cladium jamaicense), tree islands, and tropical hammock communities and a high diversity of plant species. However, relatively short hydroperiods and annual dry downs provide stressful conditions for aquatic fauna, affecting survival in the dry season when surface water is absent. Here, we present a conceptual ecological model developed for this landscape through scientific concensus, use of empirical data, and modeling. The two major societal drivers affecting the southern marl prairies are water management practices and agricultural and urban development. These drivers lead to five groups of ecosystem stressors: loss of spatial extent and connectivity, shortened hydroperiod and increased drought severity, extended hydroperiod and drying pattern reversals, introduction and spread of non-native trees, and introduction and spread of non-native fishes. Major ecological attributes include periphyton mats, plant species diversity and community mosaic, Cape Sable seaside sparrow (Ammodramus maritimus mirabilis), marsh fishes and associated aquatic fauna prey base, American alligator (Alligator mississippiensis), and wading bird early dry season foraging. Water management and development are hypothesized to have a negative effect on the ecological attributes of the southern marl prairies in the following ways. Periphyton mats have decreased in cover in areas where hydroperiod has been significantly reduced and changed in community composition due to inverse responses to increased nutrient availability. Plant species diversity and
Wielstra, Ben; Arntzen, Jan W.
If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation. PMID:24743746
Ebrahimi, Sahar; Bordbar, Ali; Rastaghi, Ahmad R Esmaeili; Parvizi, Parviz
Cutaneous leishmaniasis (CL) is a complex vector-borne disease caused by Leishmania parasites that are transmitted by the bite of several species of infected female phlebotomine sand flies. Monthly factor analysis of climatic variables indicated fundamental variables. Principal component-based regionalization was used for recognition of climatic zones using a clustering integrated method that identified five climatic zones based on factor analysis. To investigate spatial distribution of the sand fly species, the kriging method was used as an advanced geostatistical procedure in the ArcGIS modeling system that is beneficial to design measurement plans and to predict the transmission cycle in various regions of Khuzestan province, southwest of Iran. However, more than an 80% probability of P. papatasi was observed in rainy and temperate bio-climatic zones with a high potential of CL transmission. Finding P. sergenti revealed the probability of transmission and distribution patterns of a non-native vector of CL in related zones. These findings could be used as models indicating climatic zones and environmental variables connected to sand fly presence and vector distribution. Furthermore, this information is appropriate for future research efforts into the ecology of Phlebotomine sand flies and for the prevention of CL vector transmission as a public health priority.
Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A
Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process).
Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational po...
A Conceptual Framework for Evaluating the Domains of Applicability of Ecological Models and its Implementation in the Ecological Production Function Library - International Society for Ecological Modelling Conference
The use of computational ecological models to inform environmental management and policy has proliferated in the past 25 years. These models have become essential tools as linkages and feedbacks between human actions and ecological responses can be complex, and as funds for sampl...
Ibarra-Cerdeña, Carlos N.; Zaldívar-Riverón, Alejandro; Peterson, A. Townsend; Sánchez-Cordero, Víctor; Ramsey, Janine M.
The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios. PMID:25356550
Lohrmann, David K.
Background: A complementary ecological model of the coordinated school health program (CSHP) reflecting 20 years of evolved changes is proposed. Ecology refers to the complex interrelationship between intrapersonal factors, interpersonal processes and primary groups, institutional factors, community factors, and public policy. Methods: Public…
Foote, Andrew D.; Newton, Jason; Ávila-Arcos, María C.; Kampmann, Marie-Louise; Samaniego, Jose A.; Post, Klaas; Rosing-Asvid, Aqqalu; Sinding, Mikkel-Holger S.; Gilbert, M. Thomas P.
Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish. PMID:23945688
Foote, Andrew D; Newton, Jason; Ávila-Arcos, María C; Kampmann, Marie-Louise; Samaniego, Jose A; Post, Klaas; Rosing-Asvid, Aqqalu; Sinding, Mikkel-Holger S; Gilbert, M Thomas P
Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.
Dickens, Benjamin; Fisher, Charles K.; Mehta, Pankaj
A fundamental problem in community ecology is understanding how ecological processes such as selection, drift, and immigration give rise to observed patterns in species composition and diversity. Here, we analyze a recently introduced, analytically tractable, presence-absence (PA) model for community assembly, and we use it to ask how ecological traits such as the strength of competition, the amount of diversity, and demographic and environmental stochasticity affect species composition in a community. In the PA model, species are treated as stochastic binary variables that can either be present or absent in a community: species can immigrate into the community from a regional species pool and can go extinct due to competition and stochasticity. Building upon previous work, we show that, despite its simplicity, the PA model reproduces the qualitative features of more complicated models of community assembly. In agreement with recent studies of large, competitive Lotka-Volterra systems, the PA model exhibits distinct ecological behaviors organized around a special ("critical") point corresponding to Hubbell's neutral theory of biodiversity. These results suggest that the concepts of ecological "phases" and phase diagrams can provide a powerful framework for thinking about community ecology, and that the PA model captures the essential ecological dynamics of community assembly.
Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.
In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in
Background Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner. Results We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks. Conclusions These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully
Host immunity is a major driver of pathogen evolution and thus a major determinant of pathogen diversity. Explanations for pathogen diversity traditionally assume simple interactions between pathogens and the immune system, a view encapsulated by the susceptible-infected-recovered (SIR) model. However, there is growing evidence that the complexity of many host-pathogen interactions is dynamically important. This revised perspective requires broadening the definition of a pathogen's immunological phenotype, or what can be thought of as its immunological niche. After reviewing evidence that interactions between pathogens and host immunity drive much of pathogen evolution, I introduce the concept of a pathogen's immunological phenotype. Models that depart from the SIR paradigm demonstrate the utility of this perspective and show that it is particularly useful in understanding vaccine-induced evolution. This paper highlights questions in immunology, evolution, and ecology that must be answered to advance theories of pathogen diversity.
Sillero, N; Reis, M; Vieira, C P; Vieira, J; Morales-Hojas, R
The study of ecological niche evolution is fundamental for understanding how the environment influences species' geographical distributions and their adaptation to divergent environments. Here, we present a study of the ecological niche, demographic history and thermal performance (locomotor activity, developmental time and fertility/viability) of the temperate species Drosophila americana and its two chromosomal forms. Temperature is the environmental factor that contributes most to the species' and chromosomal forms' ecological niches, although precipitation is also important in the model of the southern populations. The past distribution model of the species predicts a drastic reduction in the suitable area for the distribution of the species during the last glacial maximum (LGM), suggesting a strong bottleneck. However, DNA analyses did not detect a bottleneck signature during the LGM. These contrasting results could indicate that D. americana niche preference evolves with environmental change, and thus, there is no evidence to support niche conservatism in this species. Thermal performance experiments show no difference in the locomotor activity across a temperature range of 15 to 38 °C between flies from the north and the south of its distribution. However, we found significant differences in developmental time and fertility/viability between the two chromosomal forms at the model's optimal temperatures for the two forms. However, results do not indicate that they perform better for the traits studied here in their respective optimal niche temperatures. This suggests that behaviour plays an important role in thermoregulation, supporting the capacity of this species to adapt to different climatic conditions across its latitudinal distribution.
Argôlo-Filho, Ronaldo Costa; Loguercio, Leandro Lopes
Bacillus thuringiensis (Bt) has been used successfully as a biopesticide for more than 60 years. More recently, genes encoding their toxins have been used to transform plants and other organisms. Despite the large amount of research on this bacterium, its true ecology is still a matter of debate, with two major viewpoints dominating: while some understand Bt as an insect pathogen, others see it as a saprophytic bacteria from soil. In this context, Bt’s pathogenicity to other taxa and the possibility that insects may not be the primary targets of Bt are also ideas that further complicate this scenario. The existence of conflicting research results, the difficulty in developing broader ecological and genetics studies, and the great genetic plasticity of this species has cluttered a definitive concept. In this review, we gathered information on the aspects of Bt ecology that are often ignored, in the attempt to clarify the lifestyle, mechanisms of transmission and target host range of this bacterial species. As a result, we propose an integrated view to account for Bt ecology. Although Bt is indeed a pathogenic bacterium that possesses a broad arsenal for virulence and defense mechanisms, as well as a wide range of target hosts, this seems to be an adaptation to specific ecological changes acting on a versatile and cosmopolitan environmental bacterium. Bt pathogenicity and host-specificity was favored evolutionarily by increased populations of certain insect species (or other host animals), whose availability for colonization were mostly caused by anthropogenic activities. These have generated the conditions for ecological imbalances that favored dominance of specific populations of insects, arachnids, nematodes, etc., in certain areas, with narrower genetic backgrounds. These conditions provided the selective pressure for development of new hosts for pathogenic interactions, and so, host specificity of certain strains. PMID:26462580
Dickens, Benjamin; Fisher, Charles; Mehta, Pankaj; Pankaj Mehta Biophysics Theory Group Team
A fundamental problem in community ecology is to understand how ecological processes such as selection, drift, and immigration yield observed patterns in species composition and diversity. Here, we present an analytically tractable, presence-absence (PA) model for community assembly and use it to ask how ecological traits such as the strength of competition, diversity in competition, and stochasticity affect species composition in a community. In our PA model, we treat species as stochastic binary variables that can either be present or absent in a community: species can immigrate into the community from a regional species pool and can go extinct due to competition and stochasticity. Despite its simplicity, the PA model reproduces the qualitative features of more complicated models of community assembly. In agreement with recent work on large, competitive Lotka-Volterra systems, the PA model exhibits distinct ecological behaviors organized around a special (``critical'') point corresponding to Hubbell's neutral theory of biodiversity. Our results suggest that the concepts of ``phases'' and phase diagrams can provide a powerful framework for thinking about community ecology and that the PA model captures the essential ecological dynamics of community assembly. Pm was supported by a Simons Investigator in the Mathematical Modeling of Living Systems and a Sloan Research Fellowship.
Rader, Jonathan A; Newsome, Seth D; Sabat, Pablo; Chesser, R Terry; Dillon, Michael E; Martínez Del Rio, Carlos
Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges. We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes. We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology. We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology. Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies.
Winck, Gisele R; Hatano, Fabio; Vrcibradic, Davor; VAN Sluys, Monique; Rocha, Carlos F D
Communities are structured by interactions of historical and ecological factors, which influence the use of different resources in time and space. We acquired data on time of activity, microhabitat use and diet of a lizard assemblage from a sand dune habitat in a coastal area, southeastern Brazil (Restinga de Jurubatiba). We analyzed the data of niche overlap among species in these three axes (temporal, spatial and trophic) using null models. We found a significant overlap within the trophic niche, whereas the overlap for the other axes did not differ from the expected. Based on this result, we discuss the factors acting on the structure of the local lizard community.
The niche construction model postulates that human bio-social evolution is composed of three inheritance domains, genetic, cultural and ecological, linked by feedback selection. This paper argues that many kinds of archaeological data can serve as proxies for human niche construction processes, and presents a method for investigating specific niche construction hypotheses. To illustrate this method, the repeated emergence of specialized reindeer (Rangifer tarandus) hunting/herding economies during the Late Palaeolithic (ca 14.7–11.5 kyr BP) in southern Scandinavia is analysed from a niche construction/triple-inheritance perspective. This economic relationship resulted in the eventual domestication of Rangifer. The hypothesis of whether domestication was achieved as early as the Late Palaeolithic, and whether this required the use of domesticated dogs (Canis familiaris) as hunting, herding or transport aids, is tested via a comparative analysis using material culture-based phylogenies and ecological datasets in relation to demographic/genetic proxies. Only weak evidence for sustained niche construction behaviours by prehistoric hunter–gatherer in southern Scandinavia is found, but this study nonetheless provides interesting insights into the likely processes of dog and reindeer domestication, and into processes of adaptation in Late Glacial foragers. PMID:21320895
Marx, Christopher J
Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the evolutionary and ecological processes that are occurring? For example, can we determine if a species is adapting to one niche, or if it is diversifying into multiple specialists that inhabit distinct niches? Fortunately, adaptation of populations in the laboratory can serve as a model to test our ability to make such inferences about evolution and ecology from sequencing. Even adaptation to a single niche can give rise to complex temporal dynamics due to the transient presence of multiple competing lineages. If there are multiple niches, this complexity is augmented by segmentation of the population into multiple specialists that can each continue to evolve within their own niche. For a known example of parallel diversification that occurred in the laboratory, sequencing data gave surprisingly few obvious, unambiguous signs of the ecological complexity present. Whereas experimental systems are open to direct experimentation to test hypotheses of selection or ecological interaction, the difficulty in "seeing ecology" from sequencing for even such a simple system suggests translation to communities like the human microbiome will be quite challenging. This will require both improved empirical methods to enhance the depth and time resolution for the relevant polymorphisms and novel statistical approaches to rigorously examine time-series data for signs of various evolutionary and ecological phenomena within and between species.
Kumar, Sunil; Neven, Lisa G; Zhu, Hongyu; Zhang, Runzhi
Accurate assessment of insect pest establishment risk is needed by national plant protection organizations to negotiate international trade of horticultural commodities that can potentially carry the pests and result in inadvertent introductions in the importing countries. We used mechanistic and correlative niche models to quantify and map the global patterns of the potential for establishment of codling moth (Cydia pomonella L.), a major pest of apples, peaches, pears, and other pome and stone fruits, and a quarantine pest in countries where it currently does not occur. The mechanistic model CLIMEX was calibrated using species-specific physiological tolerance thresholds, whereas the correlative model MaxEnt used species occurrences and climatic spatial data. Projected potential distribution from both models conformed well to the current known distribution of codling moth. None of the models predicted suitable environmental conditions in countries located between 20°N and 20°S potentially because of shorter photoperiod, and lack of chilling requirement (<60 d at ≤10°C) in these areas for codling moth to break diapause. Models predicted suitable conditions in South Korea and Japan where codling moth currently does not occur but where its preferred host species (i.e., apple) is present. Average annual temperature and latitude were the main environmental variables associated with codling moth distribution at global level. The predictive models developed in this study present the global risk of establishment of codling moth, and can be used for monitoring potential introductions of codling moth in different countries and by policy makers and trade negotiators in making science-based decisions.
Lai, WY; Li, YY; Mak, SK; Ho, FC; Chow, ST; Chooi, WH; Chow, CH; Leung, AY
Mesenchymal stem/stromal cells (MSCs) and osteoblasts are important niche cells for hematopoietic stem cells (HSCs) in bone marrow osteoblastic niche. Here, we aim to partially reconstitute the bone marrow HSC niche in vitro using collagen microencapsulation for investigation of the interactions between HSCs and MSCs. Mouse MSCs (mMSCs) microencapsulated in collagen were osteogenically differentiated to derive a bone-like matrix consisting of osteocalcin, osteopontin, and calcium deposits and secreted bone morphogenic protein 2 (BMP2). Decellularized bone-like matrix was seeded with fluorescence-labeled human MSCs and HSCs. Comparing with pure collagen scaffold, significantly more HSCs and HSC–MSC pairs per unit area were found in the decellularized bone-like matrix. Moreover, incubation with excess neutralizing antibody of BMP2 resulted in a significantly higher number of HSC per unit area than that without in the decellularized matrix. This work suggests that the osteogenic differentiated MSC–collagen microsphere is a valuable three-dimensional in vitro model to elucidate cell–cell and cell–matrix interactions in HSC niche. PMID:24555007
Crowther, Thomas W.; Maynard, Daniel S.; Crowther, Terence R.; Peccia, Jordan; Smith, Jeffrey R.; Bradford, Mark A.
Fungi are prominent components of most terrestrial ecosystems, both in terms of biomass and ecosystem functioning, but the hyper-diverse nature of most communities has obscured the search for unifying principles governing community organization. In particular, unlike plants and animals, observational studies provide little evidence for the existence of niche processes in structuring fungal communities at broad spatial scales. This limits our capacity to predict how communities, and their functioning, vary across landscapes. We outline how a shift in focus, from taxonomy toward functional traits, might prove to be valuable in the search for general patterns in fungal ecology. We build on theoretical advances in plant and animal ecology to provide an empirical framework for a trait-based approach in fungal community ecology. Drawing upon specific characteristics of the fungal system, we highlight the significance of drought stress and combat in structuring free-living fungal communities. We propose a conceptual model to formalize how trade-offs between stress-tolerance and combative dominance are likely to organize communities across environmental gradients. Given that the survival of a fungus in a given environment is contingent on its ability to tolerate antagonistic competitors, measuring variation in combat trait expression along environmental gradients provides a means of elucidating realized, from fundamental niche spaces. We conclude that, using a trait-based understanding of how niche processes structure fungal communities across time and space, we can ultimately link communities with ecosystem functioning. Our trait-based framework highlights fundamental uncertainties that require testing in the fungal system, given their potential to uncover general mechanisms in fungal ecology. PMID:25400630
Morrison, Sean J.; Scadden, David T.
Preface Niches are local tissue microenvironments that maintain and regulate stem cells. Haematopoiesis provides a paradigm for understanding mammalian stem cells and their niches, yet the haematopoietic stem cell (HSC) niche remains incompletely defined and beset by competing models. Here we review progress in elucidating the location and cellular components of the HSC niche in the bone marrow. The niche is perivascular, created partly by mesenchymal stromal cells and endothelial cells and often, but not always, located near trabecular bone. Outstanding questions concern the cellular complexity of the niche, the role of the endosteum, and functional heterogeneity among perivascular microenvironments. PMID:24429631
Zhdanov, Vladimir P.
Stem cells, maintaining tissue homeostasis, are nurtured in microscopic niches formed of so-called environmental cells. The kinetics of proliferation and differentiation of stem cells in such niches depend on their interaction with the messenger proteins secreted by environmental cells. We propose a generic mean-field kinetic model of the propagation of such signals. To motivate our study, we briefly describe a stem-cell niche in the Drosophila ovary. Our model is however applicable to other niches as well. In particular, it helps one to understand the necessary conditions for the niche function. For example, the model predicts that in the case of the Drosophila ovary each germline stem cell should have in the external membrane at least 700 receptors interacting with the signaling Dpp and Gpp proteins emanating from the cap cells.
Escobar, Luis E.; Qiao, Huijie; Phelps, Nicholas B. D.; Wagner, Carli K.; Larkin, Daniel J.
Nitellopsis obtusa (starry stonewort) is a dioecious green alga native to Europe and Asia that has emerged as an aquatic invasive species in North America. Nitellopsis obtusa is rare across large portions of its native range, but has spread rapidly in northern-tier lakes in the United States, where it can interfere with recreation and may displace native species. Little is known about the invasion ecology of N. obtusa, making it difficult to forecast future expansion. Using ecological niche modeling we investigated environmental variables associated with invasion risk. We used species records, climate data, and remotely sensed environmental variables to characterize the species’ multidimensional distribution. We found that N. obtusa is exploiting novel ecological niche space in its introduced range, which may help explain its invasiveness. While the fundamental niche of N. obtusa may be stable, there appears to have been a shift in its realized niche associated with invasion in North America. Large portions of the United States are predicted to constitute highly suitable habitat for N. obtusa. Our results can inform early detection and rapid response efforts targeting N. obtusa and provide testable estimates of the physiological tolerances of this species as a baseline for future empirical research. PMID:27363541
Background/Question/Methods The science of stable isotope mixing models has tended towards the development of modeling products (e.g. IsoSource, MixSIR, SIAR), where methodological advances or syntheses of the current state of the art are published in parity with software packa...
Ryan, Casey M; Williams, Mathew; Grace, John; Woollen, Emily; Lehmann, Caroline E R
Tree phenology mediates land-atmosphere mass and energy exchange and is a determinant of ecosystem structure and function. In the dry tropics, including African savannas, many trees grow new leaves during the dry season - weeks or months before the rains typically start. This syndrome of pre-rain green-up has long been recognized at small scales, but the high spatial and interspecific variability in leaf phenology has precluded regional generalizations. We used remote sensing data to show that this precocious phenology is ubiquitous across the woodlands and savannas of southern tropical Africa. In 70% of the study area, green-up preceded rain onset by > 20 d (42% > 40 d). All the main vegetation formations exhibited pre-rain green-up, by as much as 53 ± 18 d (in the wet miombo). Green-up showed low interannual variability (SD between years = 11 d), and high spatial variability (> 100 d). These results are consistent with a high degree of local phenological adaptation, and an insolation trigger of green-up. Tree-tree competition and niche separation may explain the ubiquity of this precocious phenology. The ubiquity of pre-rain green-up described here challenges existing model representations and suggests resistance (but not necessarily resilience) to the delay in rain onset predicted under climate change.
GöThlich, L.; Oschlies, A.
For marine biogeochemical models used in simulations of climate change scenarios, the ability to account for adaptability of marine ecosystems to environmental change becomes a concern. The potential for adaptation is expected to be larger for a diverse ecosystem compared to a monoculture of a single type of (model) algae, such as typically included in biogeochemical models. Recent attempts to simulate phytoplankton diversity in global marine ecosystem models display remarkable qualitative agreement with observed patterns of species distributions. However, modeled species diversity tends to be systematically lower than observed and, in many regions, is smaller than the number of potentially limiting nutrients. According to resource competition theory, the maximum number of coexisting species at equilibrium equals the number of limiting resources. By simulating phytoplankton communities in a chemostat model and in a global circulation model, we show here that a systematic underestimate of phytoplankton diversity may result from the standard modeling assumption of identical stoichiometry for the different phytoplankton types. Implementing stoichiometric variation among the different marine algae types in the models allows species to generate different resource supply niches via their own ecological impact. This is shown to increase the level of phytoplankton coexistence both in a chemostat model and in a global self-assembling ecosystem model.
Ganju, Neil K.; Brush, Mark J.; Rashleigh, Brenda; Aretxabaleta, Alfredo L.; del Barrio, Pilar; Grear, Jason S.; Harris, Lora A.; Lake, Samuel J.; McCardell, Grant; O’Donnell, James; Ralston, David K.; Signell, Richard P.; Testa, Jeremy M.; Vaudrey, Jamie M.P.
Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear, because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy. PMID:27721675
Suter, G.W., II
Ecological conceptual models are the result of the problem formulation phase of an ecological risk assessment, which is an important component of the Remedial Investigation process. They present hypotheses of how the site contaminants might affect the site ecology. The contaminant sources, routes, media, routes, and endpoint receptors are presented in the form of a flow chart. This guide is for preparing the conceptual models; use of this guide will standardize the models so that they will be of high quality, useful to the assessment process, and sufficiently consistent so that connections between sources of exposure and receptors can be extended across operable units (OU). Generic conceptual models are presented for source, aquatic integrator, groundwater integrator, and terrestrial OUs.
Sweeney, Elizabeth; Roberts, Douglas; Lin, Angela; Guldberg, Robert
Despite the appreciated interdependence of skeletal and hematopoietic development, the cell and matrix components of the hematopoietic niche remain to be fully defined. Utilizing mice with disrupted function of collagen X (ColX), a major hypertrophic cartilage matrix protein associated with endochondral ossification, our data identified a cytokine defect in trabecular bone cells at the chondro-osseous hematopoietic niche as a cause for aberrant B lymphopoiesis in these mice. Specifically, analysis of ColX transgenic and null mouse chondro-osseous regions via micro-computed tomography revealed an altered trabecular bone environment. Additionally, cocultures with hematopoietic and chondro-osseous cell types highlighted impaired hematopoietic support by ColX transgenic and null mouse derived trabecular bone cells. Further, cytokine arrays with conditioned media from the trabecular osteoblast cocultures suggested an aberrant hematopoietic cytokine milieu within the chondro-osseous niche of the ColX deficient mice. Accordingly, B lymphopoiesis was rescued in the ColX mouse derived trabecular osteoblast cocultures with interlukin-7, stem cell factor, and stromal derived factor-1 supplementation. Moreover, B cell development was restored in vivo after injections of interlukin-7. These data support our hypothesis that endrochondrally-derived trabecular bone cells and matrix constituents provide cytokine-rich niches for hematopoiesis. Furthermore, this study contributes to the emerging concept that niche defects may underlie certain immuno-osseous and hematopoietic disorders. PMID:23656481
Ecological risk assessment typically focuses on animal populations as endpoints for regulatory ecotoxicology. Scientists at USEPA are developing models for animal populations exposed to a wide range of chemicals from pesticides to emerging contaminants. Modeled taxa include aquatic and terrestrial invertebrates, fish, amphibians, and birds, and employ a wide range of methods, from matrix-based projection models to mechanistic bioenergetics models and spatially explicit population models. not applicable
Sugihara, George; Bersier, Louis-Félix; Southwood, T. Richard E.; Pimm, Stuart L.; May, Robert M.
We examine a hypothesized relationship between two descriptions of community structure: the niche-overlap dendrogram that describes the ecological similarities of species and the pattern of relative abundances. Specifically, we examine the way in which this relationship follows from the niche hierarchy model, whose fundamental assumption is a direct connection between abundances and underlying hierarchical community organization. We test three important, although correlated, predictions of the niche hierarchy model and show that they are upheld in a set of 11 communities (encompassing fishes, amphibians, lizards, and birds) where both abundances and dendrograms were reported. First, species that are highly nested in the dendrogram are on average less abundant than species from branches less subdivided. Second, and more significantly, more equitable community abundances are associated with more evenly branched dendrogram structures, whereas less equitable abundances are associated with less even dendrograms. This relationship shows that abundance patterns can give insight into less visible aspects of community organization. Third, one can recover the distribution of proportional abundances seen in assemblages containing two species by treating each branch point in the dendrogram as a two-species case. This reconstruction cannot be achieved if abundances and the dendrogram are unrelated and suggests a method for hierarchically decomposing systems. To our knowledge, this is the first test of a species abundance model based on nontrivial predictions as to the origins and causes of abundance patterns, and not simply on the goodness-of-fit of distributions. PMID:12702773
Buske, Peter; Przybilla, Jens; Loeffler, Markus; Sachs, Norman; Sato, Toshiro; Clevers, Hans; Galle, Joerg
In vitro culture of intestinal tissue has been attempted for decades. Only recently did Sato et al. [Sato, T., Vries, R. G., Snippert, H. J., van de Wetering, M., Barker, N., Stange, D. E., van Es, J. H., Abo, A., Kujala, P., Peters, P. J., et al. (2009) Nature 459, 262-265] succeed in establishing long-term intestinal culture, demonstrating that cells expressing the Lgr5 gene can give rise to organoids with crypt-like domains similar to those found in vivo. In these cultures, Paneth cells provide essential signals supporting stem cell function. We have recently developed an individual cell-based computational model of the intestinal tissue [Buske, P., Galle, J., Barker, N., Aust, G., Clevers, H. & Loeffler, M. (2011) PLoS Comput Biol 7, e1001045]. The model is capable of quantitatively reproducing a comprehensive set of experimental data on intestinal cell organization. Here, we present a significant extension of this model that allows simulation of intestinal organoid formation in silico. For this purpose, we introduce a flexible basal membrane that assigns a bending modulus to the organoid surface. This membrane may be re-organized by cells attached to it depending on their differentiation status. Accordingly, the morphology of the epithelium is self-organized. We hypothesize that local tissue curvature is a key regulatory factor in stem cell organization in the intestinal tissue by controlling Paneth cell specification. In simulation studies, our model closely resembles the spatio-temporal organization of intestinal organoids. According to our results, proliferation-induced shape fluctuations are sufficient to induce crypt-like domains, and spontaneous tissue curvature induced by Paneth cells can control cell number ratios. Thus, stem cell expansion in an organoid depends sensitively on its biomechanics. We suggest a number of experiments that will enable new insights into mechano-transduction in the intestine, and suggest model extensions in the field of gland
National Audubon Society, New York, NY.
This set of teaching aids consists of nine Audubon Nature Bulletins, providing teachers and students with informational reading on various ecological topics. The bulletins have these titles: Schoolyard Laboratories, Owls and Predators, The Forest Community, Life in Freshwater Marshes, Camouflage in the Animal World, Life in the Desert, The…
Chen, Feixing; Zhang, Zengjie
Based on field investigation and experimental data analysis, ecological economic principles were applied to study the structure and function, the characteristics of material and energy flows, and the economic and ecological benefits of a rice-crab model. The results show that rice-crab model had a higher integral benefit than rice model, and its net income, cost-benefit ratio, and labor productivity were increased by 382%, 67.7% and 295%, respectively. In view of the ecological benefits produced, the total nitrogen, alkaline-hydrolyzal nitrogen, total phosphorus, rapidly available phosphorus, rapidly available potassium, and organic matter in the soil after 1-year carb breeding were increased by 10.6%, 3.3%, 5.8%, 11.7%, 3.5% and 10.5%, respectively. Moreover, 6.375 kg N.hm-2 of non-point source pollution load could be cut down annually.
Guichard, Sylvain; Guis, Hélène; Tran, Annelise; Garros, Claire; Balenghien, Thomas; Kriticos, Darren J.
We modelled the ecoclimatic niche of Culicoides imicola, a major arthropod vector of midge-borne viral pathogens affecting ruminants and equids, at fine scale and on a global extent, so as to provide insight into current and future risks of disease epizootics, and increase current knowledge of the species' ecology. Based on the known distribution and ecology of C. imicola, the species' response to monthly climatic conditions was characterised using CLIMEX with 10′ spatial resolution climatic datasets. The species' climatic niche was projected worldwide and under future climatic scenarios. The validated model highlights the role of irrigation in supporting the occurrence of C. imicola in arid regions. In Europe, the modelled potential distribution of C. imicola extended further West than its reported distribution, raising questions regarding ongoing process of colonization and non-climatic habitat factors. The CLIMEX model highlighted similar ecological niches for C. imicola and the Australasian C. brevitarsis raising questions on biogeography and biosecurity. Under the climate change scenarios considered, its' modelled potential distribution could expand northward in the Northern hemisphere, whereas in Africa its range may contract in the future. The biosecurity risks from bluetongue and African horse sickness viruses need to be re-evaluated in regions where the vector's niche is suitable. Under a warmer climate, the risk of vector-borne epizootic pathogens such as bluetongue and African horse sickness viruses are likely to increase as the climate suitability for C. imicola shifts poleward, especially in Western Europe. PMID:25391148
Li, Weidong; Rukavina, Paul
In this review, we propose a social ecological constraint model to study inclusion of overweight or obese students in physical education by integrating key concepts and assumptions from ecological constraint theory in motor development and social ecological models in health promotion and behavior. The social ecological constraint model proposes…
Gross, Louis J.; DeAngelis, Donald L.; Scott, J. Michael; Heglund, Patricia J.; Morrison, Michael L.
The Everglades region of South Florida presents one of the major natural system management challenges facing the United States. With its assortment of alligators, crocodiles, manatees, panthers, large mixed flocks of wading birds, highly diverse subtropical flora, and sea of sawgrass, the ecosystem is unique in this country (Davis and Ogden 1994). The region is also perhaps the largest human-controlled system on the planet in that the major environmental factor influencing the region is water, and water flows are managed on a daily basis--subject to the vagaries of rainfall--by a massive system of locks, pumps, canals, and levees constructed over the past century. The changes brought about by such control have led to extensive modifications of historical patterns and magnitudes of flow, causing large declines in many native species, extensive changes in nutrient cycling and vegetation across south Florida, and great increases in pollutants such as mercury. Constrained by the conflicting demands of agriculture, urban human populations, and wildlife for control of water resources, and the varying agendas of hosts of government agencies and nongovernmental organizations, there is now an ongoing effort to plan for major changes to the system with expenditure estimates of eight billion dollars or more over the next several decades (USACOE 1999). Carrying out such planning, particularly as it impacts the natural systems of the region, provides one of the major challenges to the new field of computational ecology.
Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie
Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system–based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species’ bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification. PMID:25951051
Li, Ling-Ling; Liu, Yang; Jin, Bo; Zhang, Xue-Ming
The self-renewal and differentiation of adult stem cells are closely related to their niches. Naturally, spermatogonial stem cells (SSCs) are the only adult stem cells in the body, which can transfer genetic information into the offspring. An insight into the modulation of the self-renewal and differentiation of SSCs can help elucidate the mechanisms of spermatogenesis and investigate the proliferation and differentiation of other adult stem cells. Therefore, the SSC system provides an ideal model for researches on the adult stem cell niche. More and more evidence indicates that the self-renewal and differentiation of SSCs are regulated by their niches. Based on our previous work and other related findings recently reported, this article presents an overview on the biological properties of SSC niches and their relationship with the self-renewal and differentiation of SSCs, focusing on the basic properties and components of SSC niches and various regulatory factors they produce.
Miller, Tom E X; Rudgers, Jennifer A
Heritable symbioses can have important ecological effects and have triggered important evolutionary innovations. Current predictions for long-term symbiont prevalence are based on their fitness benefits and vertical transmission rates but ignore nonlinear competitive feedbacks among symbiotic and symbiont-free hosts. We hypothesized that such feedbacks function as stabilizing mechanisms, promoting coexistence of host types and maintaining intermediate symbiont frequency at the population scale. Using a model grass/endophyte symbiosis, we manipulated competition within and between endophyte-symbiotic (E+) and endophyte-free (E-) hosts and fit competition models to experimental data. We show for the first time that symbiont-structured competition can generate stable coexistence of E+ and E- hosts, even under perfect vertical transmission. Niche differentiation was the key to coexistence, causing hosts of each type to limit themselves more strongly than each other. These results establish roles for nonlinear competitive dynamics and niche differentiation in the ecology and evolution of heritable symbionts.
Beer, Karlyn D.; Wurtmann, Elisabeth J.; Pinel, Nicolás
Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, the ecological relevance of their behavior is not always clear because certain traits are easily lost during long-term laboratory culturing. Here, we demonstrate that despite their long tenure in the laboratory, model organisms retain “ecological memory” of complex environmental changes. We have discovered that Halobacterium salinarum NRC-1, a halophilic archaeon that dominates microbial communities in a dynamically changing hypersaline environment, simultaneously optimizes fitness to total salinity, NaCl concentration, and the [K]/[Mg] ratio. Despite being maintained under controlled conditions over the last 50 years, peaks in the three-dimensional fitness landscape occur in salinity and ionic compositions that are not replicated in laboratory culturing but are routinely observed in the natural hypersaline environment of this organism. Intriguingly, adaptation to variations in ion composition was associated with differential regulation of anaerobic metabolism genes, suggesting an intertwined relationship between responses to oxygen and salinity. Our results suggest that the ecological memory of complex environmental variations is imprinted in the networks for coordinating multiple cellular processes. These coordination networks are also essential for dealing with changes in other physicochemically linked factors present during routine laboratory culturing and, hence, retained in model organisms. PMID:24413600
DeAngelis, Donald L.; Mooij, Wolf M.
Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.
Tingley, Reid; Vallinoto, Marcelo; Sequeira, Fernando; Kearney, Michael R.
Accurate forecasts of biological invasions are crucial for managing invasion risk but are hampered by niche shifts resulting from evolved environmental tolerances (fundamental niche shifts) or the presence of novel biotic and abiotic conditions in the invaded range (realized niche shifts). Distinguishing between these kinds of niche shifts is impossible with traditional, correlative approaches to invasion forecasts, which exclusively consider the realized niche. Here we overcome this challenge by combining a physiologically mechanistic model of the fundamental niche with correlative models based on the realized niche to study the global invasion of the cane toad Rhinella marina. We find strong evidence that the success of R. marina in Australia reflects a shift in the species’ realized niche, as opposed to evolutionary shifts in range-limiting traits. Our results demonstrate that R. marina does not fill its fundamental niche in its native South American range and that areas of niche unfilling coincide with the presence of a closely related species with which R. marina hybridizes. Conversely, in Australia, where coevolved taxa are absent, R. marina largely fills its fundamental niche in areas behind the invasion front. The general approach taken here of contrasting fundamental and realized niche models provides key insights into the role of biotic interactions in shaping range limits and can inform effective management strategies not only for invasive species but also for assisted colonization under climate change. PMID:24982155
Taxonomy has far-reaching effects throughout biology, and incorrect taxonomy can be detrimental in many ways. Polymorphic species complexes, many of which exist in the bee genus Anthophora Latreille, lend themselves to such difficulties. This study employs environmental niche mapping (ENM) and tradi...
Han, Ping; Gu, Ji-Dong
A new pmoA gene-based PCR primer set was designed for detection of nitrite-dependent anaerobic oxidation of methane (n-damo) bacteria from four different ecosystems, namely rice paddy soil, freshwater reservoir, reed bed, and sludge from wastewater treatment plant. This primer set showed high specificity and efficiency in recovering n-damo bacteria from these diverse samples. The obtained sequences showed 88-94 and 90-96% similarity to nucleotide and amino acid sequences, respectively, with the known NC10 phylum bacterium. According to the UniFrac principal coordinates analysis (PCoA), DNA sequences retrieved by the new PCR primer set in this study formed a separate group from the reported sequences, indicating higher diversity of n-damo in the environment. This newly designed PCR primer is capable of amplifying not only the currently known n-damo bacteria but also those that have not been reported, providing new information on the ecological diversity and distribution of this group of microorganisms in the ecosystem.
Butsic, Van; Lewis, David J; Radeloff, Volker C
Housing growth has been widely shown to be negatively correlated with wildlife populations, avian richness, anadromous fish, and exotic invasion. Zoning is the most frequently used public policy to manage housing development and is often motivated by a desire to protect the environment. Zoning is also pervasive, taking place in all 50 states. One relevant question that has received little research concerns the effectiveness of zoning to meet ecological goals. In this paper, we examined whether minimum frontage zoning policies have made a positive impact on the lakes they were aimed to protect in Vilas County, Wisconsin, U.S.A. We used an economic model that estimated when a given lot will be subdivided and how many new lots will be created as a function of zoning. Using the economic model, we simulated the effects of multiple zoning scenarios on lakeshore development. The simulated development patterns were then input to ecological models that predicted the amount of coarse woody debris (CWD) and the growth rate of bluegills as a function of residential density. Comparison of the ecological outcomes under different simulated zoning scenarios quantified the effect of zoning policies on residential density, CWD, and bluegill growth rates. Our results showed that zoning significantly affected residential density, CWD counts, and bluegill growth rates across our study area, although the effect was less clear at the scale of individual lake. Our results suggest that homogeneous zoning (i.e., for a county) is likely to have mixed results when applied to a heterogeneous landscape. Further, our results suggest that zoning regimes with a higher minimum shoreline frontage are likely to have larger ecological effects when applied to lakes that are less developed.
Blair, M E; Sterling, E J; Dusch, M; Raxworthy, C J; Pearson, R G
Understanding ecological niche evolution over evolutionary timescales is crucial to elucidating the biogeographic history of organisms. Here, we used, for the first time, climate-based ecological niche models (ENMs) to test hypotheses about ecological divergence and speciation processes between sister species pairs of lemurs (genus Eulemur) in Madagascar. We produced ENMs for eight species, all of which had significant validation support. Among the four sister species pairs, we found nonequivalent niches between sisters, varying degrees of niche overlap in ecological and geographic space, and support for multiple divergence processes. Specifically, three sister-pair comparisons supported the null model that niches are no more divergent than the available background region. These findings are consistent with an allopatric speciation model, and for two sister pairs (E. collaris-E. cinereiceps and E. rufus-E. rufifrons), a riverine barrier has been previously proposed for driving allopatric speciation. However, for the fourth sister pair E. flavifrons-E. macaco, we found support for significant niche divergence, and consistent with their parapatric distribution on an ecotone and the lack of obvious geographic barriers, these findings most strongly support a parapatric model of speciation. These analyses thus suggest that various speciation processes have led to diversification among closely related Eulemur species.
Lang, Julien; Vigouroux, Armelle; El Sahili, Abbas; Kwasiborski, Anthony; Aumont-Nicaise, Magali; Dessaux, Yves; Shykoff, Jacqui Anne; Moréra, Solange; Faure, Denis
We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.
Laidre, Mark E
Organisms can receive not only a genetic inheritance from their ancestors but also an ecological inheritance, involving modifications their ancestors made to the environment through niche construction. Ecological inheritances may persist as a legacy, potentially generating selection pressures that favor sociality. Yet, most proposed cases of sociality being impacted by an ecological inheritance come from organisms that live among close kin and were highly social before their niche construction began. Here, I show that in terrestrial hermit crabs (Coenobita compressus)--organisms that do not live with kin and reside alone, each in its own shell--niche-construction drives social dependence, such that individuals can only survive in remodeled shells handed down from conspecifics. These results suggest that niche construction can be an important initiator of evolutionary pressures to socialize, even among unrelated and otherwise asocial organisms.
Hughes, Honore M.; Humphrey, Natalie N.; Weaver, Terri L.
The most important things learned about violence and trauma in the past 20 years are that interpersonal violence is prevalent, with different forms co-occurring, and that victims' reactions are complex. Researchers are called to consider models that include the ecological context within which victims experience violence and trauma to gain a better…
More than 40 years ago, stable isotope analysis methods used in geochemistry began to be applied to ecological studies. One common application is using mathematical mixing models to sort out the proportional contributions of various sources to a mixture. Examples include contri...
More than 40 years ago, stable isotope analysis methods used in geochemistry began to be applied to ecological studies. One common application is using mathematical mixing models to sort out the proportional contributions of various sources to a mixture. Examples include contri...
The U.S. Environmental Protection Agency (USEPA) relies on a number of ecological risk assessment models that have been developed over 30-plus years of regulating pesticide exposure and risks under Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Endangered Spe...
The U.S. Environmental Protection Agency (USEPA) relies on a number of ecological risk assessment models that have been developed over 30-plus years of regulating pesticide exposure and risks under Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Endangered Spe...
More than 40 years ago, stable isotope analysis methods used in geochemistry began to be applied to ecological studies. One common application is using mathematical mixing models to sort out the proportional contributions of various sources to a mixture. Examples include contri...
We summarize our work on integration of an economy under imperfect competition with a simple Lotka-Volterra type ecological model. Firms and households operate within a single period planning horizon, thus there is no savings or investment. Wages are set by a dominant employer. P...
Hannant, Barbara; Lim, Eng Leong; McAllum, Ruth
Dynamic Ecological Analysis (DEA) is a model of practice which increases a teams' efficacy by enabling the development of more effective interventions through collaboration and collective reflection. This process has proved to be useful in: a) clarifying thinking and problem-solving, b) transferring knowledge and thinking to significant parties,…
In recent years, there has been a growing interest among various sections of the society in the study of sustainability. Recently, a generalized mathematical model depicting a combined economic-ecological-social system has been proposed to help in the formal study of sustainabili...
Lu, Zhi Hong; Kaliberov, Sergey; Sohn, Rebecca E; Kaliberova, Lyudmila; Du, Yingqiu; Prior, Julie L; Leib, Daniel J; Chauchereau, Anne; Sehn, Jennifer K; Curiel, David T; Arbeit, Jeffrey M
While modern therapies for metastatic prostate cancer (PCa) have improved survival they are associated with an increasingly prevalent entity, aggressive variant PCa (AVPCa), lacking androgen receptor (AR) expression, enriched for cancer stem cells (CSCs), and evidencing epithelial-mesenchymal plasticity with a varying extent of neuroendocrine transdifferentiation. Parallel work revealed that endothelial cells (ECs) create a perivascular CSC niche mediated by juxtacrine and membrane tethered signaling. There is increasing interest in pharmacological metastatic niche targeting, however, targeted access has been impossible. Here, we discovered that the Gleason 7 derived, androgen receptor negative, IGR-CaP1 cell line possessed some but not all of the molecular features of AVPCa. Intracardiac injection into NOD/SCID/IL2Rg -/- (NSG) mice produced a completely penetrant bone, liver, adrenal, and brain metastatic phenotype; noninvasively and histologically detectable at 2 weeks, and necessitating sacrifice 4-5 weeks post injection. Bone metastases were osteoblastic, and osteolytic. IGR-CaP1 cells expressed the neuroendocrine marker synaptophysin, near equivalent levels of vimentin and e-cadherin, all of the EMT transcription factors, and activation of NOTCH and WNT pathways. In parallel, we created a new triple-targeted adenoviral vector containing a fiber knob RGD peptide, a hexon mutation, and an EC specific ROBO4 promoter (Ad.RGD.H5/3.ROBO4). This vector was expressed in metastatic microvessels tightly juxtaposed to IGR-CaP1 cells in bone and visceral niches. Thus, the combination of IGR-CaP1 cells and NSG mice produces a completely penetrant metastatic PCa model emulating end-stage human disease. In addition, the metastatic niche access provided by our novel Ad vector could be therapeutically leveraged for future disease control or cure.
Fraser, Hannah; Rumpff, Libby; Yen, Jian D L; Robinson, Doug; Wintle, Brendan A
Many objectives motivate ecological restoration including improving vegetation condition, increasing the range and abundance of threatened species, and improving aggregate measures of biodiversity such as richness and diversity. While ecological models have been used to examine the outcomes of ecological restoration, there are few attempts to develop models to account for multiple, potentially competing objectives. We develop the first predictive model that integrates a vegetation-focused state-and-transition model with species distribution models for birds. We demonstrate how this integrated model can be used to identify effective restoration options for vegetation and bird species under a constrained budget. For example, using a typical agricultural land management scenario from south-eastern Australia, we demonstrate how the optimal management actions for promoting the occurrence of the Brown Treecreeper, an iconic threatened species, may be suboptimal for meeting vegetation condition objectives. This highlights that any 'preferred' management decision depends on the value assigned to the different objectives. An exploration of sensitivity to value weightings highlighted that 'no management' or 'weed control' were most likely to be the best management options to meet multiple objectives in the scenario we explored. We thus illustrate an approach to using the model outputs to explore trade-offs between bird and vegetation objectives. Our approach to exploring management outcomes and trade-offs using integrated modelling and structured decision support approaches has wide application for conservation management problems in which trade-offs exist between competing objectives. This article is protected by copyright. All rights reserved.
Drysdale, Alan; Thomas, Mark; Fresa, Mark; Wheeler, Ray
Attention is given to CELSS, a critical technology for the Space Exploration Initiative. OCAM (object-oriented CELSS analysis and modeling) models carbon, hydrogen, and oxygen recycling. Multiple crops and plant types can be simulated. Resource recovery options from inedible biomass include leaching, enzyme treatment, aerobic digestion, and mushroom and fish growth. The benefit of using many small crops overlapping in time, instead of a single large crop, is demonstrated. Unanticipated results include startup transients which reduce the benefit of multiple small crops. The relative contributions of mass, energy, and manpower to system cost are analyzed in order to determine appropriate research directions.
Madigan, Daniel J.; Carlisle, Aaron B.; Gardner, Luke D.; Jayasundara, Nishad; Micheli, Fiorenza; Schaefer, Kurt M.; Fuller, Daniel W.; Block, Barbara A.
Endothermy in vertebrates has been postulated to confer physiological and ecological advantages. In endothermic fish, niche expansion into cooler waters is correlated with specific physiological traits and is hypothesized to lead to greater foraging success and increased fitness. Using the seasonal co-occurrence of three tuna species in the eastern Pacific Ocean as a model system, we used cardiac gene expression data (as a proxy for thermal tolerance to low temperatures), archival tag data, and diet analyses to examine the vertical niche expansion hypothesis for endothermy in situ. Yellowfin, albacore, and Pacific bluefin tuna (PBFT) in the California Current system used more surface, mesopelagic, and deep waters, respectively. Expression of cardiac genes for calcium cycling increased in PBFT and coincided with broader vertical and thermal niche utilization. However, the PBFT diet was less diverse and focused on energy-rich forage fishes but did not show the greatest energy gains. Ecosystem-based management strategies for tunas should thus consider species-specific differences in physiology and foraging specialization. PMID:26100889
Shenton, Will; Bond, Nicholas R; Yen, Jian D L; Mac Nally, Ralph
There have been significant diversions of water from rivers and streams around the world; natural flow regimes have been perturbed by dams, barriers and excessive extractions. Many aspects of the ecological 'health' of riverine systems have declined due to changes in water flows, which has stimulated the development of thinking about the maintenance and restoration of these systems, which we refer to as environmental flow methodologies (EFMs). Most existing EFMs cannot deliver information on the population viability of species because they: (1) use habitat suitability as a proxy for population status; (2) use historical time series (usually of short duration) to forecast future conditions and flow sequences; (3) cannot, or do not, handle extreme flow events associated with climate variability; and (4) assume process stationarity for flow sequences, which means the past sequences are treated as good indicators of the future. These assumptions undermine the capacity of EFMs to properly represent risks associated with different flow management options; assumption (4) is untenable given most climate-change predictions. We discuss these concerns and advocate the use of demographic modelling as a more appropriate tool for linking population dynamics to flow regime change. A 'meta-species' approach to demographic modelling is discussed as a useful step from habitat based models towards modelling strategies grounded in ecological theory when limited data are available on flow-demographic relationships. Data requirements of demographic models will undoubtedly expose gaps in existing knowledge, but, in so doing, will strengthen future efforts to link changes in river flows with their ecological consequences.
Shenton, Will; Bond, Nicholas R.; Yen, Jian D. L.; Mac Nally, Ralph
There have been significant diversions of water from rivers and streams around the world; natural flow regimes have been perturbed by dams, barriers and excessive extractions. Many aspects of the ecological `health' of riverine systems have declined due to changes in water flows, which has stimulated the development of thinking about the maintenance and restoration of these systems, which we refer to as environmental flow methodologies (EFMs). Most existing EFMs cannot deliver information on the population viability of species because they: (1) use habitat suitability as a proxy for population status; (2) use historical time series (usually of short duration) to forecast future conditions and flow sequences; (3) cannot, or do not, handle extreme flow events associated with climate variability; and (4) assume process stationarity for flow sequences, which means the past sequences are treated as good indicators of the future. These assumptions undermine the capacity of EFMs to properly represent risks associated with different flow management options; assumption (4) is untenable given most climate-change predictions. We discuss these concerns and advocate the use of demographic modelling as a more appropriate tool for linking population dynamics to flow regime change. A `meta-species' approach to demographic modelling is discussed as a useful step from habitat based models towards modelling strategies grounded in ecological theory when limited data are available on flow-demographic relationships. Data requirements of demographic models will undoubtedly expose gaps in existing knowledge, but, in so doing, will strengthen future efforts to link changes in river flows with their ecological consequences.
Zhu, Geng-Ping; Li, Hui-Qi; Zhao, Li; Man, Liang; Liu, Qiang
Potential distributions of endemic relic shrubs in western Ordos were poorly mapped, which hindered our implementation of proper conservation. Here we investigated the applicability of ecological niche modeling for endangered relic shrubs to detect areas of priority for biodiversity conservation and analyze differences in ecological niche spaces used by relic shrubs. We applied ordination and niche modeling techniques to assess main environmental drivers of five endemic relic shrubs in western Ordos, namely, Ammopiptanthus mongolicus, Amygdalus mongolica, Helianthemum songaricum, Potaninia mongolica, and Tetraena mongolica. We calculated niche overlap metrics in gridded environmental spaces and compared geographical projections of ecological niches to determine similarities and differences of niches occupied by relic shrubs. All studied taxa presented different responses to environmental factors, which resulted in a unique combination of niche conditions. Precipitation availability and soil quality characteristics play important roles in the distributions of most shrubs. Each relic shrub is constrained by a unique set of environmental conditions, the distribution of one species cannot be implied by the distribution of another, highlighting the inadequacy of one-fits-all type of conservation measure. Our stacked habitat suitability maps revealed regions around Yellow River, which are highly suitable for most species, thereby providing high conservation value. PMID:27199260
Colwell, Robert K.; Rangel, Thiago F.
The duality between “niche” and “biotope” proposed by G. Evelyn Hutchinson provides a powerful way to conceptualize and analyze biogeographical distributions in relation to spatial environmental patterns. Both Joseph Grinnell and Charles Elton had attributed niches to environments. Attributing niches, instead, to species, allowed Hutchinson's key innovation: the formal severing of physical place from environment that is expressed by the duality. In biogeography, the physical world (a spatial extension of what Hutchinson called the biotope) is conceived as a map, each point (or cell) of which is characterized by its geographical coordinates and the local values of n environmental attributes at a given time. Exactly the same n environmental attributes define the corresponding niche space, as niche axes, allowing reciprocal projections between the geographic distribution of a species, actual or potential, past or future, and its niche. In biogeographical terms, the realized niche has come to express not only the effects of species interactions (as Hutchinson intended), but also constraints of dispersal limitation and the lack of contemporary environments corresponding to parts of the fundamental niche. Hutchinson's duality has been used to classify and map environments; model potential species distributions under past, present, and future climates; study the distributions of invasive species; discover new species; and simulate increasingly more realistic worlds, leading to spatially explicit, stochastic models that encompass speciation, extinction, range expansion, and evolutionary adaptation to changing environments. PMID:19805163
Ramírez-Barahona, Santiago; González, Clementina; González-Rodríguez, Antonio; Ornelas, Juan Francisco
The prevalent view on genetic structuring in parasitic plants is that host-race formation is caused by varying degrees of host specificity. However, the relative importance of ecological niche divergence and host specificity to population differentiation remains poorly understood. We evaluated the factors associated with population differentiation in mistletoes of the Psittacanthus schiedeanus complex (Loranthaceae) in Mexico. We used genetic data from chloroplast sequences and nuclear microsatellites to study population genetic structure and tested its association with host preferences and climatic niche variables. Pairwise genetic differentiation was associated with environmental and host preferences, independent of geography. However, environmental predictors appeared to be more important than host preferences to explain genetic structure, supporting the hypothesis that the occurrence of the parasite is largely determined by its own climatic niche and, to a lesser degree, by host specificity. Genetic structure is significant within this mistletoe species complex, but the processes associated with this structure appear to be more complex than previously thought. Although host specificity was not supported as the major determinant of population differentiation, we consider this to be part of a more comprehensive ecological model of mistletoe host-race formation that incorporates the effects of climatic niche evolution.
Hut, Roelof A; Kronfeld-Schor, Noga; van der Vinne, Vincent; De la Iglesia, Horacio
Time as an ecological niche variable or "temporal niche" can be defined in the context of the most prominent environmental cycles, including the tidal cycle, the lunar day and month, the solar day, and the earth year. For the current review, we focus on the 24-h domain generated through the earth's rotation around its axis (solar day). The daily environmental cycles of light and temperature are a dominant ecological factor generating a variety of adaptations among animals. In this review, we describe these adaptations with a special focus on the visual system and on the adaptive plasticity of activity patterns. Our goals are: (1) Underscore the importance of the 24-h time axis as critical variable in the ecological niche. (2) Highlight cases of temporal niche switches at the evolutionary timescale (phylogenetic level). (3) Review temporal niche switching within an individual's lifespan. (4) Evaluate possible underlying mechanisms for temporal niche switching. (5) Describe a new hypothesis of circadian thermoenergetics which may explain several cases of temporal niche switching in mammals. With this, we hope to inspire experiments under natural conditions or more complex laboratory environments, aimed to reveal environmental factors and mechanisms underlying specific temporal programs.
McCabe, Marita P; Mellor, David; Ricciardelli, Lina A; Mussap, Alexander J; Hallford, David J
This study was designed to examine the health behaviors as well as the enablers and barriers to health behaviors among Indigenous Australian men. One hundred and fifty Indigenous Australian men in rural, regional, and urban locations were interviewed about their health behaviors. The results revealed several themes of importance: (a) role of community activities, (b) the Indigenous man as a leader and role model, (c) negative impact of discrimination/racism, (d) importance of partner and family, (e) positive and negative role of peer relationships, (f) central role of culturally appropriate health care facilities, and (g) association between employment and health care problems. These findings highlight the importance of broad community-based (rather than individualistic) approaches to promoting health behavior in Indigenous men.
Rato, C; Carretero, M A
Because fitness of ectotherms, including reptiles, is highly dependent on temperature and water availability, the study of ecophysiological traits, such as preferred temperature (T p) and water loss rates (WLRs), may provide mechanistic evidence on the restricting factors to the species ranges. The Moorish gecko, Tarentola mauritanica, is a species complex with a circum-Mediterranean distribution. In the Iberian Peninsula, two sister parapatric forms of the complex, known as the Iberian and the European clades, are found. Ecological models previously performed using presence records and bioclimatic variables suggest niche divergence between both lineages correlated with precipitation rather than with temperature. In this study, we test this correlative hypothesis using ecophysiological evidence. In the laboratory, we analyzed the T p and WLRs for 84 adult males from seven distinct populations ascribed to one of the two lineages present in Iberia. Specifically, we evaluated the existence of trait conservatism versus adaptation among populations, lineages, or both. In addition, we tested for a trade-off between water and thermal traits and assessed whether climate regime of sampling localities had any influence on the ecophysiological patterns found. We found that T p is quite conserved at both the population and lineage levels and independent from body size. In contrast, water loss experiments revealed some variation among populations, but the regression analysis failed to detect correlation between T p and WLR at any level. Overall, the European lineage displayed a trend for higher water loss and was more diverse among populations when compared with the Iberian lineage. The lack of correspondence between ecophysiological traits and local climatic conditions favors phylogenetic signal versus adaptation. This suggests divergent evolutionary responses to the environment, mainly acting on water ecology, in both lineages, which may account for the differences in their
Vis, Marc; Knight, Rodney; Poole, Sandra; Wolfe, William J.; Seibert, Jan; Breuer, Lutz; Kraft, Philipp
Quantification of streamflow characteristics in ungauged catchments remains a challenge. Hydrological modeling is often used to derive flow time series and to calculate streamflow characteristics for subsequent applications that may differ from those envisioned by the modelers. While the estimation of model parameters for ungauged catchments is a challenging research task in itself, it is important to evaluate whether simulated time series preserve critical aspects of the streamflow hydrograph. To address this question, seven calibration objective functions were evaluated for their ability to preserve ecologically relevant streamflow characteristics of the average annual hydrograph using a runoff model, HBV-light, at 27 catchments in the southeastern United States. Calibration trials were repeated 100 times to reduce parameter uncertainty effects on the results, and 12 ecological flow characteristics were computed for comparison. Our results showed that the most suitable calibration strategy varied according to streamflow characteristic. Combined objective functions generally gave the best results, though a clear underprediction bias was observed. The occurrence of low prediction errors for certain combinations of objective function and flow characteristic suggests that (1) incorporating multiple ecological flow characteristics into a single objective function would increase model accuracy, potentially benefitting decision-making processes; and (2) there may be a need to have different objective functions available to address specific applications of the predicted time series.
Barnagaud, Jean-Yves; Devictor, Vincent; Jiguet, Frédéric; Barbet-Massin, Morgane; Le Viol, Isabelle; Archaux, Frédéric
Predicting species' responses to the combined effects of habitat and climate changes has become a major challenge in ecology and conservation biology. However, the effects of climatic and habitat gradients on species distributions have generally been considered separately. Here, we explore the relationships between the habitat and thermal dimensions of the ecological niche in European common birds. Using data from the French Breeding Bird Survey, a large-scale bird monitoring program, we correlated the habitat and thermal positions and breadths of 74 bird species, controlling for life history traits and phylogeny. We found that cold climate species tend to have niche positions in closed habitats, as expected by the conjunction of the biogeographic history of birds' habitats, and their current continent-scale gradients. We also report a positive correlation between thermal and habitat niche breadths, a pattern consistent with macroecological predictions concerning the processes shaping species' distributions. Our results suggest that the relationships between the climatic and habitat components of the niche have to be taken into account to understand and predict changes in species' distributions.
Barnagaud, Jean-Yves; Devictor, Vincent; Jiguet, Frédéric; Barbet-Massin, Morgane; Le Viol, Isabelle; Archaux, Frédéric
Predicting species' responses to the combined effects of habitat and climate changes has become a major challenge in ecology and conservation biology. However, the effects of climatic and habitat gradients on species distributions have generally been considered separately. Here, we explore the relationships between the habitat and thermal dimensions of the ecological niche in European common birds. Using data from the French Breeding Bird Survey, a large-scale bird monitoring program, we correlated the habitat and thermal positions and breadths of 74 bird species, controlling for life history traits and phylogeny. We found that cold climate species tend to have niche positions in closed habitats, as expected by the conjunction of the biogeographic history of birds' habitats, and their current continent-scale gradients. We also report a positive correlation between thermal and habitat niche breadths, a pattern consistent with macroecological predictions concerning the processes shaping species' distributions. Our results suggest that the relationships between the climatic and habitat components of the niche have to be taken into account to understand and predict changes in species' distributions. PMID:22427891
Bonetti, Maria Fernanda; Wiens, John J
The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.
Lundgren, Marjorie R; Besnard, Guillaume; Ripley, Brad S; Lehmann, Caroline E R; Chatelet, David S; Kynast, Ralf G; Namaganda, Mary; Vorontsova, Maria S; Hall, Russell C; Elia, John; Osborne, Colin P; Christin, Pascal-Antoine
Adaptation to changing environments often requires novel traits, but how such traits directly affect the ecological niche remains poorly understood. Multiple plant lineages have evolved C4 photosynthesis, a combination of anatomical and biochemical novelties predicted to increase productivity in warm and arid conditions. Here, we infer the dispersal history across geographical and environmental space in the only known species with both C4 and non-C4 genotypes, the grass Alloteropsis semialata. While non-C4 individuals remained confined to a limited geographic area and restricted ecological conditions, C4 individuals dispersed across three continents and into an expanded range of environments, encompassing the ancestral one. This first intraspecific investigation of C4 evolutionary ecology shows that, in otherwise similar plants, C4 photosynthesis does not shift the ecological niche, but broadens it, allowing dispersal into diverse conditions and over long distances. Over macroevolutionary timescales, this immediate effect can be blurred by subsequent specialisation towards more extreme niches.
Peng, Changhui; Guiot, Joel; Wu, Haibin; Jiang, Hong; Luo, Yiqi
It is increasingly being recognized that global ecological research requires novel methods and strategies in which to combine process-based ecological models and data in cohesive, systematic ways. Model-data fusion (MDF) is an emerging area of research in ecology and palaeoecology. It provides a new quantitative approach that offers a high level of empirical constraint over model predictions based on observations using inverse modelling and data assimilation (DA) techniques. Increasing demands to integrate model and data methods in the past decade has led to MDF utilization in palaeoecology, ecology and earth system sciences. This paper reviews key features and principles of MDF and highlights different approaches with regards to DA. After providing a critical evaluation of the numerous benefits of MDF and its current applications in palaeoecology (i.e., palaeoclimatic reconstruction, palaeovegetation and palaeocarbon storage) and ecology (i.e. parameter and uncertainty estimation, model error identification, remote sensing and ecological forecasting), the paper discusses method limitations, current challenges and future research direction. In the ongoing data-rich era of today's world, MDF could become an important diagnostic and prognostic tool in which to improve our understanding of ecological processes while testing ecological theory and hypotheses and forecasting changes in ecosystem structure, function and services.
Hogan, Kathleen; Thomas, David
This study examined the cognition of five pairs of high school students over time as they built quantitative ecological models using STELLA software. One pair of students emerged as being particularly proficient at learning to model, and was able to use models productively to explore and explain ecological system behaviors. We present detailed contrasts between this and the other pairs of students' cognitive behaviors while modeling, in three areas that were crucial to their modeling productivity: (a) focusing on model output and net interactions versus on model input and individual relationships when building and revising models, (b) exploring the nature and implications of dependencies and feedbacks versus just creating these as properties of complex systems, and (c) using variables versus constants to represent continuous and periodic functions. We then apply theories of the multifaceted nature of cognition to describe object-level, metalevel, and emotional dimensions of cognitive performance that help to explain the observed differences among students' approaches to STELLA modeling. Finally, we suggest pedagogical strategies for supporting all types of students in learning the central scientific practice of model-based quantitative thinking.
Peers, Michael J. L.; Thornton, Daniel H.; Murray, Dennis L.
The long-standing view in ecology is that disparity in overall resource selection is the basis for identifying niche breadth patterns, with species having narrow selection being classified “specialists” and those with broader selection being “generalists”. The standard model of niche breadth characterizes generalists and specialists as having comparable levels of overall total resource exploitation, with specialists exploiting resources at a higher level of performance over a narrower range of conditions. This view has gone largely unchallenged. An alternate model predicts total resource use being lower for the specialized species with both peaking at a comparable level of performance over a particular resource gradient. To reconcile the niche breadth paradigm we contrasted both models by developing range-wide species distribution models for Canada lynx, Lynx canadensis, and bobcat, Lynx rufus. Using a suite of environmental factors to define each species’ niche, we determined that Canada lynx demonstrated higher total performance over a restricted set of variables, specifically those related to snow and altitude, while bobcat had higher total performance across most variables. Unlike predictions generated by the standard model, bobcat level of exploitation was not compromised by the trade-off with peak performance, and Canada lynx were not restricted to exploiting a narrower range of conditions. Instead, the emergent pattern was that specialist species have a higher total resource utilization and peak performance value within a smaller number of resources or environmental axes than generalists. Our results also indicate that relative differences in niche breadth are strongly dependent on the variable under consideration, implying that the appropriate model describing niche breadth dynamics between specialists and generalists may be more complex than either the traditional heuristic or our modified version. Our results demonstrate a need to re
Peers, Michael J L; Thornton, Daniel H; Murray, Dennis L
The long-standing view in ecology is that disparity in overall resource selection is the basis for identifying niche breadth patterns, with species having narrow selection being classified "specialists" and those with broader selection being "generalists". The standard model of niche breadth characterizes generalists and specialists as having comparable levels of overall total resource exploitation, with specialists exploiting resources at a higher level of performance over a narrower range of conditions. This view has gone largely unchallenged. An alternate model predicts total resource use being lower for the specialized species with both peaking at a comparable level of performance over a particular resource gradient. To reconcile the niche breadth paradigm we contrasted both models by developing range-wide species distribution models for Canada lynx, Lynx canadensis, and bobcat, Lynx rufus. Using a suite of environmental factors to define each species' niche, we determined that Canada lynx demonstrated higher total performance over a restricted set of variables, specifically those related to snow and altitude, while bobcat had higher total performance across most variables. Unlike predictions generated by the standard model, bobcat level of exploitation was not compromised by the trade-off with peak performance, and Canada lynx were not restricted to exploiting a narrower range of conditions. Instead, the emergent pattern was that specialist species have a higher total resource utilization and peak performance value within a smaller number of resources or environmental axes than generalists. Our results also indicate that relative differences in niche breadth are strongly dependent on the variable under consideration, implying that the appropriate model describing niche breadth dynamics between specialists and generalists may be more complex than either the traditional heuristic or our modified version. Our results demonstrate a need to re-evaluate traditional
The three-spined stickleback is a small teleost fish, native to coastal regions of the Northern Hemisphere, which has emerged as a key model organism in evolutionary biology and ecology. Sticklebacks possess a well-documented and experimentally amenable parasite fauna, and are well suited to both laboratory and field parasitological investigation. As a consequence, sticklebacks have been extensively used as model hosts in studies of host-parasite interactions, and these studies have provided considerable insight into the roles of parasites in ecology and evolutionary biology. In this review, I discuss key advances in our understanding of host-parasite interactions that have arisen from studies involving stickleback hosts, highlight areas of current research activity, and identify potentially promising areas for future research.
Finlay, Bland J
This is an exploration of contemporary protist taxonomy within an ecological perspective. As it currently stands, the 'morphospecies' does not accommodate the information that might support a truly ecological species concept for the protists. But the 'morphospecies' is merely a first step in erecting a taxonomy of the protists, and it is expected to become more meaningful in the light of genetic, physiological and ecological research in the near future. One possible way forward lies in the recognition that sexual and asexual protists may all be subject to forces of cohesion that result in (DNA) sequence-similarity clusters. A starting point would then be the detection of 'ecotypes'--where genotypic and phenotypic clusters correspond; but for that we need better information regarding the extent of clonality in protists, and better characterization of ecological niches and their boundaries. There is some progress with respect to the latter. Using the example of a community of ciliated protozoa living in the stratified water column of a freshwater pond, it is shown to be possible to gauge the potential of protists to partition their local environment into ecological niches. Around 40 morphospecies can coexist in the superimposed water layers, which presumably represent different ecological niches, but we have yet to discover if these are discrete or continuously variable. It is a myth that taxonomic problems are more severe for protists than for animals and plants. Most of the fundamental problems associated with species concepts (e.g. asexuals, sibling species, phenotypic variation) are distributed across biota in general. The recent history of the status of Pfiesteria provides a model example of an integrated approach to solving what are essentially taxonomic problems. PMID:15253347
Pugesek, Bruce H.; von Eye, Alexander; Tomer, Adrian
This book presents an introduction to the methodology of structural equation modeling, illustrates its use, and goes on to argue that it has revolutionary implications for the study of natural systems. A major theme of this book is that we have, up to this point, attempted to study systems primarily using methods (such as the univariate model) that were designed only for considering individual processes. Understanding systems requires the capacity to examine simultaneous influences and responses. Structural equation modeling (SEM) has such capabilities. It also possesses many other traits that add strength to its utility as a means of making scientific progress. In light of the capabilities of SEM, it can be argued that much of ecological theory is currently locked in an immature state that impairs its relevance. It is further argued that the principles of SEM are capable of leading to the development and evaluation of multivariate theories of the sort vitally needed for the conservation of natural systems. Supplementary information can be found at the authors website, http://www.jamesbgrace.com/. Details why multivariate analyses should be used to study ecological systems Exposes unappreciated weakness in many current popular analyses Emphasizes the future methodological developments needed to advance our understanding of ecological systems.
Woo, David James
Education systems as units of analysis have been metaphorically likened to ecologies to model change. However, ecological models to date have been ineffective in modelling educational change that is multi-scale and occurs across multiple levels of an education system. Thus, this paper advances two innovative, ecological frameworks that improve on…
Steinmetz, Robert; Garshelis, David L.; Chutipong, Wanlop; Seuaturien, Naret
Background Ecologically similar species often coexist by partitioning use of habitats or resources. Such partitioning can occur through divergent or shared niches. We investigated overlap in habitat use and spatial co-occurrence by sympatric Asiatic black bears and sun bears in three habitats in Thailand, and thereby assessed which niche model best accounts for their coexistence. Methods/Principal Findings We used density of species-specific signs to assess habitat use. Signs of both bear species occurred in all three habitats, and on >60% of sampling transects. Both species fed mostly on fruit; insect feeding signs were uncommon, and were mostly from sun bears. Significant differences in habitat use occurred only in montane forest, the habitat in which fruit was most abundant; incidence of black bear sign there was six times higher than that of sun bears. Habitat use was similar between the two species in the other habitats, which comprised 85% of the area. Of 10 habitat attributes examined, fruiting tree density was the best predictor of occurrence for both species. Models that included interspecific competition (fresh foraging activity of the other species) were less supported than the top models without competition. Conclusions/Significance Bear species co-occurrence at both coarse and fine spatial scales and use of the same resources (fruit trees) indicated common niche preferences. However, their habitat use differed in ways expected from their physical differences: larger black bears dominated in the most fruit-rich habitat, and smaller sun bears used less-preferred insects. These results indicate broadly overlapping fundamental niches combined with asymmetric competition—features consistent with the concept of shared preference niches. This model of the niche has received little attention in ecology, but appears to be relatively common in nature. PMID:21283792
Allazetta, Simone; Lutolf, Matthias P
Stem cells reside in complex niches in which their behaviour is tightly regulated by various biochemical and biophysical signals. In order to unveil some of the crucial stem cell-niche interactions and expedite the implementation of stem cells in clinical and pharmaceutical applications, in vitro methodologies are being developed to reconstruct key features of stem cell niches. Recently, droplet-based microfluidics has emerged as a promising strategy to build stem cell niche models in a miniaturized and highly precise fashion. This review highlights current advances in using droplet microfluidics in stem cell biology. We also discuss recent efforts in which microgel technology has been interfaced with high-throughput analyses to engender screening paradigms with an unparalleled potential for basic and applied biological studies.
Grace, J.B.; Michael, Anderson T.; Han, O.; Scheiner, S.M.
The use of structural equation modeling (SEM) is often motivated by its utility for investigating complex networks of relationships, but also because of its promise as a means of representing theoretical concepts using latent variables. In this paper, we discuss characteristics of ecological theory and some of the challenges for proper specification of theoretical ideas in structural equation models (SE models). In our presentation, we describe some of the requirements for classical latent variable models in which observed variables (indicators) are interpreted as the effects of underlying causes. We also describe alternative model specifications in which indicators are interpreted as having causal influences on the theoretical concepts. We suggest that this latter nonclassical specification (which involves another variable type-the composite) will often be appropriate for ecological studies because of the multifaceted nature of our theoretical concepts. In this paper, we employ the use of meta-models to aid the translation of theory into SE models and also to facilitate our ability to relate results back to our theories. We demonstrate our approach by showing how a synthetic theory of grassland biodiversity can be evaluated using SEM and data from a coastal grassland. In this example, the theory focuses on the responses of species richness to abiotic stress and disturbance, both directly and through intervening effects on community biomass. Models examined include both those based on classical forms (where each concept is represented using a single latent variable) and also ones in which the concepts are recognized to be multifaceted and modeled as such. To address the challenge of matching SE models with the conceptual level of our theory, two approaches are illustrated, compositing and aggregation. Both approaches are shown to have merits, with the former being preferable for cases where the multiple facets of a concept have widely differing effects in the
Loera, Israel; Sosa, Victoria; Ickert-Bond, Stefanie M
A lineage of 12 arid land shrubby species in the gymnosperm genus Ephedra (Gnetales) from North America is used to evaluate the influence of climate on speciation. With a long evolutionary history, and a well documented fossil record this lineage is an ideal model for understanding the process of speciation under a niche conservatism scenario. Using seven DNA molecular markers, Bayesian inference is carried out to uncover sister species and to estimate time of divergence of the lineages. Ecological niche models are generated for four parapatric and sympatric sister species and two analyses of niche evolution are performed, one based on ecological niche models and another using raw data and multivariate analysis. As previous analyses suggest, the diversification of North America Ephedra species may be the result of a recent secondary radiation. Both parapatric and sympatric species diverged mostly in a scenario of climatic niche conservatism. However, we also found strong evidence for niche divergence for one of the sister species pairs (E. californica-E. trifurca). Moreover, the multivariate analysis found environmental differences for some variables between sister species. The estimated divergence time of three pairs of sister species distributed in southwestern North America (E. cutleri-E. aspera, E. californica-E. trifurca and E. torreyana-E. viridis) is inferred to have occurred in the Late Miocene to Pliocene and for the sister species pair E. antisyphilitica-E. coryi distributed in the southern United States and northeastern Mexico, it was inferred from the Pliocene to Pleistocene. The orogenetic and climatic changes documented for these regions related to expansion of arid lands, may have contributed to the diversification in North American Ephedra, rather than adaptations to new climatic conditions.
Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien
Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.
Boucher, Florian C.; Thuiller, Wilfried; Davies, T. Jonathan; Lavergne, Sébastien
Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than adaptive scenarios. We develop a model inspired by Neutral Biodiversity Theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sample the climatic niches of species according to their geographic position and show that even when species evolved independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism, but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191
Meseguer, Andrea S; Lobo, Jorge M; Ree, Richard; Beerling, David J; Sanmartín, Isabel
In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations t