Two-species occupancy modeling accounting for species misidentification and nondetection

Science.gov (United States)

Chambert, Thierry; Grant, Evan H. Campbell; Miller, David A. W.; Nichols, James; Mulder, Kevin P.; Brand, Adrianne B,

2018-01-01

1. In occupancy studies, species misidentification can lead to false positive detections, which can cause severe estimator biases. Currently, all models that account for false positive errors only consider omnibus sources of false detections and are limited to single species occupancy. 2. However, false detections for a given species often occur because of the misidentification with another, closely-related species. To exploit this explicit source of false positive detection error, we develop a two-species occupancy model that accounts for misidentifications between two species of interest. As with other false positive models, identifiability is greatly improved by the availability of unambiguous detections at a subset of site-occasions. Here, we consider the case where some of the field observations can be confirmed using laboratory or other independent identification methods (“confirmatory data”). 3. We performed three simulation studies to (1) assess the model’s performance under various realistic scenarios, (2) investigate the influence of the proportion of confirmatory data on estimator accuracy, and (3) compare the performance of this two-species model with that of the single-species false positive model. The model shows good performance under all scenarios, even when only small proportions of detections are confirmed (e.g., 5%). It also clearly outperforms the single-species model.

Biodiversity of Aspergillus species in some important agricultural products

DEFF Research Database (Denmark)

Perrone, Giancarlo; Susca, A.,; Cozzi, G.

2007-01-01

The genus Aspergillus is one of the most important filamentous fungal genera. Aspergillus species are used in the fermentation industry, but they are also responsible of various plant and food secondary rot, with the consequence of possible accumulation of mycotoxins. The aflatoxin producing A....... flavus and A. parasiticus, and ochratoxinogenic A. niger, A. ochraceus and A. carbonarius species are frequently encountered in agricultural products. Studies on the biodiversity of toxigenic Aspergillus species is useful to clarify molecular, ecological and biochemical characteristics of the different...... occurring in agricultural fields. Altogether nine different black Aspergillus species can be found on grapes which are often difficult to identify with classical methods. The polyphasic approach used in our studies led to the identification of three new species occurring on grapes: A. brasiliensis, A...

Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

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Conor P. McGowan

2017-10-01

Full Text Available Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises in transparent and explicit ways tailored to support decision making processes related to endangered species.

Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

Science.gov (United States)

McGowan, Conor P.; Allan, Nathan; Servoss, Jeff; Hedwall, Shaula J.; Wooldridge, Brian

2017-01-01

Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises) in transparent and explicit ways tailored to support decision making processes related to endangered species.

Species invasion shifts the importance of predator dependence.

Science.gov (United States)

Griffen, Blaine D; Delaney, David G

2007-12-01

The strength of interference between foraging individuals can influence per capita consumption rates, with important consequences for predator and prey populations and system stability. Here we demonstrate how the replacement of a previously established invader, the predatory crab Carcinus maenas, by the recently invading predatory crab Hemigrapsus sanguineus shifts predation from a species that experiences strong predator interference (strong predator dependence) to one that experiences weak predator interference (weak predator dependence). We demonstrate using field experiments that differences in the strength of predator dependence persist for these species both when they forage on a single focal prey species only (the mussel Mytilus edulis) and when they forage more broadly across the entire prey community. This shift in predator dependence with species replacement may be altering the biomass across trophic levels, consistent with theoretical predictions, as we show that H. sanguineus populations are much larger than C. maenas populations throughout their invaded ranges. Our study highlights that predator dependence may differ among predator species and demonstrates that different predatory impacts of two conspicuous invasive predators may be explained at least in part by different strengths of predator dependence.

Modelling survival: exposure pattern, species sensitivity and uncertainty.

Science.gov (United States)

Ashauer, Roman; Albert, Carlo; Augustine, Starrlight; Cedergreen, Nina; Charles, Sandrine; Ducrot, Virginie; Focks, Andreas; Gabsi, Faten; Gergs, André; Goussen, Benoit; Jager, Tjalling; Kramer, Nynke I; Nyman, Anna-Maija; Poulsen, Veronique; Reichenberger, Stefan; Schäfer, Ralf B; Van den Brink, Paul J; Veltman, Karin; Vogel, Sören; Zimmer, Elke I; Preuss, Thomas G

2016-07-06

The General Unified Threshold model for Survival (GUTS) integrates previously published toxicokinetic-toxicodynamic models and estimates survival with explicitly defined assumptions. Importantly, GUTS accounts for time-variable exposure to the stressor. We performed three studies to test the ability of GUTS to predict survival of aquatic organisms across different pesticide exposure patterns, time scales and species. Firstly, using synthetic data, we identified experimental data requirements which allow for the estimation of all parameters of the GUTS proper model. Secondly, we assessed how well GUTS, calibrated with short-term survival data of Gammarus pulex exposed to four pesticides, can forecast effects of longer-term pulsed exposures. Thirdly, we tested the ability of GUTS to estimate 14-day median effect concentrations of malathion for a range of species and use these estimates to build species sensitivity distributions for different exposure patterns. We find that GUTS adequately predicts survival across exposure patterns that vary over time. When toxicity is assessed for time-variable concentrations species may differ in their responses depending on the exposure profile. This can result in different species sensitivity rankings and safe levels. The interplay of exposure pattern and species sensitivity deserves systematic investigation in order to better understand how organisms respond to stress, including humans.

Translational genomics from model species Medicago truncatula to crop legume Trifolium pratense

NARCIS (Netherlands)

Lang Chunting, Chunting

2012-01-01

The legume Trifolium pratense (red clover) is an important fodder crop and produces important secondary metabolites. This makes red clover an interesting species. In this thesis, the red clover genome is compared to the legume model species Medicago truncatula, of which the

Predicting continental-scale patterns of bird species richness with spatially explicit models

DEFF Research Database (Denmark)

Rahbek, Carsten; Gotelli, Nicholas J; Colwell, Robert K

2007-01-01

the extraordinary diversity of avian species in the montane tropics, the most species-rich region on Earth. Our findings imply that correlative climatic models substantially underestimate the importance of historical factors and small-scale niche-driven assembly processes in shaping contemporary species-richness......The causes of global variation in species richness have been debated for nearly two centuries with no clear resolution in sight. Competing hypotheses have typically been evaluated with correlative models that do not explicitly incorporate the mechanisms responsible for biotic diversity gradients....... Here, we employ a fundamentally different approach that uses spatially explicit Monte Carlo models of the placement of cohesive geographical ranges in an environmentally heterogeneous landscape. These models predict species richness of endemic South American birds (2248 species) measured...

Immigration rates in fragmented landscapes--empirical evidence for the importance of habitat amount for species persistence.

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Thomas Püttker

Full Text Available BACKGROUND: The total amount of native vegetation is an important property of fragmented landscapes and is known to exert a strong influence on population and metapopulation dynamics. As the relationship between habitat loss and local patch and gap characteristics is strongly non-linear, theoretical models predict that immigration rates should decrease dramatically at low levels of remaining native vegetation cover, leading to patch-area effects and the existence of species extinction thresholds across fragmented landscapes with different proportions of remaining native vegetation. Although empirical patterns of species distribution and richness give support to these models, direct measurements of immigration rates across fragmented landscapes are still lacking. METHODOLOGY/PRINCIPAL FINDINGS: Using the Brazilian Atlantic forest marsupial Gray Slender Mouse Opossum (Marmosops incanus as a model species and estimating demographic parameters of populations in patches situated in three landscapes differing in the total amount of remaining forest, we tested the hypotheses that patch-area effects on population density are apparent only at intermediate levels of forest cover, and that immigration rates into forest patches are defined primarily by landscape context surrounding patches. As expected, we observed a positive patch-area effect on M. incanus density only within the landscape with intermediate forest cover. Density was independent of patch size in the most forested landscape and the species was absent from the most deforested landscape. Specifically, the mean estimated numbers of immigrants into small patches were lower in the landscape with intermediate forest cover compared to the most forested landscape. CONCLUSIONS/SIGNIFICANCE: Our results reveal the crucial importance of the total amount of remaining native vegetation for species persistence in fragmented landscapes, and specifically as to the role of variable immigration rates in

Cymbopogon Species; Ethnopharmacology, Phytochemistry and the Pharmacological Importance

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Opeyemi Avoseh

2015-04-01

Full Text Available Cymbopogon genus is a member of the family of Gramineae which are herbs known worldwide for their high essential oil content. They are widely distributed across all continents where they are used for various purposes. The commercial and medicinal uses of the various species of Cymbopogon are well documented. Ethnopharmacology evidence shows that they possess a wide array of properties that justifies their use for pest control, in cosmetics and as anti-inflammation agents. These plants may also hold promise as potent anti-tumor and chemopreventive drugs. The chemo-types from this genus have been used as biomarkers for their identification and classification. Pharmacological applications of Cymbopogon citratus are well exploited, though studies show that other species may also useful pharmaceutically. Hence this literature review intends to discuss these species and explore their potential economic importance.

Bounding species distribution models

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Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

2011-10-01

Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

Bounding Species Distribution Models

Science.gov (United States)

Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

2011-01-01

Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

Modelling the potential spatial distribution of mosquito species using three different techniques

NARCIS (Netherlands)

Cianci, D.; Hartemink, N.; Ibáñez-Justicia, A.

2015-01-01

Background: Models for the spatial distribution of vector species are important tools in the assessment of the risk of establishment and subsequent spread of vector-borne diseases. The aims of this study are to define the environmental conditions suitable for several mosquito species through species

Modeling of Alkane Oxidation Using Constituents and Species

Science.gov (United States)

Bellan, Jasette; Harstad, Kenneth G.

2010-01-01

It is currently not possible to perform simulations of turbulent reactive flows due in particular to complex chemistry, which may contain thousands of reactions and hundreds of species. This complex chemistry results in additional differential equations, making the numerical solution of the equation set computationally prohibitive. Reducing the chemical kinetics mathematical description is one of several important goals in turbulent reactive flow modeling. A chemical kinetics reduction model is proposed for alkane oxidation in air that is based on a parallel methodology to that used in turbulence modeling in the context of the Large Eddy Simulation. The objective of kinetic modeling is to predict the heat release and temperature evolution. This kinetic mechanism is valid over a pressure range from atmospheric to 60 bar, temperatures from 600 K to 2,500 K, and equivalence ratios from 0.125 to 8. This range encompasses diesel, HCCI, and gas-turbine engines, including cold ignition. A computationally efficient kinetic reduction has been proposed for alkanes that has been illustrated for n-heptane using the LLNL heptane mechanism. This model is consistent with turbulence modeling in that scales were first categorized into either those modeled or those computed as progress variables. Species were identified as being either light or heavy. The heavy species were decomposed into defined 13 constituents, and their total molar density was shown to evolve in a quasi-steady manner. The light species behave either in a quasi-steady or unsteady manner. The modeled scales are the total constituent molar density, Nc, and the molar density of the quasi-steady light species. The progress variables are the total constituent molar density rate evolution and the molar densities of the unsteady light species. The unsteady equations for the light species contain contributions of the type gain/loss rates from the heavy species that are modeled consistent with the developed mathematical

Incorporating Context Dependency of Species Interactions in Species Distribution Models.

Science.gov (United States)

Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

2017-07-01

Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

The relative importance of climate and vegetation properties on patterns of North American breeding bird species richness

International Nuclear Information System (INIS)

Goetz, Scott J; Sun, Mindy; Zolkos, Scott; Hansen, Andy; Dubayah, Ralph

2014-01-01

Recent advances in remote sensing and ecological modeling warrant a timely and robust investigation of the ecological variables that underlie large-scale patterns of breeding bird species richness, particularly in the context of intensifying land use and climate change. Our objective was to address this need using an array of bioclimatic and remotely sensed data sets representing vegetation properties and structure, and other aspects of the physical environment. We first build models of bird species richness across breeding bird survey (BBS) routes, and then spatially predict richness across the coterminous US at moderately high spatial resolution (1 km). Predictor variables were derived from various sources and maps of species richness were generated for four groups (guilds) of birds with different breeding habitat affiliation (forest, grassland, open woodland, scrub/shrub), as well as all guilds combined. Predictions of forest bird distributions were strong (R 2 = 0.85), followed by grassland (0.76), scrub/shrub (0.63) and open woodland (0.60) species. Vegetation properties were generally the strongest determinants of species richness, whereas bioclimatic and lidar-derived vertical structure metrics were of variable importance and dependent upon the guild type. Environmental variables (climate and the physical environment) were also frequently selected predictors, but canopy structure variables were not as important as expected based on more local to regional scale studies. Relatively sparse sampling of canopy structure metrics from the satellite lidar sensor may have reduced their importance relative to other predictor variables across the study domain. We discuss these results in the context of the ecological drivers of species richness patterns, the spatial scale of bird diversity analyses, and the potential of next generation space-borne lidar systems relevant to vegetation and ecosystem studies. This study strengthens current understanding of bird species�

Economically important species dominate aboveground carbon storage in forests of southwestern Amazonia

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N. Galia Selaya

2017-06-01

Full Text Available Tree species in tropical forests provide economically important goods and ecosystem services. In submontane forests of southwestern Amazonia, we investigated the degree to which tree species important for subsistence and trade contribute to aboveground carbon storage (AGC. We used 41 1-hectare plots to determine the species abundance, basal area, and AGC of stems > 10 cm diameter at breast height (dbh. Economically important taxa were classified using ethnobotanical studies and according to their stem density. These taxa (n = 263 accounted for 45% of total stems, 53% of total basal area, and 56% of total AGC, significantly more than taxa with minor or unknown uses (Welch test at p 40 cm and few stems in regeneration classes of dbh < 10 to 20 cm (e.g., Bertholletia excelsa, Cariniana spp., Cedrelinga spp., Ceiba spp., Dipteryx spp., whereas dominant Tetragastris spp., and Pseudolmedia spp. had most stems in low diameter classes and a median diameter of < 30 cm. Bertholletia excelsa, with 1.5 stems per hectare, showed the highest basal area of any species and accounted for 9% of AGC (11 Mg/ha, twice that of the second-ranking species. Our study shows that economic importance and carbon stocks in trees are closely linked in southwestern Amazonia. Unplanned harvests can disrupt synergistic dual roles altering carbon stocks temporally or permanently. Precautionary measures based on species ecology, demography, and regeneration traits should be at the forefront of REDD+ to reconcile maximum harvesting limits, biodiversity conservation, and sustainable forest management.

A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically Important Brassica Species Comprising the Triangle of U

NARCIS (Netherlands)

Li, Peirong; Zhang, Shujiang; Li, Fei; Zhang, Shifan; Zhang, Hui; Wang, Xiaowu; Sun, Rifei; Bonnema, Guusje; Borm, Theo J.A.

2017-01-01

The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U’s triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus,

Present and future ecological niche modeling of garter snake species from the Trans-Mexican Volcanic Belt

Science.gov (United States)

García-Vázquez, Uri; D’Addario, Maristella

2018-01-01

Land use and climate change are affecting the abundance and distribution of species. The Trans-Mexican Volcanic Belt (TMVB) is a very diverse region due to geological history, geographic position, and climate. It is also one of the most disturbed regions in Mexico. Reptiles are particularly sensitive to environmental changes due to their low dispersal capacity and thermal ecology. In this study, we define the important environmental variables (considering climate, topography, and land use) and potential distribution (present and future) of the five Thamnophis species present in TMVB. To do so, we used the maximum entropy modeling software (MAXENT). First, we modeled to select the most important variables to explain the distribution of each species, then we modeled again using only the most important variables and projected these models to the future considering a middle-moderate climate change scenario (rcp45), and land use and vegetation variables for the year 2050 (generated according to land use changes that occurred between years 2002 and 2011). Arid vegetation had an important negative effect on habitat suitability for all species, and minimum temperature of the coldest month was important for four of the five species. Thamnophis cyrtopsis was the species with the lowest tolerance to minimum temperatures. The maximum temperature of the warmest month was important for T. scalaris and T. cyrtopsis. Low percentages of agriculture were positive for T. eques and T. melanogaster but, at higher values, agriculture had a negative effect on habitat suitability for both species. Elevation was the most important variable to explain T. eques and T. melanogaster potential distribution while distance to Abies forests was the most important variable for T. scalaris and T. scaliger. All species had a high proportion of their potential distribution in the TMVB. However, according to our models, all Thamnophis species will experience reductions in their potential

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling.

Science.gov (United States)

Wisz, Mary Susanne; Pottier, Julien; Kissling, W Daniel; Pellissier, Loïc; Lenoir, Jonathan; Damgaard, Christian F; Dormann, Carsten F; Forchhammer, Mads C; Grytnes, John-Arvid; Guisan, Antoine; Heikkinen, Risto K; Høye, Toke T; Kühn, Ingolf; Luoto, Miska; Maiorano, Luigi; Nilsson, Marie-Charlotte; Normand, Signe; Öckinger, Erik; Schmidt, Niels M; Termansen, Mette; Timmermann, Allan; Wardle, David A; Aastrup, Peter; Svenning, Jens-Christian

2013-02-01

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km(2) to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally

Thematic and spatial resolutions affect model-based predictions of tree species distribution.

Science.gov (United States)

Liang, Yu; He, Hong S; Fraser, Jacob S; Wu, ZhiWei

2013-01-01

Subjective decisions of thematic and spatial resolutions in characterizing environmental heterogeneity may affect the characterizations of spatial pattern and the simulation of occurrence and rate of ecological processes, and in turn, model-based tree species distribution. Thus, this study quantified the importance of thematic and spatial resolutions, and their interaction in predictions of tree species distribution (quantified by species abundance). We investigated how model-predicted species abundances changed and whether tree species with different ecological traits (e.g., seed dispersal distance, competitive capacity) had different responses to varying thematic and spatial resolutions. We used the LANDIS forest landscape model to predict tree species distribution at the landscape scale and designed a series of scenarios with different thematic (different numbers of land types) and spatial resolutions combinations, and then statistically examined the differences of species abundance among these scenarios. Results showed that both thematic and spatial resolutions affected model-based predictions of species distribution, but thematic resolution had a greater effect. Species ecological traits affected the predictions. For species with moderate dispersal distance and relatively abundant seed sources, predicted abundance increased as thematic resolution increased. However, for species with long seeding distance or high shade tolerance, thematic resolution had an inverse effect on predicted abundance. When seed sources and dispersal distance were not limiting, the predicted species abundance increased with spatial resolution and vice versa. Results from this study may provide insights into the choice of thematic and spatial resolutions for model-based predictions of tree species distribution.

Helminth communities of four commercially important fish species from Chetumal Bay, Mexico.

Science.gov (United States)

Aguirre-Macedo, M L; Vidal-Martínez, V M; González-Solís, D; Caballero, P I

2007-03-01

The relative importance of ecology and evolution as factors determining species richness and composition of the helminth communities of fish is a matter of current debate. Theoretical studies use host-parasite lists, but these do not include studies on a temporal or spatial scale. Local environmental conditions and host biological characteristics are shown to influence helminth species richness and composition in four fish species (Eugerres plumieri, Hexanematichthys assimilis, Oligoplites saurus, and Scomberomorus maculatus) in Chetumal Bay, Mexico. With the exception of H. assimilis, the helminth communities had not been previously studied and possible associations between environmental and host biological characteristics as factors determining helminth species richness and composition using redundancy analysis (RDA) are described. Thirty-four helminth species are identified, with the highest number of species (19 total (mean = 6.3 +/- 2.1)) and the lowest (9 (4.0 +/- 1.0)) occurring in H. assimilis and S. maculatus, respectively. The larval nematodes Contracaecum sp. and Pseudoterranova sp. were not only the helminth species shared by all four host species but also were the most prevalent and abundant. Statistical associations between helminth community parameters and local ecological variables such as host habitat use, feeding habits, mobility, and time of residence in coastal lagoons are identified. Phylogeny is important because it clearly separates all four host species by their specialist parasites, although specific habitat and feeding habits also significantly influence the differentiation between the four fish species.

Updating known distribution models for forecasting climate change impact on endangered species.

Science.gov (United States)

Muñoz, Antonio-Román; Márquez, Ana Luz; Real, Raimundo

2013-01-01

To plan endangered species conservation and to design adequate management programmes, it is necessary to predict their distributional response to climate change, especially under the current situation of rapid change. However, these predictions are customarily done by relating de novo the distribution of the species with climatic conditions with no regard of previously available knowledge about the factors affecting the species distribution. We propose to take advantage of known species distribution models, but proceeding to update them with the variables yielded by climatic models before projecting them to the future. To exemplify our proposal, the availability of suitable habitat across Spain for the endangered Bonelli's Eagle (Aquila fasciata) was modelled by updating a pre-existing model based on current climate and topography to a combination of different general circulation models and Special Report on Emissions Scenarios. Our results suggested that the main threat for this endangered species would not be climate change, since all forecasting models show that its distribution will be maintained and increased in mainland Spain for all the XXI century. We remark on the importance of linking conservation biology with distribution modelling by updating existing models, frequently available for endangered species, considering all the known factors conditioning the species' distribution, instead of building new models that are based on climate change variables only.

PDEAR model prediction of Protea species in years 2070-2100

Science.gov (United States)

Guo, Danni; Guo, Renkuan; Midgley, Guy F.; Rebelo, A. G.

2009-10-01

Global warming and climate changes are changing the environment and therefore changing the distribution and behaviour of the plant species. Plant species often move and change their distributions as they find their original habitats are no longer suitable to their needs. It is therefore important to establish a statistical model to catch up the movement and patterns of the endangered species in order to effectively manage environmental protection under the inevitable biodiversity changes that are taking place. In this paper, we are focusing on the population category of rare Proteas that has an estimated population size from 1 to 10 per sample site, which is very small. We used the partial differential equation associated regression (PDEAR) model, which merges the partial differential equation theory, (statistical) linear model theory and random fuzzy variable theory together into a efficient small-sample oriented model, for the spatial pattern changing analysis. The regression component in a PDEAR model is in nature a special random fuzzy multivariate regression model. We developed a bivariate model for investigating the impacts from rainfall and temperature on the Protea species in average sense in the population size of 1 to 10, in the Cape Floristic Region, from 1992 to 2002, South Africa. Under same the average biodiversity structure assumptions, we explore the future spatial change patterns of Protea species in the population size of 1 to 10 with future (average) predicted rainfall and temperature. The spatial distribution and patterns are clearly will help us to explore global climate changing impacts on endangered species.

Infusing considerations of trophic dependencies into species distribution modelling.

Science.gov (United States)

Trainor, Anne M; Schmitz, Oswald J

2014-12-01

Community ecology involves studying the interdependence of species with each other and their environment to predict their geographical distribution and abundance. Modern species distribution analyses characterise species-environment dependency well, but offer only crude approximations of species interdependency. Typically, the dependency between focal species and other species is characterised using other species' point occurrences as spatial covariates to constrain the focal species' predicted range. This implicitly assumes that the strength of interdependency is homogeneous across space, which is not generally supported by analyses of species interactions. This discrepancy has an important bearing on the accuracy of inferences about habitat suitability for species. We introduce a framework that integrates principles from consumer-resource analyses, resource selection theory and species distribution modelling to enhance quantitative prediction of species geographical distributions. We show how to apply the framework using a case study of lynx and snowshoe hare interactions with each other and their environment. The analysis shows how the framework offers a spatially refined understanding of species distribution that is sensitive to nuances in biophysical attributes of the environment that determine the location and strength of species interactions. © 2014 John Wiley & Sons Ltd/CNRS.

Applications of species distribution modeling to paleobiology

DEFF Research Database (Denmark)

Svenning, Jens-Christian; Fløjgaard, Camilla; Marske, Katharine Ann

2011-01-01

-Pleistocene megafaunal extinctions, past community assembly, human paleobiogeography, Holocene paleoecology, and even deep-time biogeography (notably, providing insights into biogeographic dynamics >400 million years ago). We discuss important assumptions and uncertainties that affect the SDM approach to paleobiology......Species distribution modeling (SDM: statistical and/or mechanistic approaches to the assessment of range determinants and prediction of species occurrence) offers new possibilities for estimating and studying past organism distributions. SDM complements fossil and genetic evidence by providing (i......) quantitative and potentially high-resolution predictions of the past organism distributions, (ii) statistically formulated, testable ecological hypotheses regarding past distributions and communities, and (iii) statistical assessment of range determinants. In this article, we provide an overview...

Benchmarking novel approaches for modelling species range dynamics.

Science.gov (United States)

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

2016-08-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches

How can model comparison help improving species distribution models?

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Emmanuel Stephan Gritti

Full Text Available Today, more than ever, robust projections of potential species range shifts are needed to anticipate and mitigate the impacts of climate change on biodiversity and ecosystem services. Such projections are so far provided almost exclusively by correlative species distribution models (correlative SDMs. However, concerns regarding the reliability of their predictive power are growing and several authors call for the development of process-based SDMs. Still, each of these methods presents strengths and weakness which have to be estimated if they are to be reliably used by decision makers. In this study we compare projections of three different SDMs (STASH, LPJ and PHENOFIT that lie in the continuum between correlative models and process-based models for the current distribution of three major European tree species, Fagussylvatica L., Quercusrobur L. and Pinussylvestris L. We compare the consistency of the model simulations using an innovative comparison map profile method, integrating local and multi-scale comparisons. The three models simulate relatively accurately the current distribution of the three species. The process-based model performs almost as well as the correlative model, although parameters of the former are not fitted to the observed species distributions. According to our simulations, species range limits are triggered, at the European scale, by establishment and survival through processes primarily related to phenology and resistance to abiotic stress rather than to growth efficiency. The accuracy of projections of the hybrid and process-based model could however be improved by integrating a more realistic representation of the species resistance to water stress for instance, advocating for pursuing efforts to understand and formulate explicitly the impact of climatic conditions and variations on these processes.

The importance of species name synonyms in literature searches

Science.gov (United States)

Guala, Gerald

2016-01-01

The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS) which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

The Importance of Species Name Synonyms in Literature Searches.

Science.gov (United States)

Guala, Gerald F

2016-01-01

The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS) which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

The Importance of Species Name Synonyms in Literature Searches.

Directory of Open Access Journals (Sweden)

Gerald F Guala

Full Text Available The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

Transgenerational plasticity as an important mechanism affecting response of clonal species to changing climate

OpenAIRE

M?nzbergov?, Zuzana; Hadincov?, V?roslava

2017-01-01

Abstract In spite of the increasing number of studies on the importance of transgenerational plasticity for species response to novel environments, its effects on species ability to respond to climate change are still largely unexplored. We study the importance of transgenerational plasticity for response of a clonal species Festuca rubra. Individuals from four natural populations representing two levels of temperature and two levels of precipitation were cultivated in four growth chambers th...

PCR-RFLP Method to Identify Salmonid Species of Economic Importance

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Andreea Dudu

2011-05-01

Full Text Available The identification of different fish species by molecular methods has become necessary to avoid both the incorrect labelling of individuals involved in repopulation programmes and the commercial frauds on the fish market. Different fish species of great economical importance, like the salmonids, which are very much requested for their meat, can be identified using molecular techniques such as PCR-RFLP. The method is based on the amplification of a target region from the genome by PCR reaction followed by endonucleases digestion to detect the polymorphism of restriction fragments. In our study we analysed the following salmonid species from Romania: Salmo trutta fario, Salmo labrax, Salvelinus fontinalis, Onchorhynchus mykiss, Thymallus thymallus and Hucho hucho. In order to discriminate between the analysed species we amplified a fragment of mitochondrial genome comprising tRNAGlu/ cytochrome b/ tRNAThr/ tRNAPro/ D-loop/ tRNAPhe, followed by digestion with a specific restriction enzyme. The direct digestion of unpurified PCR products generated species-specific restriction patterns and proved to be a simple, reliable, inexpensive and fast method. Thus, it may be successfully utilized in specialized laboratories for the correct identification of the fish species for multiple purposes, including the traceability of fish food products.

Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil

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Karine Pinto e Vairo

2011-09-01

Full Text Available Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.

Species distribution models of tropical deep-sea snappers.

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Céline Gomez

Full Text Available Deep-sea fisheries provide an important source of protein to Pacific Island countries and territories that are highly dependent on fish for food security. However, spatial management of these deep-sea habitats is hindered by insufficient data. We developed species distribution models using spatially limited presence data for the main harvested species in the Western Central Pacific Ocean. We used bathymetric and water temperature data to develop presence-only species distribution models for the commercially exploited deep-sea snappers Etelis Cuvier 1828, Pristipomoides Valenciennes 1830, and Aphareus Cuvier 1830. We evaluated the performance of four different algorithms (CTA, GLM, MARS, and MAXENT within the BIOMOD framework to obtain an ensemble of predicted distributions. We projected these predictions across the Western Central Pacific Ocean to produce maps of potential deep-sea snapper distributions in 32 countries and territories. Depth was consistently the best predictor of presence for all species groups across all models. Bathymetric slope was consistently the poorest predictor. Temperature at depth was a good predictor of presence for GLM only. Model precision was highest for MAXENT and CTA. There were strong regional patterns in predicted distribution of suitable habitat, with the largest areas of suitable habitat (> 35% of the Exclusive Economic Zone predicted in seven South Pacific countries and territories (Fiji, Matthew & Hunter, Nauru, New Caledonia, Tonga, Vanuatu and Wallis & Futuna. Predicted habitat also varied among species, with the proportion of predicted habitat highest for Aphareus and lowest for Etelis. Despite data paucity, the relationship between deep-sea snapper presence and their environments was sufficiently strong to predict their distribution across a large area of the Pacific Ocean. Our results therefore provide a strong baseline for designing monitoring programs that balance resource exploitation and

Detection of medically important Candida species by absolute quantitation real-time polymerase chain reaction.

Science.gov (United States)

Than, Leslie Thian Lung; Chong, Pei Pei; Ng, Kee Peng; Seow, Heng Fong

2015-01-01

The number of invasive candidiasis cases has risen especially with an increase in the number of immunosuppressed and immunocom promised patients. The early detection of Candida species which is specific and sensitive is important in determining the correct administration of antifungal drugs to patients. This study aims to develop a method for the detection, identification and quantitation of medically important Candida species through quantitative polymerase chain reaction (qPCR). The isocitrate lyase (ICL) gene which is not found in mammals was chosen as the target gene of real-time PCR. Absolute quantitation of the gene copy number was achieved by constructing the plasmid containing the ICL gene which is used to generate standard curve. Twenty fungal species, two bacterial species and human DNA were tested to check the specificity of the detection method. All eight Candida species were successfully detected, identified and quantitated based on the ICL gene. A seven-log range of the gene copy number and a minimum detection limit of 10(3) copies were achieved. A one-tube absolute quantification real-time PCR that differentiates medically important Candida species via individual unique melting temperature was achieved. Analytical sensitivity and specificity were not compromised.

Models of alien species richness show moderate predictive accuracy and poor transferability

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César Capinha

2018-06-01

Full Text Available Robust predictions of alien species richness are useful to assess global biodiversity change. Nevertheless, the capacity to predict spatial patterns of alien species richness remains largely unassessed. Using 22 data sets of alien species richness from diverse taxonomic groups and covering various parts of the world, we evaluated whether different statistical models were able to provide useful predictions of absolute and relative alien species richness, as a function of explanatory variables representing geographical, environmental and socio-economic factors. Five state-of-the-art count data modelling techniques were used and compared: Poisson and negative binomial generalised linear models (GLMs, multivariate adaptive regression splines (MARS, random forests (RF and boosted regression trees (BRT. We found that predictions of absolute alien species richness had a low to moderate accuracy in the region where the models were developed and a consistently poor accuracy in new regions. Predictions of relative richness performed in a superior manner in both geographical settings, but still were not good. Flexible tree ensembles-type techniques (RF and BRT were shown to be significantly better in modelling alien species richness than parametric linear models (such as GLM, despite the latter being more commonly applied for this purpose. Importantly, the poor spatial transferability of models also warrants caution in assuming the generality of the relationships they identify, e.g. by applying projections under future scenario conditions. Ultimately, our results strongly suggest that predictability of spatial variation in richness of alien species richness is limited. The somewhat more robust ability to rank regions according to the number of aliens they have (i.e. relative richness, suggests that models of aliens species richness may be useful for prioritising and comparing regions, but not for predicting exact species numbers.

New trends in species distribution modelling

Science.gov (United States)

Zimmermann, Niklaus E.; Edwards, Thomas C.; Graham, Catherine H.; Pearman, Peter B.; Svenning, Jens-Christian

2010-01-01

Species distribution modelling has its origin in the late 1970s when computing capacity was limited. Early work in the field concentrated mostly on the development of methods to model effectively the shape of a species' response to environmental gradients (Austin 1987, Austin et al. 1990). The methodology and its framework were summarized in reviews 10–15 yr ago (Franklin 1995, Guisan and Zimmermann 2000), and these syntheses are still widely used as reference landmarks in the current distribution modelling literature. However, enormous advancements have occurred over the last decade, with hundreds – if not thousands – of publications on species distribution model (SDM) methodologies and their application to a broad set of conservation, ecological and evolutionary questions. With this special issue, originating from the third of a set of specialized SDM workshops (2008 Riederalp) entitled 'The Utility of Species Distribution Models as Tools for Conservation Ecology', we reflect on current trends and the progress achieved over the last decade.

Richards-like two species population dynamics model.

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Ribeiro, Fabiano; Cabella, Brenno Caetano Troca; Martinez, Alexandre Souto

2014-12-01

The two-species population dynamics model is the simplest paradigm of inter- and intra-species interaction. Here, we present a generalized Lotka-Volterra model with intraspecific competition, which retrieves as particular cases, some well-known models. The generalization parameter is related to the species habitat dimensionality and their interaction range. Contrary to standard models, the species coupling parameters are general, not restricted to non-negative values. Therefore, they may represent different ecological regimes, which are derived from the asymptotic solution stability analysis and are represented in a phase diagram. In this diagram, we have identified a forbidden region in the mutualism regime, and a survival/extinction transition with dependence on initial conditions for the competition regime. Also, we shed light on two types of predation and competition: weak, if there are species coexistence, or strong, if at least one species is extinguished.

Asymmetric biotic interactions and abiotic niche differences revealed by a dynamic joint species distribution model.

Science.gov (United States)

Lany, Nina K; Zarnetske, Phoebe L; Schliep, Erin M; Schaeffer, Robert N; Orians, Colin M; Orwig, David A; Preisser, Evan L

2018-05-01

A species' distribution and abundance are determined by abiotic conditions and biotic interactions with other species in the community. Most species distribution models correlate the occurrence of a single species with environmental variables only, and leave out biotic interactions. To test the importance of biotic interactions on occurrence and abundance, we compared a multivariate spatiotemporal model of the joint abundance of two invasive insects that share a host plant, hemlock woolly adelgid (HWA; Adelges tsugae) and elongate hemlock scale (EHS; Fiorina externa), to independent models that do not account for dependence among co-occurring species. The joint model revealed that HWA responded more strongly to abiotic conditions than EHS. Additionally, HWA appeared to predispose stands to subsequent increase of EHS, but HWA abundance was not strongly dependent on EHS abundance. This study demonstrates how incorporating spatial and temporal dependence into a species distribution model can reveal the dependence of a species' abundance on other species in the community. Accounting for dependence among co-occurring species with a joint distribution model can also improve estimation of the abiotic niche for species affected by interspecific interactions. © 2018 by the Ecological Society of America.

Important LiDAR metrics for discriminating forest tree species in Central Europe

Science.gov (United States)

Shi, Yifang; Wang, Tiejun; Skidmore, Andrew K.; Heurich, Marco

2018-03-01

Numerous airborne LiDAR-derived metrics have been proposed for classifying tree species. Yet an in-depth ecological and biological understanding of the significance of these metrics for tree species mapping remains largely unexplored. In this paper, we evaluated the performance of 37 frequently used LiDAR metrics derived under leaf-on and leaf-off conditions, respectively, for discriminating six different tree species in a natural forest in Germany. We firstly assessed the correlation between these metrics. Then we applied a Random Forest algorithm to classify the tree species and evaluated the importance of the LiDAR metrics. Finally, we identified the most important LiDAR metrics and tested their robustness and transferability. Our results indicated that about 60% of LiDAR metrics were highly correlated to each other (|r| > 0.7). There was no statistically significant difference in tree species mapping accuracy between the use of leaf-on and leaf-off LiDAR metrics. However, combining leaf-on and leaf-off LiDAR metrics significantly increased the overall accuracy from 58.2% (leaf-on) and 62.0% (leaf-off) to 66.5% as well as the kappa coefficient from 0.47 (leaf-on) and 0.51 (leaf-off) to 0.58. Radiometric features, especially intensity related metrics, provided more consistent and significant contributions than geometric features for tree species discrimination. Specifically, the mean intensity of first-or-single returns as well as the mean value of echo width were identified as the most robust LiDAR metrics for tree species discrimination. These results indicate that metrics derived from airborne LiDAR data, especially radiometric metrics, can aid in discriminating tree species in a mixed temperate forest, and represent candidate metrics for tree species classification and monitoring in Central Europe.

Montane and coastal species diversification in the economically important Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).

Science.gov (United States)

Pedraza-Lara, Carlos; Barrientos-Lozano, Ludivina; Rocha-Sánchez, Aurora Y; Zaldívar-Riverón, Alejandro

2015-03-01

The genus Sphenarium (Pyrgomorphidae) is a small group of grasshoppers endemic to México and Guatemala that are economically and culturally important both as a food source and as agricultural pests. However, its taxonomy has been largely neglected mainly due to its conserved interspecific external morphology and the considerable intraspecific variation in colour pattern of some taxa. Here we examined morphological as well as mitochondrial and nuclear DNA sequence data to assess the species boundaries and evolutionary history in Sphenarium. Our morphological identification and DNA sequence-based species delimitation, carried out with three different approaches (DNA barcoding, general mixed Yule-coalescent model, Bayesian species delimitation), all recovered a higher number of putative species of Sphenarium than previously recognised. We unambiguously delimit seven species, and between five and ten additional species depending on the data/method analysed. Phylogenetic relationships within the genus strongly support two main clades, one exclusively montane, the other coastal. Divergence time estimates suggest late Miocene to Pliocene ages for the origin and most of the early diversification events in the genus, which were probably influenced by the formation of the Trans-Mexican Volcanic Belt. A series of Pleistocene events could have led to the current species diversification in both montane and coastal regions. This study not only reveals an overlooked species richness for the most popular edible insect in Mexico, but also highlights the influence of the dynamic geological and climatic history of the region in shaping its current diversity. Copyright © 2015 Elsevier Inc. All rights reserved.

Animal models: an important tool in mycology.

Science.gov (United States)

Capilla, Javier; Clemons, Karl V; Stevens, David A

2007-12-01

Animal models of fungal infections are, and will remain, a key tool in the advancement of the medical mycology. Many different types of animal models of fungal infection have been developed, with murine models the most frequently used, for studies of pathogenesis, virulence, immunology, diagnosis, and therapy. The ability to control numerous variables in performing the model allows us to mimic human disease states and quantitatively monitor the course of the disease. However, no single model can answer all questions and different animal species or different routes of infection can show somewhat different results. Thus, the choice of which animal model to use must be made carefully, addressing issues of the type of human disease to mimic, the parameters to follow and collection of the appropriate data to answer those questions being asked. This review addresses a variety of uses for animal models in medical mycology. It focuses on the most clinically important diseases affecting humans and cites various examples of the different types of studies that have been performed. Overall, animal models of fungal infection will continue to be valuable tools in addressing questions concerning fungal infections and contribute to our deeper understanding of how these infections occur, progress and can be controlled and eliminated.

Brine shrimp bioassay: importance of correct taxonomic identification of Artemia (Anostraca) species.

Science.gov (United States)

Ruebhart, David R; Cock, Ian E; Shaw, Glen R

2008-08-01

Despite the common use of the brine shrimp bioassay in toxicology, there is confusion in the literature regarding citation of the correct taxonomic identity of the Artemia species used. The genus Artemia, once thought to be represented by a single species Artemia salina, is now known to be composed of several bisexual species as well as parthenogenetic populations. Artemia franciscana is the best studied of the Artemia species and is considered to represent the vast majority of studies in which Artemia is used as an experimental test organism. We found that in studies referring to the use of A. salina, the zoogeography of the cyst harvest site indicated that the species used was actually A. franciscana. Those performing bioassays with Artemia need to exercise diligence in assigning correct species identification, as the identity of the test organism is an important parameter in assuring the validity of the results of the assay.

Construction of analytically solvable models for interacting species. [biological species competition

Science.gov (United States)

Rosen, G.

1976-01-01

The basic form of a model representation for systems of n interacting biological species is a set of essentially nonlinear autonomous ordinary differential equations. A generic canonical expression for the rate functions in the equations is reported which permits the analytical general solution to be obtained by elementary computation. It is shown that a general analytical solution is directly obtainable for models where the rate functions are prescribed by the generic canonical expression from the outset. Some illustrative examples are given which demonstrate that the generic canonical expression can be used to construct analytically solvable models for two interacting species with limit-cycle dynamics as well as for a three-species interdependence.

Using Species Distribution Models to Predict Potential Landscape Restoration Effects on Puma Conservation.

Science.gov (United States)

Angelieri, Cintia Camila Silva; Adams-Hosking, Christine; Ferraz, Katia Maria Paschoaletto Micchi de Barros; de Souza, Marcelo Pereira; McAlpine, Clive Alexander

2016-01-01

A mosaic of intact native and human-modified vegetation use can provide important habitat for top predators such as the puma (Puma concolor), avoiding negative effects on other species and ecological processes due to cascade trophic interactions. This study investigates the effects of restoration scenarios on the puma's habitat suitability in the most developed Brazilian region (São Paulo State). Species Distribution Models incorporating restoration scenarios were developed using the species' occurrence information to (1) map habitat suitability of pumas in São Paulo State, Southeast, Brazil; (2) test the relative contribution of environmental variables ecologically relevant to the species habitat suitability and (3) project the predicted habitat suitability to future native vegetation restoration scenarios. The Maximum Entropy algorithm was used (Test AUC of 0.84 ± 0.0228) based on seven environmental non-correlated variables and non-autocorrelated presence-only records (n = 342). The percentage of native vegetation (positive influence), elevation (positive influence) and density of roads (negative influence) were considered the most important environmental variables to the model. Model projections to restoration scenarios reflected the high positive relationship between pumas and native vegetation. These projections identified new high suitability areas for pumas (probability of presence >0.5) in highly deforested regions. High suitability areas were increased from 5.3% to 8.5% of the total State extension when the landscapes were restored for ≥ the minimum native vegetation cover rule (20%) established by the Brazilian Forest Code in private lands. This study highlights the importance of a landscape planning approach to improve the conservation outlook for pumas and other species, including not only the establishment and management of protected areas, but also the habitat restoration on private lands. Importantly, the results may inform environmental

Modeling of spatial distribution for scorpions of medical importance in the São Paulo State, Brazil

Directory of Open Access Journals (Sweden)

José Brites-Neto

2015-07-01

Full Text Available Aim: In this work, we aimed to develop maps of modeling geographic distribution correlating to environmental suitability for the two species of scorpions of medical importance at São Paulo State and to develop spatial configuration parameters for epidemiological surveillance of these species of venomous animals. Materials and Methods: In this study, 54 georeferenced points for Tityus serrulatus and 86 points for Tityus bahiensis and eight environmental indicators, were used to generate species distribution models in Maxent (maximum entropy modeling of species geographic distributions version 3.3.3k using 70% of data for training (n=38 to T. serrulatus and n=60 to T. bahiensis and 30% to test the models (n=16 for T. serrulatus and n=26 for T. bahiensis. The logistic threshold used to cut models in converting the continuous probability model into a binary model was the “maximum test sensitivity plus specificity,” provided by Maxent, with results of 0.4143 to T. serrulatus and of 0.3401 to T. bahiensis. The models were evaluated by the area under the curve (AUC, using the omission error and the binomial probability. With the data generated by Maxent, distribution maps were produced using the “ESRI® ArcGIS 10.2.2 for Desktop” software. Results: The models had high predictive success (AUC=0.7698±0.0533, omission error=0.2467 and p<0.001 for T. serrulatus and AUC=0.8205±0.0390, omission error=0.1917 and p<0.001 for T. bahiensis and the resultant maps showed a high environmental suitability in the north, central, and southeast of the state, confirming the increasing spread of these species. The environmental variables that mostly contributed to the scorpions species distribution model were rain precipitation (28.9% and tree cover (28.2% for the T. serrulatus and temperature (45.8% and thermal amplitude (12.6% for the T. bahiensis. Conclusion: The distribution model of these species of medical importance scorpions in São Paulo State

General extrapolation model for an important chemical dose-rate effect

International Nuclear Information System (INIS)

Gillen, K.T.; Clough, R.L.

1984-12-01

In order to extrapolate material accelerated aging data, methodologies must be developed based on sufficient understanding of the processes leading to material degradation. One of the most important mechanisms leading to chemical dose-rate effects in polymers involves the breakdown of intermediate hydroperoxide species. A general model for this mechanism is derived based on the underlying chemical steps. The results lead to a general formalism for understanding dose rate and sequential aging effects when hydroperoxide breakdown is important. We apply the model to combined radiation/temperature aging data for a PVC material and show that this data is consistent with the model and that model extrapolations are in excellent agreement with 12-year real-time aging results from an actual nuclear plant. This model and other techniques discussed in this report can aid in the selection of appropriate accelerated aging methods and can also be used to compare and select materials for use in safety-related components. This will result in increased assurance that equipment qualification procedures are adequate

Complementary models of tree species-soil relationships in old-growth temperate forests

Science.gov (United States)

Cross, Alison; Perakis, Steven S.

2011-01-01

Ecosystem level studies identify plant soil feed backs as important controls on soil nutrient availability,particularly for nitrogen and phosphorus. Although site and species specific studies of tree species soil relationships are relatively common,comparatively fewer studies consider multiple coexisting speciesin old-growth forests across a range of sites that vary underlying soil fertility. We characterized patterns in forest floor and mineral soil nutrients associated with four common tree species across eight undisturbed old-growth forests in Oregon, USA, and used two complementary conceptual models to assess tree species soil relationships. Plant soil feedbacks that could reinforce sitelevel differences in nutrient availability were assessed using the context dependent relationships model, where by relative species based differences in each soil nutrient divergedorconvergedas nutrient status changed across sites. Tree species soil relationships that did not reflect strong feedbacks were evaluated using a site independent relationships model, where by forest floor and surface mineral soil nutrient tools differed consistently by tree species across sites,without variation in deeper mineral soils. We found that theorganically cycled elements carbon, nitrogen, and phosphorus exhibited context-dependent differences among species in both forest floor and mineral soil, and most of ten followed adivergence model,where by species differences were greatest at high-nutrient sites. These patterns are consistent with the oryemphasizing biotic control of these elements through plant soil feedback mechanisms. Site independent species differences were strongest for pool so if the weather able cations calcium, magnesium, potassium,as well as phosphorus, in mineral soils. Site independent species differences in forest floor nutrients we reattributable too nespecies that displayed significant greater forest floor mass accumulation. Our finding confirmed that site-independent and

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

Directory of Open Access Journals (Sweden)

Benkman Craig W

2010-03-01

Full Text Available Abstract Background Massively parallel sequencing of cDNA is now an efficient route for generating enormous sequence collections that represent expressed genes. This approach provides a valuable starting point for characterizing functional genetic variation in non-model organisms, especially where whole genome sequencing efforts are currently cost and time prohibitive. The large and complex genomes of pines (Pinus spp. have hindered the development of genomic resources, despite the ecological and economical importance of the group. While most genomic studies have focused on a single species (P. taeda, genomic level resources for other pines are insufficiently developed to facilitate ecological genomic research. Lodgepole pine (P. contorta is an ecologically important foundation species of montane forest ecosystems and exhibits substantial adaptive variation across its range in western North America. Here we describe a sequencing study of expressed genes from P. contorta, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies. Results We obtained 586,732 sequencing reads from a 454 GS XLR70 Titanium pyrosequencer (mean length: 306 base pairs. A combination of reference-based and de novo assemblies yielded 63,657 contigs, with 239,793 reads remaining as singletons. Based on sequence similarity with known proteins, these sequences represent approximately 17,000 unique genes, many of which are well covered by contig sequences. This sequence collection also included a surprisingly large number of retrotransposon sequences, suggesting that they are highly transcriptionally active in the tissues we sampled. We located and characterized thousands of simple sequence repeats and single nucleotide polymorphisms as potential molecular markers in our assembled and annotated sequences. High quality PCR primers were designed for a substantial number of the SSR loci

Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

Directory of Open Access Journals (Sweden)

Teja P. Muha

2017-12-01

Full Text Available Species Distribution Models (SDMs have been reported as a useful tool for the risk assessment and modeling of the pathways of dispersal of freshwater invasive alien species (IAS. Environmental DNA (eDNA is a novel tool that can help detect IAS at their early stage of introduction and additionally improve the data available for a more efficient management. SDMs rely on presence and absence of the species in the study area to infer the predictors affecting species distributions. Presence is verified once a species is detected, but confirmation of absence can be problematic because this depends both on the detectability of the species and the sampling strategy. eDNA is a technique that presents higher detectability and accuracy in comparison to conventional sampling techniques, and can effectively differentiate between presence or absence of specific species or entire communities by using a barcoding or metabarcoding approach. However, a number of potential bias can be introduced during (i sampling, (ii amplification, (iii sequencing, or (iv through the usage of bioinformatics pipelines. Therefore, it is important to report and conduct the field and laboratory procedures in a consistent way, by (i introducing eDNA independent observations, (ii amplifying and sequencing control samples, (iii achieving quality sequence reads by appropriate clean-up steps, (iv controlling primer amplification preferences, (v introducing PCR-free sequence capturing, (vi estimating primer detection capabilities through controlled experiments and/or (vii post-hoc introduction of “site occupancy-detection models.” With eDNA methodology becoming increasingly routine, its use is strongly recommended to retrieve species distributional data for SDMs.

Drought resilience across ecologically dominant species: An experiment-model integration approach

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Felton, A. J.; Warren, J.; Ricciuto, D. M.; Smith, M. D.

2017-12-01

Poorly understood are the mechanisms contributing to variability in ecosystem recovery following drought. Grasslands of the central U.S. are ecologically and economically important ecosystems, yet are also highly sensitive to drought. Although characteristics of these ecosystems change across gradients of temperature and precipitation, a consistent feature among these systems is the presence of highly abundant, dominant grass species that control biomass production. As a result, the incorporation of these species' traits into terrestrial biosphere models may constrain predictions amid increases in climatic variability. Here we report the results of a modeling-experiment (MODEX) research approach. We investigated the physiological, morphological and growth responses of the dominant grass species from each of the four major grasslands of the central U.S. (ranging from tallgrass prairie to desert grassland) following severe drought. Despite significant differences in baseline values, full recovery in leaf physiological function was evident across species, of which was consistently driven by the production of new leaves. Further, recovery in whole-plant carbon uptake tended to be driven by shifts in allocation from belowground to aboveground structures. However, there was clear variability among species in the magnitude of this dynamic as well as the relative allocation to stem versus leaf production. As a result, all species harbored the physiological capacity to recover from drought, yet we posit that variability in the recovery of whole-plant carbon uptake to be more strongly driven by variability in the sensitivity of species' morphology to soil moisture increases. The next step of this project will be to incorporate these and other existing data on these species and ecosystems into the community land model in an effort to test the sensitivity of this model to these data.

Modelling patterns of pollinator species richness and diversity using satellite image texture.

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Sylvia Hofmann

Full Text Available Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010-2013 from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3-5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees. While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity.

Modelling patterns of pollinator species richness and diversity using satellite image texture.

Science.gov (United States)

Hofmann, Sylvia; Everaars, Jeroen; Schweiger, Oliver; Frenzel, Mark; Bannehr, Lutz; Cord, Anna F

2017-01-01

Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS) can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010-2013) from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3-5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees). While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity.

Transgenerational plasticity as an important mechanism affecting response of clonal species to changing climate.

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Münzbergová, Zuzana; Hadincová, Věroslava

2017-07-01

In spite of the increasing number of studies on the importance of transgenerational plasticity for species response to novel environments, its effects on species ability to respond to climate change are still largely unexplored. We study the importance of transgenerational plasticity for response of a clonal species Festuca rubra . Individuals from four natural populations representing two levels of temperature and two levels of precipitation were cultivated in four growth chambers that simulate the temperature and precipitation of origin of the populations (maternal phase). Each population was represented in each growth chamber. After 6 months, single young ramets of these plants were reshuffled among the growth chambers and let to grow for additional 2 months (offspring phase). The results show that transgenerational effects (i.e., maternal phase conditions) significantly modify species response to novel climates, and the direction and intensity of the response depend on the climate of origin of the plants. For traits related to recourse acquisition, the conditions of maternal phase, either alone or in interaction mainly with climate of origin, had stronger effect than the conditions of cultivation. Overall, the maternal climate interacted more intensively with the climate of origin than with the offspring climate. The direction of the effect of the maternal climate was of different directions and intensities depending on plant origin and trait studied. The data demonstrated strong significant effects of conditions during maternal phase on species response to novel climates. These transgenerational affects were, however, not adaptive. Still, transgenerational plasticity may be an important driver of species response to novel conditions across clonal generations. These effects thus need to be carefully considered in future studies exploring species response to novel climates. This will also have strong effects on species performance under increasingly variable

Importance of riparian remnants for frog species diversity in a highly fragmented rainforest.

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Rodríguez-Mendoza, Clara; Pineda, Eduardo

2010-12-23

Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest.

Effects of model complexity and priors on estimation using sequential importance sampling/resampling for species conservation

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Dunham, Kylee; Grand, James B.

2016-01-01

We examined the effects of complexity and priors on the accuracy of models used to estimate ecological and observational processes, and to make predictions regarding population size and structure. State-space models are useful for estimating complex, unobservable population processes and making predictions about future populations based on limited data. To better understand the utility of state space models in evaluating population dynamics, we used them in a Bayesian framework and compared the accuracy of models with differing complexity, with and without informative priors using sequential importance sampling/resampling (SISR). Count data were simulated for 25 years using known parameters and observation process for each model. We used kernel smoothing to reduce the effect of particle depletion, which is common when estimating both states and parameters with SISR. Models using informative priors estimated parameter values and population size with greater accuracy than their non-informative counterparts. While the estimates of population size and trend did not suffer greatly in models using non-informative priors, the algorithm was unable to accurately estimate demographic parameters. This model framework provides reasonable estimates of population size when little to no information is available; however, when information on some vital rates is available, SISR can be used to obtain more precise estimates of population size and process. Incorporating model complexity such as that required by structured populations with stage-specific vital rates affects precision and accuracy when estimating latent population variables and predicting population dynamics. These results are important to consider when designing monitoring programs and conservation efforts requiring management of specific population segments.

BAYESIAN MODELS FOR SPECIES DISTRIBUTION MODELLING WITH ONLY-PRESENCE RECORDS

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Bartolo de Jesús Villar-Hernández

2015-08-01

Full Text Available One of the central issues in ecology is the study of geographical distribution of species of flora and fauna through Species Distribution Models (SDM. Recently, scientific interest has focused on presence-only records. Two recent approaches have been proposed for this problem: a model based on maximum likelihood method (Maxlike and an inhomogeneous poisson process model (IPP. In this paper we discussed two bayesian approaches called MaxBayes and IPPBayes based on Maxlike and IPP model, respectively. To illustrate these proposals, we implemented two study examples: (1 both models were implemented on a simulated dataset, and (2 we modeled the potencial distribution of genus Dalea in the Tehuacan-Cuicatlán biosphere reserve with both models, the results was compared with that of Maxent. The results show that both models, MaxBayes and IPPBayes, are viable alternatives when species distribution are modeled with only-presence records. For simulated dataset, MaxBayes achieved prevalence estimation, even when the number of records was small. In the real dataset example, both models predict similar potential distributions like Maxent does. Â

Focus stacking technique in identification of forensically important Chrysomya species (Diptera: Calliphoridae

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Noha A. Elleboudy

2016-09-01

Recommendations: Further studies on the blowfly species that occur in Egypt and documentation of their key for identification are recommended to facilitate the diverse applications of these important insects in forensic investigations.

Towards an integrated approach to modelling the risks and impacts of invasive forest species

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Denys Yemshanov; Daniel McKenney; John Pedlar; Frank Koch; David Cook

2009-01-01

In this paper we provide an overview of an integrated approach to modelling the risks and impacts associated with non-indigenous forest pest species. This is a broad and important topic given the scale of ecological and economic consequences associated with non-indigenous species in north america and elsewhere. Assessments of risk and impacts remain difficult due to...

Temperature-dependent development of the parasitoid Tachinaephagus zealandicus on five forensically important carrion fly species.

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Voss, S C; Spafford, H; Dadour, I R

2010-06-01

The influences of temperature and host species on the development of the forensically important parasitoid Tachinaephagus zealandicus Ashmead (Hymenoptera: Encyrtidae) were studied at six constant temperatures in the range of 15-30 degrees C. T. zealandicus completed development successfully between 15 degrees C and 27 degrees C on five species of Calliphoridae, Calliphora albifrontalis Malloch, Calliphora dubia Macquart, Lucilia sericata Meigen, Chrysomya rufifacies Macquart and Chrysomya megacephala Fabricius. No adult parasitoids emerged from any of the host species reared at 30 degrees C. Temperature and host species significantly influenced development time, emergence success and progeny size. Development was significantly longer on Ch. megacephala and Ch. rufifacies at 18-24 degrees C and significantly longer on Ch. rufifacies and C. albifrontalis at 15 degrees C and 27 degrees C. Parasitoid emergence success was greatest at 21 degrees C, declined at the temperature extremes (15 degrees C and 27 degrees C) and was significantly lower on Ch. megacephala and Ch. rufifacies than on the three other host species. Progeny numbers per host pupa were highest at 21-24 degrees C, declined on either side of this temperature range and were significantly lower on L. sericata, Ch. rufifacies and Ch. megacephala than on either C. dubia or C. albifrontalis. An effect of host species on sex ratio was only observed at 27 degrees C, at which a higher proportion of T. zealandicus females emerged from Ch. megacephala and Ch. rufifacies than from the other host species. The thermal requirements for development (developmental thresholds, thermal constant, optimum temperature) of T. zealandicus in each host species were estimated using linear and non-linear models. Upper and lower developmental thresholds ranged between 29.90 degrees C and 31.73 degrees C, and 9.73 degrees C and 10.08 degrees C, respectively. The optimum temperature for development was estimated at between 25

Molecular characterization of Fasciola species isolated from imported sheep in Taif region (Saudi Arabia).

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Shalaby, I; Gherbawy, Y; Banaja, A

2013-03-01

Accurate identification of Fasciola species, followed by biological and ecological characterization, is important with concern to the planning for field control. Because there are many variations in morphological characteristics, exact distinguishing of Fasciola species is usually difficult by simple traditional microscopic measurements and, therefore, the morphometric characterization may be insufficient for the species identification. Hence, the present work was proposed to collect 100 liver samples from 100 imported sheep from Sudan from slaughterhouses in Taif region. The samples were firstly examined macroscopically and microscopically to ensure the presence or absence of infection. The collected worms were subjected for RAPD-PCR analysis using different primers and ITS1 sequences for accurate identification. Using RAPD-PCR analysis, two primers were selected to amplify the DNA of each Fasciola. The results show that the amplification fragments were between 500 and 1500 bp and, the use of random genetic markers allowed to discriminate among the different collected species. Using Internal transcribed spacer region (ITS) sequencing, the imported sheep in Taif region consisted of 630 bps including complete ITS1, partial 18S and 5.8S and had 5 variable nucleotide positions. This is the first demonstration of the existence of both F. hepatica, F. gigantica and hybrid and/or introgressed populations of liver flukes bearing genetic material from both F. hepatica and F. gigantica in the imported sheep in Saudi Arabia by a genetic approach.

Species Distribution modeling as a tool to unravel determinants of palm distribution in Thailand

DEFF Research Database (Denmark)

Tovaranonte, Jantrararuk; Barfod, Anders S.; Balslev, Henrik

2011-01-01

As a consequence of the decimation of the forest cover in Thailand from 50% to ca. 20 % since the 1950ies, it is difficult to gain insight in the drivers behind past, present and future distribution ranges of plant species. Species distribution modeling allows visualization of potential species...... distribution under specific sets of assumptions. In this study we used maximum entropy to map potential distributions of 103 species of palms for which more than 5 herbarium records exist. Palms constitute key-stone plant group from both an ecological, economical and conservation perspective. The models were......) and the Area Under the Curve (AUC). All models performed well with AUC scores above 0.95. The predicted distribution ranges showed high suitability for palms in the southern region of Thailand. It also shows that spatial predictor variables are important in cases where historical processes may explain extant...

Patterns of among- and within-species variation in heterospecific pollen receipt: The importance of ecological generalization.

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Arceo-Gómez, Gerardo; Abdala-Roberts, Luis; Jankowiak, Anneka; Kohler, Clare; Meindl, George A; Navarro-Fernández, Carmen M; Parra-Tabla, Víctor; Ashman, Tia-Lynn; Alonso, Conchita

2016-03-01

Coflowering plants are at risk for receiving pollen from heterospecifics as well as conspecifics, yet evidence shows wide variation in the degree that heterospecific pollen transfer occurs. Evaluation of patterns and correlates of among- and within-species variation in heterospecific pollen (HP) receipt is key to understanding its importance for floral evolution and species coexistence; however, the rarity of deeply sampled multispecies comparisons has precluded such an evaluation. We evaluated patterns of among- and within-species variation in HP load size and diversity in 19 species across three distinct plant communities. We assessed the importance of phenotypic specialization (floral phenotype), ecological specialization (contemporary visitor assemblage), and conspecific flower density as determinants of among-species variation. We present hypotheses for different accrual patterns of HP within species based on the evenness and quality of floral visitors and evaluated these by characterizing the relationship between conspecific pollen (CP) and HP receipt. We found that within-species variation in HP receipt was greater than among-species and among-communities variation. Among species, ecological generalization emerged as the strongest driver of variation in HP receipt irrespective of phenotypic specialization. Within-species variation in HP load size and diversity was predicted most often from two CP-HP relationships (linear or exponentially decreasing), suggesting that two distinct types of plant-pollinator interactions prevail. Our results give important insights into the potential drivers of among- and within-species variation in HP receipt. They also highlight the value of explorations of patterns at the intraspecific level, which can ultimately shed light on plant-pollinator-mediated selection in diverse plant communities. © 2016 Botanical Society of America.

Pollen Deposition Is More Important than Species Richness for Seed Set in Luffa Gourd.

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Ali, M; Saeed, S; Sajjad, A

2016-10-01

In the context of global biodiversity decline, it is imperative to understand the different aspects of bee communities for sustaining the vital ecosystem service of pollination. Bee species can be assigned to functional groups (average difference among species in functionally related traits) on the basis of complementarity (trait variations exhibited by individual organisms) in their behavior but is not yet known which functional group trait is most important for seed set. In this study, first, the functional groups of bees were made based on their five selected traits (pollen deposition, visitation rate, stay time, visiting time of the day, body size) and then related to the seed set of obligate cross-pollinated Luffa gourd (Luffa aegyptiaca). We found that bee diversity and abundance differed significantly among the studied plots, but only the bee species richness was positively related to the seed set. Functional group diversity in terms of pollen deposition explained even more of the variance in seed set (r 2  = 0.74) than did the species richness (r 2  = 0.53) making it the most important trait of bee species for predicting the crop reproductive success.

A simple model for skewed species-lifetime distributions

KAUST Repository

Murase, Yohsuke

2010-06-11

A simple model of a biological community assembly is studied. Communities are assembled by successive migrations and extinctions of species. In the model, species are interacting with each other. The intensity of the interaction between each pair of species is denoted by an interaction coefficient. At each time step, a new species is introduced to the system with randomly assigned interaction coefficients. If the sum of the coefficients, which we call the fitness of a species, is negative, the species goes extinct. The species-lifetime distribution is found to be well characterized by a stretched exponential function with an exponent close to 1/2. This profile agrees not only with more realistic population dynamics models but also with fossil records. We also find that an age-independent and inversely diversity-dependent mortality, which is confirmed in the simulation, is a key mechanism accounting for the distribution. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil

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Karine Pinto e Vairo

2011-09-01

Full Text Available Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.Chave pictórica para a identificação das espécies de Sarcophagidae (Diptera de potencial importância forense do sul do Brasil. Espécies da subfamília Sarcophaginae são importantes para a entomologia forense devido ao seu hábito necrófago. Este trabalho apresenta uma chave pictórica para a identificação de 22 espécies de Sarcophaginae de 10 gêneros encontradas na região sul do Brasil. São fornecidas fotografias dos principais estruturas das espécies, principalmente da terminália masculina.

Nyala and Bushbuck I: A Competing Species Model.

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Fay, Temple H.; Greeff, Johanna C.

1999-01-01

Introduces a model of differential equations for students--a very real overpopulation problem is occurring in the Ndumu Game Reserve in KwaZulu-Natal, South Africa, where one species of antelope, the Nyala, is crowding out another species, the Bushbuck. Constructs a competing species model to mathematically describe what is occurring in Ndumu.…

Standardization of a two-step real-time polymerase chain reaction based method for species-specific detection of medically important Aspergillus species.

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Das, P; Pandey, P; Harishankar, A; Chandy, M; Bhattacharya, S; Chakrabarti, A

2017-01-01

Standardization of Aspergillus polymerase chain reaction (PCR) poses two technical challenges (a) standardization of DNA extraction, (b) optimization of PCR against various medically important Aspergillus species. Many cases of aspergillosis go undiagnosed because of relative insensitivity of conventional diagnostic methods such as microscopy, culture or antigen detection. The present study is an attempt to standardize real-time PCR assay for rapid sensitive and specific detection of Aspergillus DNA in EDTA whole blood. Three nucleic acid extraction protocols were compared and a two-step real-time PCR assay was developed and validated following the recommendations of the European Aspergillus PCR Initiative in our setup. In the first PCR step (pan-Aspergillus PCR), the target was 28S rDNA gene, whereas in the second step, species specific PCR the targets were beta-tubulin (for Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus), gene and calmodulin gene (for Aspergillus niger). Species specific identification of four medically important Aspergillus species, namely, A. fumigatus, A. flavus, A. niger and A. terreus were achieved by this PCR. Specificity of the PCR was tested against 34 different DNA source including bacteria, virus, yeast, other Aspergillus sp., other fungal species and for human DNA and had no false-positive reactions. The analytical sensitivity of the PCR was found to be 102 CFU/ml. The present protocol of two-step real-time PCR assays for genus- and species-specific identification for commonly isolated species in whole blood for diagnosis of invasive Aspergillus infections offers a rapid, sensitive and specific assay option and requires clinical validation at multiple centers.

Incorporating spatial autocorrelation into species distribution models alters forecasts of climate-mediated range shifts.

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Crase, Beth; Liedloff, Adam; Vesk, Peter A; Fukuda, Yusuke; Wintle, Brendan A

2014-08-01

Species distribution models (SDMs) are widely used to forecast changes in the spatial distributions of species and communities in response to climate change. However, spatial autocorrelation (SA) is rarely accounted for in these models, despite its ubiquity in broad-scale ecological data. While spatial autocorrelation in model residuals is known to result in biased parameter estimates and the inflation of type I errors, the influence of unmodeled SA on species' range forecasts is poorly understood. Here we quantify how accounting for SA in SDMs influences the magnitude of range shift forecasts produced by SDMs for multiple climate change scenarios. SDMs were fitted to simulated data with a known autocorrelation structure, and to field observations of three mangrove communities from northern Australia displaying strong spatial autocorrelation. Three modeling approaches were implemented: environment-only models (most frequently applied in species' range forecasts), and two approaches that incorporate SA; autologistic models and residuals autocovariate (RAC) models. Differences in forecasts among modeling approaches and climate scenarios were quantified. While all model predictions at the current time closely matched that of the actual current distribution of the mangrove communities, under the climate change scenarios environment-only models forecast substantially greater range shifts than models incorporating SA. Furthermore, the magnitude of these differences intensified with increasing increments of climate change across the scenarios. When models do not account for SA, forecasts of species' range shifts indicate more extreme impacts of climate change, compared to models that explicitly account for SA. Therefore, where biological or population processes induce substantial autocorrelation in the distribution of organisms, and this is not modeled, model predictions will be inaccurate. These results have global importance for conservation efforts as inaccurate

Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

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Franklin, J.; Wejnert, K.E.; Hathaway, S.A.; Rochester, C.J.; Fisher, R.N.

2009-01-01

Aim: Several studies have found that more accurate predictive models of species' occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species' survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location: Coastal southern California, USA. Methods: Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver-operating characteristic (ROC) plot based on twofold cross-validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results: Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions: Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the

Species distribution modeling in regions of high need and limited data: waterfowl of China

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Prosser, Diann J.; Ding, Changqing; Erwin, R. Michael; Mundkur, Taej; Sullivan, Jeffery D.; Ellis, Erle C.

2018-01-01

BackgroundA number of conservation and societal issues require understanding how species are distributed on the landscape, yet ecologists are often faced with a lack of data to develop models at the resolution and extent desired, resulting in inefficient use of conservation resources. Such a situation presented itself in our attempt to develop waterfowl distribution models as part of a multi-disciplinary team targeting the control of the highly pathogenic H5N1 avian influenza virus in China.MethodsFaced with limited data, we built species distribution models using a habitat suitability approach for China’s breeding and non-breeding (hereafter, wintering) waterfowl. An extensive review of the literature was used to determine model parameters for habitat modeling. Habitat relationships were implemented in GIS using land cover covariates. Wintering models were validated using waterfowl census data, while breeding models, though developed for many species, were only validated for the one species with sufficient telemetry data available.ResultsWe developed suitability models for 42 waterfowl species (30 breeding and 39 wintering) at 1 km resolution for the extent of China, along with cumulative and genus level species richness maps. Breeding season models showed highest waterfowl suitability in wetlands of the high-elevation west-central plateau and northeastern China. Wintering waterfowl suitability was highest in the lowland regions of southeastern China. Validation measures indicated strong performance in predicting species presence. Comparing our model outputs to China’s protected areas indicated that breeding habitat was generally better covered than wintering habitat, and identified locations for which additional research and protection should be prioritized.ConclusionsThese suitability models are the first available for many of China’s waterfowl species, and have direct utility to conservation and habitat planning and prioritizing management of critically

Fit-for-purpose: species distribution model performance depends on evaluation criteria - Dutch Hoverflies as a case study.

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Aguirre-Gutiérrez, Jesús; Carvalheiro, Luísa G; Polce, Chiara; van Loon, E Emiel; Raes, Niels; Reemer, Menno; Biesmeijer, Jacobus C

2013-01-01

Understanding species distributions and the factors limiting them is an important topic in ecology and conservation, including in nature reserve selection and predicting climate change impacts. While Species Distribution Models (SDM) are the main tool used for these purposes, choosing the best SDM algorithm is not straightforward as these are plentiful and can be applied in many different ways. SDM are used mainly to gain insight in 1) overall species distributions, 2) their past-present-future probability of occurrence and/or 3) to understand their ecological niche limits (also referred to as ecological niche modelling). The fact that these three aims may require different models and outputs is, however, rarely considered and has not been evaluated consistently. Here we use data from a systematically sampled set of species occurrences to specifically test the performance of Species Distribution Models across several commonly used algorithms. Species range in distribution patterns from rare to common and from local to widespread. We compare overall model fit (representing species distribution), the accuracy of the predictions at multiple spatial scales, and the consistency in selection of environmental correlations all across multiple modelling runs. As expected, the choice of modelling algorithm determines model outcome. However, model quality depends not only on the algorithm, but also on the measure of model fit used and the scale at which it is used. Although model fit was higher for the consensus approach and Maxent, Maxent and GAM models were more consistent in estimating local occurrence, while RF and GBM showed higher consistency in environmental variables selection. Model outcomes diverged more for narrowly distributed species than for widespread species. We suggest that matching study aims with modelling approach is essential in Species Distribution Models, and provide suggestions how to do this for different modelling aims and species' data

The Importance of Landscape Elements for Bat Activity and Species Richness in Agricultural Areas.

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Olga Heim

Full Text Available Landscape heterogeneity is regarded as a key factor for maintaining biodiversity and ecosystem function in production landscapes. We investigated whether grassland sites at close vicinity to forested areas are more frequently used by bats. Considering that bats are important consumers of herbivorous insects, including agricultural pest, this is important for sustainable land management. Bat activity and species richness were assessed using repeated monitoring from May to September in 2010 with acoustic monitoring surveys on 50 grassland sites in the Biosphere Reserve Schorfheide-Chorin (North-East Germany. Using spatial analysis (GIS, we measured the closest distance of each grassland site to potentially connecting landscape elements (e.g., trees, linear vegetation, groves, running and standing water. In addition, we assessed the distance to and the percent land cover of forest remnants and urban areas in a 200 m buffer around the recording sites to address differences in the local landscape setting. Species richness and bat activity increased significantly with higher forest land cover in the 200 m buffer and at smaller distance to forested areas. Moreover, species richness increased in proximity to tree groves. Larger amount of forest land cover and smaller distance to forest also resulted in a higher activity of bats on grassland sites in the beginning of the year during May, June and July. Landscape elements near grassland sites also influenced species composition of bats and species richness of functional groups (open, edge and narrow space foragers. Our results highlight the importance of forested areas, and suggest that agricultural grasslands that are closer to forest remnants might be better buffered against outbreaks of agricultural pest insects due to higher species richness and higher bat activity. Furthermore, our data reveals that even for highly mobile species such as bats, a very dense network of connecting elements within the

PCR-RFLP on β-tubulin gene for rapid identification of the most clinically important species of Aspergillus.

Science.gov (United States)

Nasri, Tuba; Hedayati, Mohammad Taghi; Abastabar, Mahdi; Pasqualotto, Alessandro C; Armaki, Mojtaba Taghizadeh; Hoseinnejad, Akbar; Nabili, Mojtaba

2015-10-01

Aspergillus species are important agents of life-threatening infections in immunosuppressed patients. Proper speciation in the Aspergilli has been justified based on varied fungal virulence, clinical presentations, and antifungal resistance. Accurate identification of Aspergillus species usually relies on fungal DNA sequencing but this requires expensive equipment that is not available in most clinical laboratories. We developed and validated a discriminative low-cost PCR-based test to discriminate Aspergillus isolates at the species level. The Beta tubulin gene of various reference strains of Aspergillus species was amplified using the universal fungal primers Bt2a and Bt2b. The PCR products were subjected to digestion with a single restriction enzyme AlwI. All Aspergillus isolates were subjected to DNA sequencing for final species characterization. The PCR-RFLP test generated unique patterns for six clinically important Aspergillus species, including Aspergillus flavus, Aspergillus fumigatus, Aspergillus nidulans, Aspergillus terreus, Aspergillus clavatus and Aspergillus nidulans. The one-enzyme PCR-RFLP on Beta tubulin gene designed in this study is a low-cost tool for the reliable and rapid differentiation of the clinically important Aspergillus species. Copyright © 2015 Elsevier B.V. All rights reserved.

Larval morphology of Chrysomya nigripes (Diptera: Calliphoridae), a fly species of forensic importance.

Science.gov (United States)

Sukontason, Kabkaew L; Vogtsberger, Roy C; Boonchu, Noppawan; Chaiwong, Tarinee; Sripakdee, Duanghatai; Ngern-Klun, Radchadawan; Piangjai, Somsak; Sukontason, Kom

2005-05-01

The morphology of all instars of Chrysomya nigripes Aubertin, a blow fly species of forensic importance, is presented with the aid of both light microscopy and scanning electron microscopy (SEM). Morphological features of the cephalopharyngeal skeleton, anterior spiracle, posterior spiracle, and dorsal spines between the prothorax and mesothorax are highlighted. No consistent features were found, even using SEM, for distinguishing the first instar of C. nigripes from that of Chrysomya megacephala (F.) or Chrysomya rufifacies (Macquart), two other commonly associated blow fly species in corpses in Thailand. Several features observed in second and third instars proved to be valuable characteristics for separating these species.

Trees of Laos and Vietnam: a field guide to 100 economically or ecologically important species

NARCIS (Netherlands)

Sam, Hoang Van; Nanthavong, Khamseng; Keßler, P.J.A.

2004-01-01

This field guide to 100 economically or ecologically important tree species from Laos and Vietnam enables the user to identify the included taxa with user-friendly keys. It includes scientific names, botanical descriptions of families, genera, and species. Specific information on distribution,

A simple model for skewed species-lifetime distributions

KAUST Repository

Murase, Yohsuke; Shimada, Takashi; Ito, Nobuyasu

2010-01-01

A simple model of a biological community assembly is studied. Communities are assembled by successive migrations and extinctions of species. In the model, species are interacting with each other. The intensity of the interaction between each pair

Bias correction in species distribution models: pooling survey and collection data for multiple species.

Science.gov (United States)

Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A

2015-04-01

Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence-absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence-absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model's performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence-absence data for a given species is scarceIf we have only presence-only data and no presence-absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species' geographic range.

Species distribution modeling for the invasive raccoon dog (Nyctereutes procyonoides) in Austria and first range predictions for alpine environments

OpenAIRE

Duscher Tanja; Nopp-Mayr Ursula

2017-01-01

Species distribution models are important tools for wildlife management planning, particularly in the case of invasive species. We employed a recent framework for niche-based invasive species distribution modeling to predict the probability of presence for the invasive raccoon dog (Nyctereutes procyonoides) in Austria. The raccoon dog is an adaptive, mobile and highly reproductive Asiatic canid that has successfully invaded many parts of Europe. It is known...

EVALUATING THE NOVEL METHODS ON SPECIES DISTRIBUTION MODELING IN COMPLEX FOREST

Directory of Open Access Journals (Sweden)

C. H. Tu

2012-07-01

Full Text Available The prediction of species distribution has become a focus in ecology. For predicting a result more effectively and accurately, some novel methods have been proposed recently, like support vector machine (SVM and maximum entropy (MAXENT. However, high complexity in the forest, like that in Taiwan, will make the modeling become even harder. In this study, we aim to explore which method is more applicable to species distribution modeling in the complex forest. Castanopsis carlesii (long-leaf chinkapin, LLC, growing widely in Taiwan, was chosen as the target species because its seeds are an important food source for animals. We overlaid the tree samples on the layers of altitude, slope, aspect, terrain position, and vegetation index derived from SOPT-5 images, and developed three models, MAXENT, SVM, and decision tree (DT, to predict the potential habitat of LLCs. We evaluated these models by two sets of independent samples in different site and the effect on the complexity of forest by changing the background sample size (BSZ. In the forest with low complex (small BSZ, the accuracies of SVM (kappa = 0.87 and DT (0.86 models were slightly higher than that of MAXENT (0.84. In the more complex situation (large BSZ, MAXENT kept high kappa value (0.85, whereas SVM (0.61 and DT (0.57 models dropped significantly due to limiting the habitat close to samples. Therefore, MAXENT model was more applicable to predict species’ potential habitat in the complex forest; whereas SVM and DT models would tend to underestimate the potential habitat of LLCs.

Fit-for-purpose: species distribution model performance depends on evaluation criteria -Dutch hoverflies as a case study

NARCIS (Netherlands)

Aguirre-Gutiérrez, J.; Carvalheiro, L.G.; Polce, C.; van Loon, E.E.; Raes, N.; Reemer, M.; Biesmeijer, J.C.

2013-01-01

Understanding species distributions and the factors limiting them is an important topic in ecology and conservation, including in nature reserve selection and predicting climate change impacts. While Species Distribution Models (SDM) are the main tool used for these purposes, choosing the best SDM

A nonlocal and periodic reaction-diffusion-advection model of a single phytoplankton species.

Science.gov (United States)

Peng, Rui; Zhao, Xiao-Qiang

2016-02-01

In this article, we are concerned with a nonlocal reaction-diffusion-advection model which describes the evolution of a single phytoplankton species in a eutrophic vertical water column where the species relies solely on light for its metabolism. The new feature of our modeling equation lies in that the incident light intensity and the death rate are assumed to be time periodic with a common period. We first establish a threshold type result on the global dynamics of this model in terms of the basic reproduction number R0. Then we derive various characterizations of R0 with respect to the vertical turbulent diffusion rate, the sinking or buoyant rate and the water column depth, respectively, which in turn give rather precise conditions to determine whether the phytoplankton persist or become extinct. Our theoretical results not only extend the existing ones for the time-independent case, but also reveal new interesting effects of the modeling parameters and the time-periodic heterogeneous environment on persistence and extinction of the phytoplankton species, and thereby suggest important implications for phytoplankton growth control.

Species-free species distribution models describe macroecological properties of protected area networks.

Science.gov (United States)

Robinson, Jason L; Fordyce, James A

2017-01-01

Among the greatest challenges facing the conservation of plants and animal species in protected areas are threats from a rapidly changing climate. An altered climate creates both challenges and opportunities for improving the management of protected areas in networks. Increasingly, quantitative tools like species distribution modeling are used to assess the performance of protected areas and predict potential responses to changing climates for groups of species, within a predictive framework. At larger geographic domains and scales, protected area network units have spatial geoclimatic properties that can be described in the gap analysis typically used to measure or aggregate the geographic distributions of species (stacked species distribution models, or S-SDM). We extend the use of species distribution modeling techniques in order to model the climate envelope (or "footprint") of individual protected areas within a network of protected areas distributed across the 48 conterminous United States and managed by the US National Park System. In our approach we treat each protected area as the geographic range of a hypothetical endemic species, then use MaxEnt and 5 uncorrelated BioClim variables to model the geographic distribution of the climatic envelope associated with each protected area unit (modeling the geographic area of park units as the range of a species). We describe the individual and aggregated climate envelopes predicted by a large network of 163 protected areas and briefly illustrate how macroecological measures of geodiversity can be derived from our analysis of the landscape ecological context of protected areas. To estimate trajectories of change in the temporal distribution of climatic features within a protected area network, we projected the climate envelopes of protected areas in current conditions onto a dataset of predicted future climatic conditions. Our results suggest that the climate envelopes of some parks may be locally unique or have

The geography of demography: long-term demographic studies and species distribution models reveal a species border limited by adaptation.

Science.gov (United States)

Eckhart, V M; Geber, M A; Morris, W F; Fabio, E S; Tiffin, P; Moeller, D A

2011-10-01

Potential causes of species' geographic distribution limits fall into two broad classes: (1) limited adaptation across spatially variable environments and (2) limited opportunities to colonize unoccupied areas. Combining demographic studies, analyses of demographic responses to environmental variation, and species distribution models, we investigated the causes of range limits in a model system, the eastern border of the California annual plant Clarkia xantiana ssp. xantiana. Vital rates of 20 populations varied with growing season temperature and precipitation: fruit number and overwinter survival of 1-year-old seeds declined steeply, while current-year seed germination increased modestly along west-to-east gradients in decreasing temperature, decreasing mean precipitation, and increasing variation in precipitation. Long-term stochastic finite rate of increase, λ(s), exhibited a fourfold range and varied among geologic surface materials as well as with temperature and precipitation. Growth rate declined significantly toward the eastern border, falling below 1 in three of the five easternmost populations. Distribution models employing demographically important environmental variables predicted low habitat favorability beyond the eastern border. Models that filtered or weighted population presences by λ(s) predicted steeper eastward declines in favorability and assigned greater roles in setting the distribution to among-year variation in precipitation and to geologic surface material. These analyses reveal a species border likely set by limited adaptation to declining environmental quality.

An Overview of Important Ethnomedicinal Herbs of Phyllanthus Species: Present Status and Future Prospects

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Bharti Sarin

2014-01-01

Full Text Available The genus Phyllanthus consists of more than 1000 species, of which many are used as traditional medicines. The plant extracts have been used since ancient times, for treating hypertension, diabetes, hepatic, urinary, and sexual disorders, and other common ailments. Modern day scientific investigations have now confirmed pharmacognostic properties of Phyllanthus herbs. The phytochemicals attributing these medicinal properties have been identified in many of the Phyllanthus herbs. The morphologically similar herbs of Phyllanthus grow together and admixture of species during collection for manufacture of herbal medicines is quite common. Hence, along with pharmacognostic and phytochemical studies, appropriate protocols for correct identification of species are also important. As the use of these herbs as green medicines is becoming more popular, it is imperative to assess its genetic diversity and phylogenetic relatedness for future conservation strategies. This review is an attempt to present an overview of the existing studies on pharmacognostics, phytochemistry, species identification, and genetic diversity of Phyllanthus herbs and consequently (i highlight areas where further research is needed and (ii draw attention towards extending similar studies in underutilized but potentially important herbs such as P. maderaspatensis, P. kozhikodianus, P. rheedii, P. scabrifolius, and P. rotundifolius.

Spectral Data Captures Important Variability Between and Among Species and Functional Types

Science.gov (United States)

Townsend, P. A.; Serbin, S. P.; Kingdon, C.; Singh, A.; Couture, J. J.; Gamon, J. A.

2013-12-01

Narrowband spectral data in the visible, near and shortwave infrared (400-2500 nm) are being used increasingly in plant ecology to characterize the biochemical, physiological and water status of vegetation, as well as community composition. In particular, spectroscopic data have recently received considerable attention for their capacity to discriminate plants according to functional properties or 'optical types.' Such measurements can be acquired from airborne/satellite remote sensing imagery or field spectrometers and are commonly used to directly estimate or infer properties important to photosynthesis, carbon and water fluxes, nutrient dynamics, phenology, and disturbance. Spectral data therefore represent proxies for measurements that are otherwise time consuming or expensive to make, and - more importantly - provide the opportunity to characterize the spatial and temporal variability of taxonomic or functional groups. We have found that spectral variation within species and functional types can in fact exceed the variation between types. As such, we recommend that the traditional quantification of characteristics defining species and/or functional types must be modified to include the range of variability in those properties. We provide four examples of the importance of spectral data for describing within-species/functional type variation. First, within temperate forests, the spectral properties of foliage vary considerably with canopy position. This variability is strongly related to differences in specific leaf area between shade- and sun-lit leaves, and the resulting differences among leaves in strategies for light harvesting, photosynthesis, and leaf longevity. These results point to the need to better characterize leaf optical properties throughout a canopy, rather than basing the characterization of ecosystem functioning on only the sunlit portion of the canopy crown. Second, we show considerable differences in optical properties of foliage from

The importance of plot size and the number of sampling seasons on capturing macrofungal species richness.

Science.gov (United States)

Li, Huili; Ostermann, Anne; Karunarathna, Samantha C; Xu, Jianchu; Hyde, Kevin D; Mortimer, Peter E

2018-07-01

The species-area relationship is an important factor in the study of species diversity, conservation biology, and landscape ecology. A deeper understanding of this relationship is necessary, in order to provide recommendations on how to improve the quality of data collection on macrofungal diversity in different land use systems in future studies, a systematic assessment of methodological parameters, in particular optimal plot sizes. The species-area relationship of macrofungi in tropical and temperate climatic zones and four different land use systems were investigated by determining the macrofungal species richness in plot sizes ranging from 100 m 2 to 10 000 m 2 over two sampling seasons. We found that the effect of plot size on recorded species richness significantly differed between land use systems with the exception of monoculture systems. For both climate zones, land use system needs to be considered when determining optimal plot size. Using an optimal plot size was more important than temporal replication (over two sampling seasons) in accurately recording species richness. Copyright © 2018 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Are ecologically important tree species the most useful? A case study from indigenous people in the Bolivian Amazon.

Science.gov (United States)

Guèze, Maximilien; Luz, Ana Catarina; Paneque-Gálvez, Jaime; Macía, Manuel J; Orta-Martínez, Martí; Pino, Joan; Reyes-García, Victoria

2014-03-01

Researchers have argued that indigenous peoples preferably use the most apparent plant species, particularly for medicinal uses. However, the association between the ecological importance of a species and its usefulness remains unclear. In this paper we quantify such association for six use categories (firewood, construction, materials, food, medicines and other uses). We collected data on the uses of 58 tree species, as reported by 93 informants in 22 villages in the Tsimane' territory (Bolivian Amazon). We calculated the ecological importance of the same species by deriving their importance value index (IVI) in 48 0.1-ha old-growth forest plots. Matching both data sets, we found a positive relation between the IVI of a species and its overall use value (UV) as well as with its UV for construction and materials. We found a negative relation between IVI and UV for species that were reportedly used for medicine and food uses, and no clear pattern for the other categories. We hypothesize that species used for construction or crafting purposes because of their physical properties are more easily substitutable than species used for medicinal or edible purposes because of their chemical properties.

Modeling abundance using N-mixture models: the importance of considering ecological mechanisms.

Science.gov (United States)

Joseph, Liana N; Elkin, Ché; Martin, Tara G; Possinghami, Hugh P

2009-04-01

Predicting abundance across a species' distribution is useful for studies of ecology and biodiversity management. Modeling of survey data in relation to environmental variables can be a powerful method for extrapolating abundances across a species' distribution and, consequently, calculating total abundances and ultimately trends. Research in this area has demonstrated that models of abundance are often unstable and produce spurious estimates, and until recently our ability to remove detection error limited the development of accurate models. The N-mixture model accounts for detection and abundance simultaneously and has been a significant advance in abundance modeling. Case studies that have tested these new models have demonstrated success for some species, but doubt remains over the appropriateness of standard N-mixture models for many species. Here we develop the N-mixture model to accommodate zero-inflated data, a common occurrence in ecology, by employing zero-inflated count models. To our knowledge, this is the first application of this method to modeling count data. We use four variants of the N-mixture model (Poisson, zero-inflated Poisson, negative binomial, and zero-inflated negative binomial) to model abundance, occupancy (zero-inflated models only) and detection probability of six birds in South Australia. We assess models by their statistical fit and the ecological realism of the parameter estimates. Specifically, we assess the statistical fit with AIC and assess the ecological realism by comparing the parameter estimates with expected values derived from literature, ecological theory, and expert opinion. We demonstrate that, despite being frequently ranked the "best model" according to AIC, the negative binomial variants of the N-mixture often produce ecologically unrealistic parameter estimates. The zero-inflated Poisson variant is preferable to the negative binomial variants of the N-mixture, as it models an ecological mechanism rather than a

Microplastics as contaminants in commercially important seafood species.

Science.gov (United States)

Santillo, David; Miller, Kathryn; Johnston, Paul

2017-05-01

The ingestion of microplastic fragments, spheres, and fibers by marine mollusks, crustaceans, and fish, including a number of commercially important species, appears to be a widespread and pervasive phenomenon. Evidence is also growing for direct impacts of microplastic ingestion on physiology, reproductive success and survival of exposed marine organisms, and transfer through food webs, although the ecological implications are not yet known. Concerns also remain over the capacity for microplastics to act as vectors for harmful chemical pollutants, including plastic additives and persistent organic pollutants, although their contribution must be evaluated alongside other known sources. The potential for humans, as top predators, to consume microplastics as contaminants in seafood is very real, and its implications for health need to be considered. An urgent need also exists to extend the geographical scope of studies of microplastic contamination in seafood species to currently underrepresented areas, and to finalize and adopt standardized methods and quality-assurance protocols for the isolation, identification, and quantification of microplastic contaminants from biological tissues. Such developments would enable more robust investigation of spatial and temporal trends, thereby contributing further evidence as a sound basis for regulatory controls. Despite the existence of considerable uncertainties and unknowns, there is already a compelling case for urgent actions to identify, control, and, where possible, eliminate key sources of both primary and secondary microplastics before they reach the marine environment. Integr Environ Assess Manag 2017;13:516-521. © 2017 SETAC. © 2017 SETAC.

Habitat-Based Density Models for Three Cetacean Species off Southern California Illustrate Pronounced Seasonal Differences

Directory of Open Access Journals (Sweden)

Elizabeth A. Becker

2017-05-01

Full Text Available Managing marine species effectively requires spatially and temporally explicit knowledge of their density and distribution. Habitat-based density models, a type of species distribution model (SDM that uses habitat covariates to estimate species density and distribution patterns, are increasingly used for marine management and conservation because they provide a tool for assessing potential impacts (e.g., from fishery bycatch, ship strikes, anthropogenic sound over a variety of spatial and temporal scales. The abundance and distribution of many pelagic species exhibit substantial seasonal variability, highlighting the importance of predicting density specific to the season of interest. This is particularly true in dynamic regions like the California Current, where significant seasonal shifts in cetacean distribution have been documented at coarse scales. Finer scale (10 km habitat-based density models were previously developed for many cetacean species occurring in this region, but most models were limited to summer/fall. The objectives of our study were two-fold: (1 develop spatially-explicit density estimates for winter/spring to support management applications, and (2 compare model-predicted density and distribution patterns to previously developed summer/fall model results in the context of species ecology. We used a well-established Generalized Additive Modeling framework to develop cetacean SDMs based on 20 California Cooperative Oceanic Fisheries Investigations (CalCOFI shipboard surveys conducted during winter and spring between 2005 and 2015. Models were fit for short-beaked common dolphin (Delphinus delphis delphis, Dall's porpoise (Phocoenoides dalli, and humpback whale (Megaptera novaeangliae. Model performance was evaluated based on a variety of established metrics, including the percentage of explained deviance, ratios of observed to predicted density, and visual inspection of predicted and observed distributions. Final models were

Important biological factors for utilizing native plant species

Science.gov (United States)

Loren E. Wiesner

1999-01-01

Native plant species are valuable resources for revegetation of disturbed ecosystems. The success of these plantings is dependent on the native species selected, quality of seed used, condition of the soil, environmental conditions before and after planting, planting equipment used, time of planting, and other factors. Most native species contain dormant seed. Dormancy...

Scaling local species-habitat relations to the larger landscape with a hierarchical spatial count model

Science.gov (United States)

Thogmartin, W.E.; Knutson, M.G.

2007-01-01

Much of what is known about avian species-habitat relations has been derived from studies of birds at local scales. It is entirely unclear whether the relations observed at these scales translate to the larger landscape in a predictable linear fashion. We derived habitat models and mapped predicted abundances for three forest bird species of eastern North America using bird counts, environmental variables, and hierarchical models applied at three spatial scales. Our purpose was to understand habitat associations at multiple spatial scales and create predictive abundance maps for purposes of conservation planning at a landscape scale given the constraint that the variables used in this exercise were derived from local-level studies. Our models indicated a substantial influence of landscape context for all species, many of which were counter to reported associations at finer spatial extents. We found land cover composition provided the greatest contribution to the relative explained variance in counts for all three species; spatial structure was second in importance. No single spatial scale dominated any model, indicating that these species are responding to factors at multiple spatial scales. For purposes of conservation planning, areas of predicted high abundance should be investigated to evaluate the conservation potential of the landscape in their general vicinity. In addition, the models and spatial patterns of abundance among species suggest locations where conservation actions may benefit more than one species. ?? 2006 Springer Science+Business Media B.V.

Species Sorting of Benthic Invertebrates in a Salinity Gradient - Importance of Dispersal Limitation.

Directory of Open Access Journals (Sweden)

Alf B Josefson

Full Text Available The relative importance of environment and dispersal related processes for community assembly has attracted great interest over recent decades, but few empirical studies from the marine/estuarine realm have examined the possible effects of these two types of factors in the same system. Importance of these processes was investigated in a hypothetical metacommunity of benthic invertebrates in 16 micro-tidal estuaries connected to the same open sea area. The estuaries differed in size and connectivity to the open sea and represented a salinity gradient across the estuaries. The Elements of Metacommunity Structure (EMS approach on estuary scale was complemented with a mechanistic variance partitioning approach on sample scale to disentangle effects of factors affecting assembly of three trait groups of species with different dispersivity. A quasi-Clementsian pattern was observed for all three traits, a likely response to some latent gradient. The primary axis in the pattern was most strongly related to gradients in estuary salinity and estuary entrance width and correlation with richness indicated nestedness only in the matrix of the most dispersive trait group. In the variance partitioning approach measures of turnover and nestedness between paired samples each from different estuaries were related to environmental distance in different gradients. Distance between estuaries was unimportant suggesting importance of factors characterizing the estuaries. While the high dispersive species mainly were sorted in the salinity gradient, apparently according to their tolerance ranges towards salinity, the two less dispersive traits were additionally affected by estuary entrance width and possibly also area. The results exemplify a mechanism of community assembly in the marine realm where the niche factor salinity in conjunction with differential dispersal structure invertebrates in a metacommunity of connected estuaries, and support the idea that dispersive

Species Sorting of Benthic Invertebrates in a Salinity Gradient - Importance of Dispersal Limitation.

Science.gov (United States)

Josefson, Alf B

2016-01-01

The relative importance of environment and dispersal related processes for community assembly has attracted great interest over recent decades, but few empirical studies from the marine/estuarine realm have examined the possible effects of these two types of factors in the same system. Importance of these processes was investigated in a hypothetical metacommunity of benthic invertebrates in 16 micro-tidal estuaries connected to the same open sea area. The estuaries differed in size and connectivity to the open sea and represented a salinity gradient across the estuaries. The Elements of Metacommunity Structure (EMS) approach on estuary scale was complemented with a mechanistic variance partitioning approach on sample scale to disentangle effects of factors affecting assembly of three trait groups of species with different dispersivity. A quasi-Clementsian pattern was observed for all three traits, a likely response to some latent gradient. The primary axis in the pattern was most strongly related to gradients in estuary salinity and estuary entrance width and correlation with richness indicated nestedness only in the matrix of the most dispersive trait group. In the variance partitioning approach measures of turnover and nestedness between paired samples each from different estuaries were related to environmental distance in different gradients. Distance between estuaries was unimportant suggesting importance of factors characterizing the estuaries. While the high dispersive species mainly were sorted in the salinity gradient, apparently according to their tolerance ranges towards salinity, the two less dispersive traits were additionally affected by estuary entrance width and possibly also area. The results exemplify a mechanism of community assembly in the marine realm where the niche factor salinity in conjunction with differential dispersal structure invertebrates in a metacommunity of connected estuaries, and support the idea that dispersive species are more

Strong thermal acclimation of photosynthesis in tropical and temperate wet-forest tree species: the importance of altered Rubisco content.

Science.gov (United States)

Scafaro, Andrew P; Xiang, Shuang; Long, Benedict M; Bahar, Nur H A; Weerasinghe, Lasantha K; Creek, Danielle; Evans, John R; Reich, Peter B; Atkin, Owen K

2017-07-01

Understanding of the extent of acclimation of light-saturated net photosynthesis (A n ) to temperature (T), and associated underlying mechanisms, remains limited. This is a key knowledge gap given the importance of thermal acclimation for plant functioning, both under current and future higher temperatures, limiting the accuracy and realism of Earth system model (ESM) predictions. Given this, we analysed and modelled T-dependent changes in photosynthetic capacity in 10 wet-forest tree species: six from temperate forests and four from tropical forests. Temperate and tropical species were each acclimated to three daytime growth temperatures (T growth ): temperate - 15, 20 and 25 °C; tropical - 25, 30 and 35 °C. CO 2 response curves of A n were used to model maximal rates of RuBP (ribulose-1,5-bisphosphate) carboxylation (V cmax ) and electron transport (J max ) at each treatment's respective T growth and at a common measurement T (25 °C). SDS-PAGE gels were used to determine abundance of the CO 2 -fixing enzyme, Rubisco. Leaf chlorophyll, nitrogen (N) and mass per unit leaf area (LMA) were also determined. For all species and T growth , A n at current atmospheric CO 2 partial pressure was Rubisco-limited. Across all species, LMA decreased with increasing T growth . Similarly, area-based rates of V cmax at a measurement T of 25 °C (V cmax 25 ) linearly declined with increasing T growth , linked to a concomitant decline in total leaf protein per unit leaf area and Rubisco as a percentage of leaf N. The decline in Rubisco constrained V cmax and A n for leaves developed at higher T growth and resulted in poor predictions of photosynthesis by currently widely used models that do not account for T growth -mediated changes in Rubisco abundance that underpin the thermal acclimation response of photosynthesis in wet-forest tree species. A new model is proposed that accounts for the effect of T growth -mediated declines in V cmax 25 on A n , complementing current

Endangered species toxicity extrapolation using ICE models

Science.gov (United States)

The National Research Council’s (NRC) report on assessing pesticide risks to threatened and endangered species (T&E) included the recommendation of using interspecies correlation models (ICE) as an alternative to general safety factors for extrapolating across species. ...

From models to crop species: caveats and solutions for translational metabolomics

Directory of Open Access Journals (Sweden)

Takayuki eTohge

2011-10-01

Full Text Available Although plant metabolomics is largely carried out on Arabidopsis it is essentially genome-independent, and thus potentially applicable to a wide range of species. However, transfer of between species, or even between different tissues of the same species, is not facile. This is because the reliability of protocols for harvesting, handling and analysis depends on the biological features and chemical composition of the plant tissue. In parallel with the diversification of model species it is important to establish good handling and analytic practice, in order to augment computational comparisons between tissues and species. LC-MS-based metabolomics is one of the powerful approaches for metabolite profiling. By using a combination of different extraction methods, separation columns and ion detection, a very wide range of metabolites can be analysed. However, its application requires careful attention to exclude potential pitfalls, including artifactual changes in metabolite levels during sample preparation and analytic errors due to ion-suppression. Here we provide case studies with two different LC-MS-based metabolomics platforms and four species (Arabidopsis thaliana, Chlamydomonas reinhardtii, Solanum lycopersicum and Oryza sativa that illustrate how such dangers can be detected and circumvented.

Important sources and chemical species of ambient fine particles related to adverse health effects

Science.gov (United States)

Heo, J.

2017-12-01

Although many epidemiological studies have reported that exposure to ambient fine particulate matter (PM2.5) has been linked to increases in mortality and mobidity health outcomes, the key question of which chemical species and sources of PM2.5 are most harmful to public health remains unanswered in the air pollution research area. This study was designed to address the key question with evaluating the risks of exposure to chemical species and source-specific PM2.5 mass on morbidity. Hourly measurements of PM2.5 mass and its major chemical species, including organic carbon, elemental carbon, ions, and trace elements, were observed from January 1 to December 31, 2013 at four of the PM2.5 supersites in urban environments in Korea and the reuslts were used in a positive matrix factorization to estimate source contributions to PM2.5 mass. Nine sources, including secondary sulfate, secondary nitrate, mobile, biomass burning, roadway emission, industry, oil combustion, soil, and aged sea salt, were identified and secondary inorganic aerosol factors (i.e. secondary sulfalte, and secondary nitrate) were the dominant sources contributing to 40% of the total PM2.5 mass in the study region. In order to evaluate the risks of exposure to chemical species and sources of PM2.5 on morbidity, emergency room visits for cardivascular disease and respiratory disease were considered. Hourly health outcomes were compared with hourly measurments of the PM2.5 chemical species and sources using a poission generalized linear model incorporating natural splines, as well as time-stratified case-crossover design. The PM2.5 mass and speveral chemical components, such as organic carbon, elemetal carbon, zinc, and potassium, were strongly associated with morbidity. Source-apporitionmened PM2.5 mass derived from biomass burning, and mobile sources, was significantly associated with cardiovascular and respiratory diseases. The findings represent that local combustion may be particularly important

Inferential monitoring of global change impact on biodiversity through remote sensing and species distribution modeling

Science.gov (United States)

Sangermano, Florencia

2009-12-01

The world is suffering from rapid changes in both climate and land cover which are the main factors affecting global biodiversity. These changes may affect ecosystems by altering species distributions, population sizes, and community compositions, which emphasizes the need for a rapid assessment of biodiversity status for conservation and management purposes. Current approaches on monitoring biodiversity rely mainly on long term observations of predetermined sites, which require large amounts of time, money and personnel to be executed. In order to overcome problems associated with current field monitoring methods, the main objective of this dissertation is the development of framework for inferential monitoring of the impact of global change on biodiversity based on remotely sensed data coupled with species distribution modeling techniques. Several research pieces were performed independently in order to fulfill this goal. First, species distribution modeling was used to identify the ranges of 6362 birds, mammals and amphibians in South America. Chapter 1 compares the power of different presence-only species distribution methods for modeling distributions of species with different response curves to environmental gradients and sample sizes. It was found that there is large variability in the power of the methods for modeling habitat suitability and species ranges, showing the importance of performing, when possible, a preliminary gradient analysis of the species distribution before selecting the method to be used. Chapter 2 presents a new methodology for the redefinition of species range polygons. Using a method capable of establishing the uncertainty in the definition of existing range polygons, the automated procedure identifies the relative importance of bioclimatic variables for the species, predicts their ranges and generates a quality assessment report to explore prediction errors. Analysis using independent validation data shows the power of this

Modeling Ecosystem Services for Park Trees: Sensitivity of i-Tree Eco Simulations to Light Exposure and Tree Species Classification

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Rocco Pace

2018-02-01

Full Text Available Ecosystem modeling can help decision making regarding planting of urban trees for climate change mitigation and air pollution reduction. Algorithms and models that link the properties of plant functional types, species groups, or single species to their impact on specific ecosystem services have been developed. However, these models require a considerable effort for initialization that is inherently related to uncertainties originating from the high diversity of plant species in urban areas. We therefore suggest a new automated method to be used with the i-Tree Eco model to derive light competition for individual trees and investigate the importance of this property. Since competition depends also on the species, which is difficult to determine from increasingly used remote sensing methodologies, we also investigate the impact of uncertain tree species classification on the ecosystem services by comparing a species-specific inventory determined by field observation with a genus-specific categorization and a model initialization for the dominant deciduous and evergreen species only. Our results show how the simulation of competition affects the determination of carbon sequestration, leaf area, and related ecosystem services and that the proposed method provides a tool for improving estimations. Misclassifications of tree species can lead to large deviations in estimates of ecosystem impacts, particularly concerning biogenic volatile compound emissions. In our test case, monoterpene emissions almost doubled and isoprene emissions decreased to less than 10% when species were estimated to belong only to either two groups instead of being determined by species or genus. It is discussed that this uncertainty of emission estimates propagates further uncertainty in the estimation of potential ozone formation. Overall, we show the importance of using an individual light competition approach and explicitly parameterizing all ecosystem functions at the

Trees of Laos and Vietnam: a field guide to 100 economically or ecologically important species

OpenAIRE

Sam, Hoang Van; Nanthavong, Khamseng; Keßler, P.J.A.

2004-01-01

This field guide to 100 economically or ecologically important tree species from Laos and Vietnam enables the user to identify the included taxa with user-friendly keys. It includes scientific names, botanical descriptions of families, genera, and species. Specific information on distribution, habitat, ecology, and uses has been compiled. All specimens examined have been listed.

Finessing atlas data for species distribution models

NARCIS (Netherlands)

Niamir, A.; Skidmore, A.K.; Toxopeus, A.G.; Munoz, A.R.; Real, R.

2011-01-01

Aim The spatial resolution of species atlases and therefore resulting model predictions are often too coarse for local applications. Collecting distribution data at a finer resolution for large numbers of species requires a comprehensive sampling effort, making it impractical and expensive. This

Tackling Biocomplexity with Meta-models for Species Risk Assessment

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Philip J. Nyhus

2007-06-01

Full Text Available We describe results of a multi-year effort to strengthen consideration of the human dimension into endangered species risk assessments and to strengthen research capacity to understand biodiversity risk assessment in the context of coupled human-natural systems. A core group of social and biological scientists have worked with a network of more than 50 individuals from four countries to develop a conceptual framework illustrating how human-mediated processes influence biological systems and to develop tools to gather, translate, and incorporate these data into existing simulation models. A central theme of our research focused on (1 the difficulties often encountered in identifying and securing diverse bodies of expertise and information that is necessary to adequately address complex species conservation issues; and (2 the development of quantitative simulation modeling tools that could explicitly link these datasets as a way to gain deeper insight into these issues. To address these important challenges, we promote a "meta-modeling" approach where computational links are constructed between discipline-specific models already in existence. In this approach, each model can function as a powerful stand-alone program, but interaction between applications is achieved by passing data structures describing the state of the system between programs. As one example of this concept, an integrated meta-model of wildlife disease and population biology is described. A goal of this effort is to improve science-based capabilities for decision making by scientists, natural resource managers, and policy makers addressing environmental problems in general, and focusing on biodiversity risk assessment in particular.

Regional climate model downscaling may improve the prediction of alien plant species distributions

Science.gov (United States)

Liu, Shuyan; Liang, Xin-Zhong; Gao, Wei; Stohlgren, Thomas J.

2014-12-01

Distributions of invasive species are commonly predicted with species distribution models that build upon the statistical relationships between observed species presence data and climate data. We used field observations, climate station data, and Maximum Entropy species distribution models for 13 invasive plant species in the United States, and then compared the models with inputs from a General Circulation Model (hereafter GCM-based models) and a downscaled Regional Climate Model (hereafter, RCM-based models).We also compared species distributions based on either GCM-based or RCM-based models for the present (1990-1999) to the future (2046-2055). RCM-based species distribution models replicated observed distributions remarkably better than GCM-based models for all invasive species under the current climate. This was shown for the presence locations of the species, and by using four common statistical metrics to compare modeled distributions. For two widespread invasive taxa ( Bromus tectorum or cheatgrass, and Tamarix spp. or tamarisk), GCM-based models failed miserably to reproduce observed species distributions. In contrast, RCM-based species distribution models closely matched observations. Future species distributions may be significantly affected by using GCM-based inputs. Because invasive plants species often show high resilience and low rates of local extinction, RCM-based species distribution models may perform better than GCM-based species distribution models for planning containment programs for invasive species.

Stakeholder perspectives on the importance of rare-species research for deep-sea environmental management

Science.gov (United States)

Turner, Phillip J.; Campbell, Lisa M.; Van Dover, Cindy L.

2017-07-01

The apparent prevalence of rare species (rarity) in the deep sea is a concern for environmental management and conservation of biodiversity. Rare species are often considered at risk of extinction and, in terrestrial and shallow water environments, have been shown to play key roles within an ecosystem. In the deep-sea environment, current research focuses primarily on abundant species and deep-sea stakeholders are questioning the importance of rare species in ecosystem functioning. This study asks whether deep-sea stakeholders (primarily scientists) view rare-species research as a priority in guiding environmental management. Delphi methodology (i.e., an iterative survey approach) was used to understand views about whether or not 'deep-sea scientists should allocate more resources to research on rare species in the deep sea, even if this means less resources might be available for abundant-species research.' Results suggest little consensus regarding the prioritization of resources for rare-species research. From Survey 1 to Survey 3, the average participant response shifted toward a view that rare-species research is not a priority if it comes at a cost to research on abundant species. Participants pointed to the need for a balanced approach and highlighted knowledge gaps about even the most fundamental questions, including whether rare species are truly 'rare' or simply under-sampled. Participants emphasized the lack of basic biological knowledge for rare and abundant species, particularly abundant meio- and microscopic species, as well as uncertainty in the roles rare and abundant species play in ecosystem processes. Approaches that jointly consider the role of rare and abundant species in ecosystem functioning (e.g., biological trait analysis) may help to clarify the extent to which rare species need to be incorporated into deep-sea environment management in order to maintain ecosystem functioning.

Determining the factors affecting the distribution of Muscari latifolium, an endemic plant of Turkey, and a mapping species distribution model.

Science.gov (United States)

Yilmaz, Hatice; Yilmaz, Osman Yalçın; Akyüz, Yaşar Feyza

2017-02-01

Species distribution modeling was used to determine factors among the large predictor candidate data set that affect the distribution of Muscari latifolium , an endemic bulbous plant species of Turkey, to quantify the relative importance of each factor and make a potential spatial distribution map of M. latifolium . Models were built using the Boosted Regression Trees method based on 35 presence and 70 absence records obtained through field sampling in the Gönen Dam watershed area of the Kazdağı Mountains in West Anatolia. Large candidate variables of monthly and seasonal climate, fine-scale land surface, and geologic and biotic variables were simplified using a BRT simplifying procedure. Analyses performed on these resources, direct and indirect variables showed that there were 14 main factors that influence the species' distribution. Five of the 14 most important variables influencing the distribution of the species are bedrock type, Quercus cerris density, precipitation during the wettest month, Pinus nigra density, and northness. These variables account for approximately 60% of the relative importance for determining the distribution of the species. Prediction performance was assessed by 10 random subsample data sets and gave a maximum the area under a receiver operating characteristic curve (AUC) value of 0.93 and an average AUC value of 0.8. This study provides a significant contribution to the knowledge of the habitat requirements and ecological characteristics of this species. The distribution of this species is explained by a combination of biotic and abiotic factors. Hence, using biotic interaction and fine-scale land surface variables in species distribution models improved the accuracy and precision of the model. The knowledge of the relationships between distribution patterns and environmental factors and biotic interaction of M. latifolium can help develop a management and conservation strategy for this species.

Using the Developmental Gene Bicoid to Identify Species of Forensically Important Blowflies (Diptera: Calliphoridae

Directory of Open Access Journals (Sweden)

Seong Hwan Park

2013-01-01

Full Text Available Identifying species of insects used to estimate postmortem interval (PMI is a major subject in forensic entomology. Because forensic insect specimens are morphologically uniform and are obtained at various developmental stages, DNA markers are greatly needed. To develop new autosomal DNA markers to identify species, partial genomic sequences of the bicoid (bcd genes, containing the homeobox and its flanking sequences, from 12 blowfly species (Aldrichina grahami, Calliphora vicina, Calliphora lata, Triceratopyga calliphoroides, Chrysomya megacephala, Chrysomya pinguis, Phormia regina, Lucilia ampullacea, Lucilia caesar, Lucilia illustris, Hemipyrellia ligurriens and Lucilia sericata; Calliphoridae: Diptera were determined and analyzed. This study first sequenced the ten blowfly species other than C. vicina and L. sericata. Based on the bcd sequences of these 12 blowfly species, a phylogenetic tree was constructed that discriminates the subfamilies of Calliphoridae (Luciliinae, Chrysomyinae, and Calliphorinae and most blowfly species. Even partial genomic sequences of about 500 bp can distinguish most blowfly species. The short intron 2 and coding sequences downstream of the bcd homeobox in exon 3 could be utilized to develop DNA markers for forensic applications. These gene sequences are important in the evolution of insect developmental biology and are potentially useful for identifying insect species in forensic science.

Using the Developmental Gene Bicoid to Identify Species of Forensically Important Blowflies (Diptera: Calliphoridae)

Science.gov (United States)

Park, Seong Hwan; Park, Chung Hyun; Zhang, Yong; Piao, Huguo; Chung, Ukhee; Kim, Seong Yoon; Ko, Kwang Soo; Yi, Cheong-Ho; Jo, Tae-Ho; Hwang, Juck-Joon

2013-01-01

Identifying species of insects used to estimate postmortem interval (PMI) is a major subject in forensic entomology. Because forensic insect specimens are morphologically uniform and are obtained at various developmental stages, DNA markers are greatly needed. To develop new autosomal DNA markers to identify species, partial genomic sequences of the bicoid (bcd) genes, containing the homeobox and its flanking sequences, from 12 blowfly species (Aldrichina grahami, Calliphora vicina, Calliphora lata, Triceratopyga calliphoroides, Chrysomya megacephala, Chrysomya pinguis, Phormia regina, Lucilia ampullacea, Lucilia caesar, Lucilia illustris, Hemipyrellia ligurriens and Lucilia sericata; Calliphoridae: Diptera) were determined and analyzed. This study first sequenced the ten blowfly species other than C. vicina and L. sericata. Based on the bcd sequences of these 12 blowfly species, a phylogenetic tree was constructed that discriminates the subfamilies of Calliphoridae (Luciliinae, Chrysomyinae, and Calliphorinae) and most blowfly species. Even partial genomic sequences of about 500 bp can distinguish most blowfly species. The short intron 2 and coding sequences downstream of the bcd homeobox in exon 3 could be utilized to develop DNA markers for forensic applications. These gene sequences are important in the evolution of insect developmental biology and are potentially useful for identifying insect species in forensic science. PMID:23586044

Integrative modelling reveals mechanisms linking productivity and plant species richness.

Science.gov (United States)

Grace, James B; Anderson, T Michael; Seabloom, Eric W; Borer, Elizabeth T; Adler, Peter B; Harpole, W Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M; Pärtel, Meelis; Bakker, Jonathan D; Buckley, Yvonne M; Crawley, Michael J; Damschen, Ellen I; Davies, Kendi F; Fay, Philip A; Firn, Jennifer; Gruner, Daniel S; Hector, Andy; Knops, Johannes M H; MacDougall, Andrew S; Melbourne, Brett A; Morgan, John W; Orrock, John L; Prober, Suzanne M; Smith, Melinda D

2016-01-21

How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

Citizen Science and Open Data: a Model for Invasive Alien Plant Species in Kenya's Northern Rangelands

Science.gov (United States)

Amirazodi, S.; Griffin, R.; Flores Cordova, A. I.; Ouko, E.; Omondi, S.; Mugo, R. M.; Farah, H.; Flores Cordova, A. I.; Adams, E. C.

2017-12-01

Invasive species in African savannas pose great threat to the native biodiversity and changes ecosystem functioning. In the forest sector, for instance Acacia species are important sources of fuel-wood, yet at the same time they have increased strain on water resources and shrunken forage spaces for both livestock and wildlife. In recently infested regions, invasive species can progress through the stages of introduction, establishment and dispersal to a full range. Currently there is much worldwide interest in predicting distributions of invasive species, and several organizations are faced with questions of whether and how to tackle such environmental challenges, or how to interpret predictions from the science community. Conservation practioners require mapped estimates of where species could persist in a given region, and this is associated to information about the biotope - i.e. the geographic location of the species' niche. The process of collecting species distribution data for identifying the potential distribution of the invasive species in the invaded ranges has become a challenge both in terms of resource and time allocation. This study highlights innovative approaches in crowdsourcing validation data in mapping and modelling invasive species (Acacia reficiens and Cactus) through involvement of the local communities. The general approach was to model the distribution of A. reficiens and Cactus (Opuntia Spp) using occurrence records from native range, then project the model into new regions to assess susceptibility to invasion using climatic and topographic environmental variables. The models performed better than random prediction (P 0.75.

An exactly solvable coarse-grained model for species diversity

Science.gov (United States)

Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

2012-07-01

We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

An exactly solvable coarse-grained model for species diversity

International Nuclear Information System (INIS)

Suweis, Samir; Maritan, Amos; Rinaldo, Andrea

2012-01-01

We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth–death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology. (paper)

Nest survival modelling using a multi-species approach in forests managed for timber and biofuel feedstock

Science.gov (United States)

Loman, Zachary G.; Monroe, Adrian; Riffell, Samuel K.; Miller, Darren A.; Vilella, Francisco; Wheat, Bradley R.; Rush, Scott A.; Martin, James A.

2018-01-01

Switchgrass (Panicum virgatum) intercropping is a novel forest management practice for biomass production intended to generate cellulosic feedstocks within intensively managed loblolly pine‐dominated landscapes. These pine plantations are important for early‐successional bird species, as short rotation times continually maintain early‐successional habitat. We tested the efficacy of using community models compared to individual surrogate species models in understanding influences on nest survival. We analysed nest data to test for differences in habitat use for 14 bird species in plots managed for switchgrass intercropping and controls within loblolly pine (Pinus taeda) plantations in Mississippi, USA.We adapted hierarchical models using hyper‐parameters to incorporate information from both common and rare species to understand community‐level nest survival. This approach incorporates rare species that are often discarded due to low sample sizes, but can inform community‐level demographic parameter estimates. We illustrate use of this approach in generating both species‐level and community‐wide estimates of daily survival rates for songbird nests. We were able to include rare species with low sample size (minimum n = 5) to inform a hyper‐prior, allowing us to estimate effects of covariates on daily survival at the community level, then compare this with a single‐species approach using surrogate species. Using single‐species models, we were unable to generate estimates below a sample size of 21 nests per species.Community model species‐level survival and parameter estimates were similar to those generated by five single‐species models, with improved precision in community model parameters.Covariates of nest placement indicated that switchgrass at the nest site (<4 m) reduced daily nest survival, although intercropping at the forest stand level increased daily nest survival.Synthesis and applications. Community models represent a viable

Using maximum topology matching to explore differences in species distribution models

Science.gov (United States)

Poco, Jorge; Doraiswamy, Harish; Talbert, Marian; Morisette, Jeffrey; Silva, Claudio

2015-01-01

Species distribution models (SDM) are used to help understand what drives the distribution of various plant and animal species. These models are typically high dimensional scalar functions, where the dimensions of the domain correspond to predictor variables of the model algorithm. Understanding and exploring the differences between models help ecologists understand areas where their data or understanding of the system is incomplete and will help guide further investigation in these regions. These differences can also indicate an important source of model to model uncertainty. However, it is cumbersome and often impractical to perform this analysis using existing tools, which allows for manual exploration of the models usually as 1-dimensional curves. In this paper, we propose a topology-based framework to help ecologists explore the differences in various SDMs directly in the high dimensional domain. In order to accomplish this, we introduce the concept of maximum topology matching that computes a locality-aware correspondence between similar extrema of two scalar functions. The matching is then used to compute the similarity between two functions. We also design a visualization interface that allows ecologists to explore SDMs using their topological features and to study the differences between pairs of models found using maximum topological matching. We demonstrate the utility of the proposed framework through several use cases using different data sets and report the feedback obtained from ecologists.

Improving the performance of indicator groups for the identification of important areas for species conservation

DEFF Research Database (Denmark)

Larsen, Frank Wugt; Bladt, Jesper; Rahbek, Carsten

2007-01-01

Indicator groups may be important tools with which to guide the selection of networks of areas for conservation. Nevertheless, the literature provides little guidance as to what makes some groups of species more suitable than others to guide area selection. Using distributional data on all sub...... diversity by systematically varying the number of distinct genera and families within the indicator groups. We selected area networks based on the indicator groups and tested their ability to represent a set of species, which, in terms of species composition, is independent of the indicator group....... Increasing the proportion of threatened, endemic, and range-restricted species in the indicator groups improved effectiveness of the selected area networks; in particular it improved the effectiveness in representing other threatened and range-restricted species. In contrast increasing the proportion...

Species delimitation in asexual insects of economic importance: The case of black scale (Parasaissetia nigra, a cosmopolitan parthenogenetic pest scale insect.

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Yen-Po Lin

Full Text Available Asexual lineages provide a challenge to species delimitation because species concepts either have little biological meaning for them or are arbitrary, since every individual is monophyletic and reproductively isolated from all other individuals. However, recognition and naming of asexual species is important to conservation and economic applications. Some scale insects are widespread and polyphagous pests of plants, and several species have been found to comprise cryptic species complexes. Parasaissetia nigra (Nietner, 1861 (Hemiptera: Coccidae is a parthenogenetic, cosmopolitan and polyphagous pest that feeds on plant species from more than 80 families. Here, we implement multiple approaches to assess the species status of P. nigra, including coalescence-based analyses of mitochondrial and nuclear genes, and ecological niche modelling. Our results indicate that the sampled specimens of P. nigra should be considered to comprise at least two ecotypes (or "species" that are ecologically differentiated, particularly in relation to temperature and moisture. The presence of more than one ecotype under the current concept of P. nigra has implications for biosecurity because the geographic extent of each type is not fully known: some countries may currently have only one of the biotypes. Introduction of additional lineages could expand the geographic extent of damage by the pest in some countries.

The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species.

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Thibaud Rougier

Full Text Available Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa, an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5. We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local

Past, present and future distributions of an Iberian Endemic, Lepus granatensis: ecological and evolutionary clues from species distribution models.

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Pelayo Acevedo

Full Text Available The application of species distribution models (SDMs in ecology and conservation biology is increasing and assuming an important role, mainly because they can be used to hindcast past and predict current and future species distributions. However, the accuracy of SDMs depends on the quality of the data and on appropriate theoretical frameworks. In this study, comprehensive data on the current distribution of the Iberian hare (Lepus granatensis were used to i determine the species' ecogeographical constraints, ii hindcast a climatic model for the last glacial maximum (LGM, relating it to inferences derived from molecular studies, and iii calibrate a model to assess the species future distribution trends (up to 2080. Our results showed that the climatic factor (in its pure effect and when it is combined with the land-cover factor is the most important descriptor of the current distribution of the Iberian hare. In addition, the model's output was a reliable index of the local probability of species occurrence, which is a valuable tool to guide species management decisions and conservation planning. Climatic potential obtained for the LGM was combined with molecular data and the results suggest that several glacial refugia may have existed for the species within the major Iberian refugium. Finally, a high probability of occurrence of the Iberian hare in the current species range and a northward expansion were predicted for future. Given its current environmental envelope and evolutionary history, we discuss the macroecology of the Iberian hare and its sensitivity to climate change.

Past, present and future distributions of an Iberian Endemic, Lepus granatensis: ecological and evolutionary clues from species distribution models.

Science.gov (United States)

Acevedo, Pelayo; Melo-Ferreira, José; Real, Raimundo; Alves, Paulo Célio

2012-01-01

The application of species distribution models (SDMs) in ecology and conservation biology is increasing and assuming an important role, mainly because they can be used to hindcast past and predict current and future species distributions. However, the accuracy of SDMs depends on the quality of the data and on appropriate theoretical frameworks. In this study, comprehensive data on the current distribution of the Iberian hare (Lepus granatensis) were used to i) determine the species' ecogeographical constraints, ii) hindcast a climatic model for the last glacial maximum (LGM), relating it to inferences derived from molecular studies, and iii) calibrate a model to assess the species future distribution trends (up to 2080). Our results showed that the climatic factor (in its pure effect and when it is combined with the land-cover factor) is the most important descriptor of the current distribution of the Iberian hare. In addition, the model's output was a reliable index of the local probability of species occurrence, which is a valuable tool to guide species management decisions and conservation planning. Climatic potential obtained for the LGM was combined with molecular data and the results suggest that several glacial refugia may have existed for the species within the major Iberian refugium. Finally, a high probability of occurrence of the Iberian hare in the current species range and a northward expansion were predicted for future. Given its current environmental envelope and evolutionary history, we discuss the macroecology of the Iberian hare and its sensitivity to climate change.

Molluscan indicator species and their potential use in ecological status assessment using species distribution modeling.

Science.gov (United States)

Moraitis, Manos L; Tsikopoulou, Irini; Geropoulos, Antonios; Dimitriou, Panagiotis D; Papageorgiou, Nafsika; Giannoulaki, Marianna; Valavanis, Vasilis D; Karakassis, Ioannis

2018-05-24

Marine habitat assessment using indicator species through Species Distribution Modeling (SDM) was investigated. The bivalves: Corbula gibba and Flexopecten hyalinus were the indicator species characterizing disturbed and undisturbed areas respectively in terms of chlorophyll a concentration in Greece. The habitat suitability maps of these species reflected the overall ecological status of the area. The C. gibba model successfully predicted the occurrence of this species in areas with increased physical disturbance driven by chlorophyll a concentration, whereas the habitat map for F. hyalinus showed an increased probability of occurrence in chlorophyll-poor areas, affected mainly by salinity. We advocate the use of C. gibba as a proxy for eutrophication and the incorporation of this species in monitoring studies through SDM methods. For the Mediterranean Sea we suggest the use of F. hyalinus in SDM as an indicator of environmental stability and a possible forecasting tool for salinity fluctuations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Using habitat suitability models to target invasive plant species surveys.

Science.gov (United States)

Crall, Alycia W; Jarnevich, Catherine S; Panke, Brendon; Young, Nick; Renz, Mark; Morisette, Jeffrey

2013-01-01

Managers need new tools for detecting the movement and spread of nonnative, invasive species. Habitat suitability models are a popular tool for mapping the potential distribution of current invaders, but the ability of these models to prioritize monitoring efforts has not been tested in the field. We tested the utility of an iterative sampling design (i.e., models based on field observations used to guide subsequent field data collection to improve the model), hypothesizing that model performance would increase when new data were gathered from targeted sampling using criteria based on the initial model results. We also tested the ability of habitat suitability models to predict the spread of invasive species, hypothesizing that models would accurately predict occurrences in the field, and that the use of targeted sampling would detect more species with less sampling effort than a nontargeted approach. We tested these hypotheses on two species at the state scale (Centaurea stoebe and Pastinaca sativa) in Wisconsin (USA), and one genus at the regional scale (Tamarix) in the western United States. These initial data were merged with environmental data at 30-m2 resolution for Wisconsin and 1-km2 resolution for the western United States to produce our first iteration models. We stratified these initial models to target field sampling and compared our models and success at detecting our species of interest to other surveys being conducted during the same field season (i.e., nontargeted sampling). Although more data did not always improve our models based on correct classification rate (CCR), sensitivity, specificity, kappa, or area under the curve (AUC), our models generated from targeted sampling data always performed better than models generated from nontargeted data. For Wisconsin species, the model described actual locations in the field fairly well (kappa = 0.51, 0.19, P guiding invasive species monitoring, and we support the use of an iterative sampling design for

Application of Tissue Culture and Transformation Techniques in Model Species Brachypodium distachyon.

Science.gov (United States)

Sogutmaz Ozdemir, Bahar; Budak, Hikmet

2018-01-01

Brachypodium distachyon has recently emerged as a model plant species for the grass family (Poaceae) that includes major cereal crops and forage grasses. One of the important traits of a model species is its capacity to be transformed and ease of growing both in tissue culture and in greenhouse conditions. Hence, plant transformation technology is crucial for improvements in agricultural studies, both for the study of new genes and in the production of new transgenic plant species. In this chapter, we review an efficient tissue culture and two different transformation systems for Brachypodium using most commonly preferred gene transfer techniques in plant species, microprojectile bombardment method (biolistics) and Agrobacterium-mediated transformation.In plant transformation studies, frequently used explant materials are immature embryos due to their higher transformation efficiencies and regeneration capacity. However, mature embryos are available throughout the year in contrast to immature embryos. We explain a tissue culture protocol for Brachypodium using mature embryos with the selected inbred lines from our collection. Embryogenic calluses obtained from mature embryos are used to transform Brachypodium with both plant transformation techniques that are revised according to previously studied protocols applied in the grasses, such as applying vacuum infiltration, different wounding effects, modification in inoculation and cocultivation steps or optimization of bombardment parameters.

When Ontogeny Matters: A New Japanese Species of Brittle Star Illustrates the Importance of Considering both Adult and Juvenile Characters in Taxonomic Practice.

Science.gov (United States)

Martynov, Alexander; Ishida, Yoshiaki; Irimura, Seiichi; Tajiri, Rie; O'Hara, Timothy; Fujita, Toshihiko

2015-01-01

Current taxonomy offers numerous approaches and methods for species delimitation and description. However, most of them are based on the adult characters and rarely suggest a dynamic representation of developmental transformations of taxonomically important features. Here we show how the underestimation of ontogenetic changes may result in long term lack of recognition of a new species of one of the most common ophiacanthid brittle stars (Echinodermata: Ophiuroidea) from the North Pacific. Based on vast material collected predominantly by various Japanese expeditions in the course of more than 50 years, and thorough study of appropriate type material, we revise the complex of three common species of the ophiuroid genus Ophiacantha which have been persistently confused with each other. The present study thus reveals the previously unrecognized new species Ophiacantha kokusai sp.nov. which is commonly distributed off the Pacific coast of Japan. The new species shows developmental differentiation from the closely related species Ophiacantha rhachophora H. L. Clark, 1911 and retains clearly expressed early juvenile features in the adult morphology. Another species, Ophiacantha clypeata Kyte, 1977, which had been separated from O. rhachophora, is in turn shown to be just a juvenile stage of another North Pacific species, Ophiacantha trachybactra H.L. Clark, 1911. For every species, detailed morphological data from both adult and juvenile specimens based on scanning electron microscopy are presented. A special grinding method showing complex internal features has been utilized for the first time. For all three species in this complex, a clear bathymetric differentiation is revealed: O. rhachophora predominantly inhabits shallow waters, 0-250 m, the new species O. kokusai lives deeper, at 250-600 m, and the third species, O. trachybactra, is found at 500-2,000 m. The present case clearly highlights the importance of considering developmental transformations, not only for

Francisella-Like Endosymbionts and Rickettsia Species in Local and Imported Hyalomma Ticks.

Science.gov (United States)

Azagi, Tal; Klement, Eyal; Perlman, Gidon; Lustig, Yaniv; Mumcuoglu, Kosta Y; Apanaskevich, Dmitry A; Gottlieb, Yuval

2017-09-15

Hyalomma ticks (Acari: Ixodidae) are hosts for Francisella -like endosymbionts (FLE) and may serve as vectors of zoonotic disease agents. This study aimed to provide an initial characterization of the interaction between Hyalomma and FLE and to determine the prevalence of pathogenic Rickettsia in these ticks. Hyalomma marginatum , Hyalomma rufipes , Hyalomma dromedarii , Hyalomma aegyptium , and Hyalomma excavatum ticks, identified morphologically and molecularly, were collected from different hosts and locations representing the distribution of the genus Hyalomma in Israel, as well as from migratory birds. A high prevalence of FLE was found in all Hyalomma species (90.6%), as well as efficient maternal transmission of FLE (91.8%), and the localization of FLE in Malpighian tubules, ovaries, and salivary glands in H. marginatum Furthermore, we demonstrated strong cophylogeny between FLE and their host species. Contrary to FLE, the prevalence of Rickettsia ranged from 2.4% to 81.3% and was significantly different between Hyalomma species, with a higher prevalence in ticks collected from migratory birds. Using ompA gene sequences, most of the Rickettsia spp. were similar to Rickettsia aeschlimannii , while a few were similar to Rickettsia africae of the spotted fever group (SFG). Given their zoonotic importance, 249 ticks were tested for Crimean Congo hemorrhagic fever virus infection, and all were negative. The results imply that Hyalomma and FLE have obligatory symbiotic interactions, indicating a potential SFG Rickettsia zoonosis risk. A further understanding of the possible influence of FLE on Hyalomma development, as well as on its infection with Rickettsia pathogens, may lead to novel ways to control tick-borne zoonoses. IMPORTANCE This study shows that Francisella -like endosymbionts were ubiquitous in Hyalomma , were maternally transmitted, and cospeciated with their hosts. These findings imply that the interaction between FLE and Hyalomma is of an obligatory

Species Sorting of Benthic Invertebrates in a Salinity Gradient – Importance of Dispersal Limitation

Science.gov (United States)

Josefson, Alf B.

2016-01-01

The relative importance of environment and dispersal related processes for community assembly has attracted great interest over recent decades, but few empirical studies from the marine/estuarine realm have examined the possible effects of these two types of factors in the same system. Importance of these processes was investigated in a hypothetical metacommunity of benthic invertebrates in 16 micro-tidal estuaries connected to the same open sea area. The estuaries differed in size and connectivity to the open sea and represented a salinity gradient across the estuaries. The Elements of Metacommunity Structure (EMS) approach on estuary scale was complemented with a mechanistic variance partitioning approach on sample scale to disentangle effects of factors affecting assembly of three trait groups of species with different dispersivity. A quasi-Clementsian pattern was observed for all three traits, a likely response to some latent gradient. The primary axis in the pattern was most strongly related to gradients in estuary salinity and estuary entrance width and correlation with richness indicated nestedness only in the matrix of the most dispersive trait group. In the variance partitioning approach measures of turnover and nestedness between paired samples each from different estuaries were related to environmental distance in different gradients. Distance between estuaries was unimportant suggesting importance of factors characterizing the estuaries. While the high dispersive species mainly were sorted in the salinity gradient, apparently according to their tolerance ranges towards salinity, the two less dispersive traits were additionally affected by estuary entrance width and possibly also area. The results exemplify a mechanism of community assembly in the marine realm where the niche factor salinity in conjunction with differential dispersal structure invertebrates in a metacommunity of connected estuaries, and support the idea that dispersive species are more

CARBON-CHAIN SPECIES IN WARM-UP MODELS

International Nuclear Information System (INIS)

Hassel, George E.; Harada, Nanase; Herbst, Eric

2011-01-01

In previous warm-up chemical models of the low-mass star-forming region L1527, we investigated the evolution of carbon-chain unsaturated hydrocarbon species when the envelope temperature is slightly elevated to T ≈ 30 K. These models demonstrated that enhanced abundances of such species can be explained by gas-phase ion-molecule chemistry following the partial sublimation of methane from grain surfaces. We also concluded that the abundances of hydrocarbon radicals such as the C n H family should be further enhanced as the temperatures increase to higher values, but this conclusion stood in contrast with the lack of unambiguous detection of these species toward hot core and corino sources. Meanwhile, observational surveys have identified C 2 H, C 4 H, CH 3 CCH, and CH 3 OH toward hot corinos (especially IRAS 16293–2422) as well as toward L1527, with lower abundances for the carbon-chain radicals and higher abundances for the other two species toward the hot corinos. In addition, the Herschel Space Telescope has detected the bare linear chain C 3 in 50 K material surrounding young high-mass stellar objects. To understand these new results, we revisit previous warm-up models with an augmented gas-grain network that incorporated reactions from a gas-phase network that was constructed for use with increased temperature up to 800 K. Some of the newly adopted reactions between carbon-chain species and abundant H 2 possess chemical activation energy barriers. The revised model results now better reproduce the observed abundances of unsaturated carbon chains under hot corino (100 K) conditions and make predictions for the abundances of bare carbon chains in the 50 K regions observed by the Herschel HIFI detector.

Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties.

Science.gov (United States)

Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M Aminur; Islam, Mohamad Tofazzal

2017-10-17

Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural-activity relationships (SARs) of sea cucumber glycosides are also discussed briefly.

Effects of stand composition and thinning in mixed-species forests : a modeling approach applied to Douglas-fir and beech

NARCIS (Netherlands)

Bartelink, H.H.

2000-01-01

Models estimating growth and yield of forest stands provide important tools for forest management. Pure stands have been modeled extensively and successfully for decades; however, relatively few models for mixed-species stands have been developed. A spatially explicit, mechanistic model (COMMIX) is

Species Distribution Modelling: Contrasting presence-only models with plot abundance data.

Science.gov (United States)

Gomes, Vitor H F; IJff, Stéphanie D; Raes, Niels; Amaral, Iêda Leão; Salomão, Rafael P; de Souza Coelho, Luiz; de Almeida Matos, Francisca Dionízia; Castilho, Carolina V; de Andrade Lima Filho, Diogenes; López, Dairon Cárdenas; Guevara, Juan Ernesto; Magnusson, William E; Phillips, Oliver L; Wittmann, Florian; de Jesus Veiga Carim, Marcelo; Martins, Maria Pires; Irume, Mariana Victória; Sabatier, Daniel; Molino, Jean-François; Bánki, Olaf S; da Silva Guimarães, José Renan; Pitman, Nigel C A; Piedade, Maria Teresa Fernandez; Mendoza, Abel Monteagudo; Luize, Bruno Garcia; Venticinque, Eduardo Martins; de Leão Novo, Evlyn Márcia Moraes; Vargas, Percy Núñez; Silva, Thiago Sanna Freire; Manzatto, Angelo Gilberto; Terborgh, John; Reis, Neidiane Farias Costa; Montero, Juan Carlos; Casula, Katia Regina; Marimon, Beatriz S; Marimon, Ben-Hur; Coronado, Euridice N Honorio; Feldpausch, Ted R; Duque, Alvaro; Zartman, Charles Eugene; Arboleda, Nicolás Castaño; Killeen, Timothy J; Mostacedo, Bonifacio; Vasquez, Rodolfo; Schöngart, Jochen; Assis, Rafael L; Medeiros, Marcelo Brilhante; Simon, Marcelo Fragomeni; Andrade, Ana; Laurance, William F; Camargo, José Luís; Demarchi, Layon O; Laurance, Susan G W; de Sousa Farias, Emanuelle; Nascimento, Henrique Eduardo Mendonça; Revilla, Juan David Cardenas; Quaresma, Adriano; Costa, Flavia R C; Vieira, Ima Célia Guimarães; Cintra, Bruno Barçante Ladvocat; Castellanos, Hernán; Brienen, Roel; Stevenson, Pablo R; Feitosa, Yuri; Duivenvoorden, Joost F; Aymard C, Gerardo A; Mogollón, Hugo F; Targhetta, Natalia; Comiskey, James A; Vicentini, Alberto; Lopes, Aline; Damasco, Gabriel; Dávila, Nállarett; García-Villacorta, Roosevelt; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Emilio, Thaise; Alonso, Alfonso; Neill, David; Dallmeier, Francisco; Ferreira, Leandro Valle; Araujo-Murakami, Alejandro; Praia, Daniel; do Amaral, Dário Dantas; Carvalho, Fernanda Antunes; de Souza, Fernanda Coelho; Feeley, Kenneth; Arroyo, Luzmila; Pansonato, Marcelo Petratti; Gribel, Rogerio; Villa, Boris; Licona, Juan Carlos; Fine, Paul V A; Cerón, Carlos; Baraloto, Chris; Jimenez, Eliana M; Stropp, Juliana; Engel, Julien; Silveira, Marcos; Mora, Maria Cristina Peñuela; Petronelli, Pascal; Maas, Paul; Thomas-Caesar, Raquel; Henkel, Terry W; Daly, Doug; Paredes, Marcos Ríos; Baker, Tim R; Fuentes, Alfredo; Peres, Carlos A; Chave, Jerome; Pena, Jose Luis Marcelo; Dexter, Kyle G; Silman, Miles R; Jørgensen, Peter Møller; Pennington, Toby; Di Fiore, Anthony; Valverde, Fernando Cornejo; Phillips, Juan Fernando; Rivas-Torres, Gonzalo; von Hildebrand, Patricio; van Andel, Tinde R; Ruschel, Ademir R; Prieto, Adriana; Rudas, Agustín; Hoffman, Bruce; Vela, César I A; Barbosa, Edelcilio Marques; Zent, Egleé L; Gonzales, George Pepe Gallardo; Doza, Hilda Paulette Dávila; de Andrade Miranda, Ires Paula; Guillaumet, Jean-Louis; Pinto, Linder Felipe Mozombite; de Matos Bonates, Luiz Carlos; Silva, Natalino; Gómez, Ricardo Zárate; Zent, Stanford; Gonzales, Therany; Vos, Vincent A; Malhi, Yadvinder; Oliveira, Alexandre A; Cano, Angela; Albuquerque, Bianca Weiss; Vriesendorp, Corine; Correa, Diego Felipe; Torre, Emilio Vilanova; van der Heijden, Geertje; Ramirez-Angulo, Hirma; Ramos, José Ferreira; Young, Kenneth R; Rocha, Maira; Nascimento, Marcelo Trindade; Medina, Maria Natalia Umaña; Tirado, Milton; Wang, Ophelia; Sierra, Rodrigo; Torres-Lezama, Armando; Mendoza, Casimiro; Ferreira, Cid; Baider, Cláudia; Villarroel, Daniel; Balslev, Henrik; Mesones, Italo; Giraldo, Ligia Estela Urrego; Casas, Luisa Fernanda; Reategui, Manuel Augusto Ahuite; Linares-Palomino, Reynaldo; Zagt, Roderick; Cárdenas, Sasha; Farfan-Rios, William; Sampaio, Adeilza Felipe; Pauletto, Daniela; Sandoval, Elvis H Valderrama; Arevalo, Freddy Ramirez; Huamantupa-Chuquimaco, Isau; Garcia-Cabrera, Karina; Hernandez, Lionel; Gamarra, Luis Valenzuela; Alexiades, Miguel N; Pansini, Susamar; Cuenca, Walter Palacios; Milliken, William; Ricardo, Joana; Lopez-Gonzalez, Gabriela; Pos, Edwin; Ter Steege, Hans

2018-01-17

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.

SESAM – a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages

DEFF Research Database (Denmark)

Guisan, Antoine; Rahbek, Carsten

2011-01-01

Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S-SDM) starts...

Incorporating uncertainty in predictive species distribution modelling.

Science.gov (United States)

Beale, Colin M; Lennon, Jack J

2012-01-19

Motivated by the need to solve ecological problems (climate change, habitat fragmentation and biological invasions), there has been increasing interest in species distribution models (SDMs). Predictions from these models inform conservation policy, invasive species management and disease-control measures. However, predictions are subject to uncertainty, the degree and source of which is often unrecognized. Here, we review the SDM literature in the context of uncertainty, focusing on three main classes of SDM: niche-based models, demographic models and process-based models. We identify sources of uncertainty for each class and discuss how uncertainty can be minimized or included in the modelling process to give realistic measures of confidence around predictions. Because this has typically not been performed, we conclude that uncertainty in SDMs has often been underestimated and a false precision assigned to predictions of geographical distribution. We identify areas where development of new statistical tools will improve predictions from distribution models, notably the development of hierarchical models that link different types of distribution model and their attendant uncertainties across spatial scales. Finally, we discuss the need to develop more defensible methods for assessing predictive performance, quantifying model goodness-of-fit and for assessing the significance of model covariates.

Deriving field-based species sensitivity distributions (f-SSDs) from stacked species distribution models (S-SDMs).

Science.gov (United States)

Schipper, Aafke M; Posthuma, Leo; de Zwart, Dick; Huijbregts, Mark A J

2014-12-16

Quantitative relationships between species richness and single environmental factors, also called species sensitivity distributions (SSDs), are helpful to understand and predict biodiversity patterns, identify environmental management options and set environmental quality standards. However, species richness is typically dependent on a variety of environmental factors, implying that it is not straightforward to quantify SSDs from field monitoring data. Here, we present a novel and flexible approach to solve this, based on the method of stacked species distribution modeling. First, a species distribution model (SDM) is established for each species, describing its probability of occurrence in relation to multiple environmental factors. Next, the predictions of the SDMs are stacked along the gradient of each environmental factor with the remaining environmental factors at fixed levels. By varying those fixed levels, our approach can be used to investigate how field-based SSDs for a given environmental factor change in relation to changing confounding influences, including for example optimal, typical, or extreme environmental conditions. This provides an asset in the evaluation of potential management measures to reach good ecological status.

Sample sizes and model comparison metrics for species distribution models

Science.gov (United States)

B.B. Hanberry; H.S. He; D.C. Dey

2012-01-01

Species distribution models use small samples to produce continuous distribution maps. The question of how small a sample can be to produce an accurate model generally has been answered based on comparisons to maximum sample sizes of 200 observations or fewer. In addition, model comparisons often are made with the kappa statistic, which has become controversial....

The effects of model and data complexity on predictions from species distributions models

DEFF Research Database (Denmark)

García-Callejas, David; Bastos, Miguel

2016-01-01

How complex does a model need to be to provide useful predictions is a matter of continuous debate across environmental sciences. In the species distributions modelling literature, studies have demonstrated that more complex models tend to provide better fits. However, studies have also shown...... that predictive performance does not always increase with complexity. Testing of species distributions models is challenging because independent data for testing are often lacking, but a more general problem is that model complexity has never been formally described in such studies. Here, we systematically...

Phylogeographic structure of the commercially important tropical tree species Dryobalanops aromatica Gaertn. F. (Dipterocarpaceae revealed by microsatellite markers

Directory of Open Access Journals (Sweden)

Fifi Gus Dwiyanti

2014-12-01

Full Text Available Dryobalanops aromatica Gaertn. F. (Kapur is an economically important timber     species in Southeast Asia that can serve as a good model for studying the impact of the Pleistocene glaciations on the genetic diversity and distribution of species in tropical regions. Seven polymorphic microsatellite markers were        analyzed in five natural populations of D. aromatica (N = 120 individuals: Gunung Panti in Malay Peninsula, Lingga Island in Lingga Archipelago, Lambir Hills National Park, Limbang and Similajau National Park in Borneo. The level of gene diversity (HE for the five populations was relatively high with a range from 0.571 (Similajau to 0.729 (Gunung Panti. The high genetic diversity in the present study could be attributed to the larger refugia population sizes of D. aromatica than that of other species. The population genetic structure revealed two distinct groups: the Malay Peninsula-Lingga Archipelago and Borneo. This pattern suggests that populations in each geographical area might be the consequence of post-glacial expansion from one or two refugia, but that gene flow between different glacial refugia was fairly restricted. 

Predicting Environmental Suitability for a Rare and Threatened Species (Lao Newt, Laotriton laoensis) Using Validated Species Distribution Models

Science.gov (United States)

Chunco, Amanda J.; Phimmachak, Somphouthone; Sivongxay, Niane; Stuart, Bryan L.

2013-01-01

The Lao newt (Laotriton laoensis) is a recently described species currently known only from northern Laos. Little is known about the species, but it is threatened as a result of overharvesting. We integrated field survey results with climate and altitude data to predict the geographic distribution of this species using the niche modeling program Maxent, and we validated these predictions by using interviews with local residents to confirm model predictions of presence and absence. The results of the validated Maxent models were then used to characterize the environmental conditions of areas predicted suitable for L. laoensis. Finally, we overlaid the resulting model with a map of current national protected areas in Laos to determine whether or not any land predicted to be suitable for this species is coincident with a national protected area. We found that both area under the curve (AUC) values and interview data provided strong support for the predictive power of these models, and we suggest that interview data could be used more widely in species distribution niche modeling. Our results further indicated that this species is mostly likely geographically restricted to high altitude regions (i.e., over 1,000 m elevation) in northern Laos and that only a minute fraction of suitable habitat is currently protected. This work thus emphasizes that increased protection efforts, including listing this species as endangered and the establishment of protected areas in the region predicted to be suitable for L. laoensis, are urgently needed. PMID:23555808

Modelling the spatial distribution of the nuisance mosquito species Anopheles plumbeus (Diptera: Culicidae) in the Netherlands.

Science.gov (United States)

Ibañez-Justicia, Adolfo; Cianci, Daniela

2015-05-01

Landscape modifications, urbanization or changes of use of rural-agricultural areas can create more favourable conditions for certain mosquito species and therefore indirectly cause nuisance problems for humans. This could potentially result in mosquito-borne disease outbreaks when the nuisance is caused by mosquito species that can transmit pathogens. Anopheles plumbeus is a nuisance mosquito species and a potential malaria vector. It is one of the most frequently observed species in the Netherlands. Information on the distribution of this species is essential for risk assessments. The purpose of the study was to investigate the potential spatial distribution of An. plumbeus in the Netherlands. Random forest models were used to link the occurrence and the abundance of An. plumbeus with environmental features and to produce distribution maps in the Netherlands. Mosquito data were collected using a cross-sectional study design in the Netherlands, from April to October 2010-2013. The environmental data were obtained from satellite imagery and weather stations. Statistical measures (accuracy for the occurrence model and mean squared error for the abundance model) were used to evaluate the models performance. The models were externally validated. The maps show that forested areas (centre of the Netherlands) and the east of the country were predicted as suitable for An. plumbeus. In particular high suitability and high abundance was predicted in the south-eastern provinces Limburg and North Brabant. Elevation, precipitation, day and night temperature and vegetation indices were important predictors for calculating the probability of occurrence for An. plumbeus. The probability of occurrence, vegetation indices and precipitation were important for predicting its abundance. The AUC value was 0.73 and the error in the validation was 0.29; the mean squared error value was 0.12. The areas identified by the model as suitable and with high abundance of An. plumbeus, are

An analytically tractable model for community ecology with many species

Science.gov (United States)

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.

A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling.

Science.gov (United States)

Dalmaris, Eleftheria; Ramalho, Cristina E; Poot, Pieter; Veneklaas, Erik J; Byrne, Margaret

2015-11-01

A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia. Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM). A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction. Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had

Near infra-red spectroscopy quantitative modelling of bivalve protein, lipid and glycogen composition using single-species versus multi-species calibration and validation sets

Science.gov (United States)

Bartlett, Jill K.; Maher, William A.; Purss, Matthew B. J.

2018-03-01

Near infrared spectroscopy (NIRS) quantitative modelling was used to measure the protein, lipid and glycogen composition of five marine bivalve species (Saccostrea glomerata, Ostrea angasi, Crassostrea gigas, Mytilus galloprovincialis and Anadara trapezia) from multiple locations and seasons. Predictive models were produced for each component using individual species and aggregated sample populations for the three oyster species (S. glomerata, O. angasi and C. gigas) and for all five bivalve species. Whole animal tissues were freeze dried, ground to > 20 μm and scanned by NIRS. Protein, lipid and glycogen composition were determined by traditional chemical analyses and calibration models developed to allow rapid NIRS-measurement of these components in the five bivalve species. Calibration modelling was performed using wavelet selection, genetic algorithms and partial least squares analysis. Model quality was assessed using RPIQ and RMESP. For protein composition, single species model results had RPIQ values between 2.4 and 3.5 and RMSEP between 8.6 and 18%, the three oyster model had an RPIQ of 2.6 and an RMSEP of 10.8% and the five bivalve species had an RPIQ of 3.6 and RMSEP of 8.7% respectively. For lipid composition, single species models achieved RPIQ values between 2.9 and 5.3 with RMSEP between 9.1 and 11.2%, the oyster model had an RPIQ of 3.6 and RMSEP of 6.8 and the five bivalve model had an RPIQ of 5.2 and RMSEP of 6.8% respectively. For glycogen composition, the single species models had RPIQs between 3.8 and 18.9 with RMSEP between 3.5 and 9.2%, the oyster model had an RPIQ of 5.5 and RMSEP of 7.1% and the five bivalve model had an RPIQ of 4 and RMSEP of 7.6% respectively. Comparison between individual species models and aggregated models for three oyster species and five bivalve species for each component indicate that aggregating data from like species produces high quality models with robust and reliable quantitative application. The benefit of

A comparison of fisheries biological reference points estimated from temperature-specific multi-species and single-species climate-enhanced stock assessment models

Science.gov (United States)

Holsman, Kirstin K.; Ianelli, James; Aydin, Kerim; Punt, André E.; Moffitt, Elizabeth A.

2016-12-01

Multi-species statistical catch at age models (MSCAA) can quantify interacting effects of climate and fisheries harvest on species populations, and evaluate management trade-offs for fisheries that target several species in a food web. We modified an existing MSCAA model to include temperature-specific growth and predation rates and applied the modified model to three fish species, walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus) and arrowtooth flounder (Atheresthes stomias), from the eastern Bering Sea (USA). We fit the model to data from 1979 through 2012, with and without trophic interactions and temperature effects, and use projections to derive single- and multi-species biological reference points (BRP and MBRP, respectively) for fisheries management. The multi-species model achieved a higher over-all goodness of fit to the data (i.e. lower negative log-likelihood) for pollock and Pacific cod. Variability from water temperature typically resulted in 5-15% changes in spawning, survey, and total biomasses, but did not strongly impact recruitment estimates or mortality. Despite this, inclusion of temperature in projections did have a strong effect on BRPs, including recommended yield, which were higher in single-species models for Pacific cod and arrowtooth flounder that included temperature compared to the same models without temperature effects. While the temperature-driven multi-species model resulted in higher yield MBPRs for arrowtooth flounder than the same model without temperature, we did not observe the same patterns in multi-species models for pollock and Pacific cod, where variability between harvest scenarios and predation greatly exceeded temperature-driven variability in yield MBRPs. Annual predation on juvenile pollock (primarily cannibalism) in the multi-species model was 2-5 times the annual harvest of adult fish in the system, thus predation represents a strong control on population dynamics that exceeds temperature

Exploration of genetic diversity among medicinally important genus Epimedium species based on genomic and EST-SSR marker.

Science.gov (United States)

Yousaf, Zubaida; Hu, Weiming; Zhang, Yanjun; Zeng, Shaohua; Wang, Ying

2015-01-01

Epimedium species has gained prime importance due to their medicinal and economic values. Therefore, in this study, 26 genomic SSR and 10 EST-SSR markers were developed for 13 medicinal species of the Epimedium genus and one out-group species Vancouveria hexandra W. J. Hooker to explore the existing genetic diversity. A total of 100 alleles by genomic SSR and 65 by EST-SSR were detected. The genomic SSR markers were presented between 2-7 alleles per locus. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 4.5 and 0.0254 to 2.8108, respectively. Similarly, for EST-SSR, these values were ranged from 3.00 to 4.00 and 1.9650 to 2.7142. The number of alleles for EST-SSR markers ranged from 3 to 10 with an average of 3.51 per loci. It has been concluded that medicinally important species of the genus Epimedium possesses lower intraspecific genetic variation.

Biomass models to estimate carbon stocks for hardwood tree species

Energy Technology Data Exchange (ETDEWEB)

Ruiz-Peinado, R.; Montero, G.; Rio, M. del

2012-11-01

To estimate forest carbon pools from forest inventories it is necessary to have biomass models or biomass expansion factors. In this study, tree biomass models were developed for the main hardwood forest species in Spain: Alnus glutinosa, Castanea sativa, Ceratonia siliqua, Eucalyptus globulus, Fagus sylvatica, Fraxinus angustifolia, Olea europaea var. sylvestris, Populus x euramericana, Quercus canariensis, Quercus faginea, Quercus ilex, Quercus pyrenaica and Quercus suber. Different tree biomass components were considered: stem with bark, branches of different sizes, above and belowground biomass. For each species, a system of equations was fitted using seemingly unrelated regression, fulfilling the additivity property between biomass components. Diameter and total height were explored as independent variables. All models included tree diameter whereas for the majority of species, total height was only considered in the stem biomass models and in some of the branch models. The comparison of the new biomass models with previous models fitted separately for each tree component indicated an improvement in the accuracy of the models. A mean reduction of 20% in the root mean square error and a mean increase in the model efficiency of 7% in comparison with recently published models. So, the fitted models allow estimating more accurately the biomass stock in hardwood species from the Spanish National Forest Inventory data. (Author) 45 refs.

Abundance modelling of invasive and indigenous Culicoides species in Spain

Directory of Open Access Journals (Sweden)

Els Ducheyne

2013-11-01

Full Text Available In this paper we present a novel methodology applied in Spain to model spatial abundance patterns of potential vectors of disease at a medium spatial resolution of 5 x 5 km using a countrywide database with abundance data for five Culicoides species, random regression Forest modelling and a spatial dataset of ground measured and remotely sensed eco-climatic and environmental predictor variables. First the probability of occurrence was computed. In a second step a direct regression between the probability of occurrence and trap abundance was established to verify the linearity of the relationship. Finally the probability of occurrence was used in combination with the set of predictor variables to model abundance. In each case the variable importance of the predictors was used to biologically interpret results and to compare both model outputs, and model performance was assessed using four different accuracy measures. Results are shown for C. imicola, C. newsteadii, C. pulicaris group, C. punctatus and C. obsoletus group. In each case the probability of occurrence is a good predictor of abundance at the used spatial resolution of 5 x 5 km. In addition, the C. imicola and C. obsoletus group are highly driven by summer rainfall. The spatial pattern is inverse between the two species, indicating that the lower and upper thresholds are different. C. pulicaris group is mainly driven by temperature. The patterns for C. newsteadii and C. punctatus are less clear. It is concluded that the proposed methodology can be used as an input to transmission-infection-recovery (TIR models and R0 models. The methodology will become available to the general public as part of the VECMAPTM software.

Practical Modeling of aluminum species in high-pH waste

International Nuclear Information System (INIS)

Reynolds, D.A.

1995-10-01

One of the main components of the nuclear waste stored at the Hanford Site is aluminum. As efforts are made to dispose of the waste, the need to predict the various phases of the aluminum becomes important for modeling of the disposal processes. Current databases of the aluminum species are not adequate as they stand. This study is not an attempt to present a rigorous discussion of aluminum chemistry, but to approach aluminum solubility as a practical application. The approach considers two different forms of aluminate; Al(OH) 4 - and AlO 2 - . By taking both of these forms of aluminate into consideration, a workable system of aluminium chemistry is formed that can be used to model the various waste disposal processes

Preliminary investigation of Culicidae species in South Pantanal, Brazil and their potential importance in arbovirus transmission.

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Pauvolid-Corrêa, Alex; Tavares, Fernando Neto; Alencar, Jeronimo; Silva, Julia dos Santos; Murta, Michele; Serra-Freire, Nicolau Maués; Pellegrin, Aiesca Oliveira; Gil-Santana, Hélcio; Guimarães, Anthony Erico; Silva, Edson Elias da

2010-01-01

In view of the high circulation of migratory birds and the environmental and climatic conditions which favor the proliferation of arthropods, the Brazilian Pantanal is susceptible to circulation of arboviruses. However, the amount of data concerning arbovirus vectors in this area is scarce; therefore the aim of this study was to conduct a preliminary investigation of Culicidae species in the Nhecolândia Sub-region of South Pantanal, Brazil and their potential importance in the arbovirus transmission. A total of 3684 specimens of mosquitoes were captured, 1689 of which caught in the rainy season of 2007, were divided into 78 pools and submitted to viral isolation, Semi-Nested RT-PCR and Nested RT-PCR, with a view to identifying the most important arboviruses in Brazil. Simultaneously, 70 specimens of ticks found blood-feeding on horses were also submitted to the same virological assays. No virus was isolated and viral nucleic-acid detection by RT-PCR was also negative. Nevertheless, a total of 22 Culicidae species were identified, ten of which had previously been reported as vectors of important arboviruses. The diversity of species found blood-feeding on human and horse hosts together with the arboviruses circulation previously reported suggest that the Nhecolândia Sub-region of South Pantanal is an important area for arbovirus surveillance in Brazil.

Model-based uncertainty in species range prediction

DEFF Research Database (Denmark)

Pearson, R. G.; Thuiller, Wilfried; Bastos Araujo, Miguel

2006-01-01

Aim Many attempts to predict the potential range of species rely on environmental niche (or 'bioclimate envelope') modelling, yet the effects of using different niche-based methodologies require further investigation. Here we investigate the impact that the choice of model can have on predictions...

Species distribution modelling for conservation of an endangered endemic orchid.

Science.gov (United States)

Wang, Hsiao-Hsuan; Wonkka, Carissa L; Treglia, Michael L; Grant, William E; Smeins, Fred E; Rogers, William E

2015-04-21

Concerns regarding the long-term viability of threatened and endangered plant species are increasingly warranted given the potential impacts of climate change and habitat fragmentation on unstable and isolated populations. Orchidaceae is the largest and most diverse family of flowering plants, but it is currently facing unprecedented risks of extinction. Despite substantial conservation emphasis on rare orchids, populations continue to decline. Spiranthes parksii (Navasota ladies' tresses) is a federally and state-listed endangered terrestrial orchid endemic to central Texas. Hence, we aimed to identify potential factors influencing the distribution of the species, quantify the relative importance of each factor and determine suitable habitat for future surveys and targeted conservation efforts. We analysed several geo-referenced variables describing climatic conditions and landscape features to identify potential factors influencing the likelihood of occurrence of S. parksii using boosted regression trees. Our model classified 97 % of the cells correctly with regard to species presence and absence, and indicated that probability of existence was correlated with climatic conditions and landscape features. The most influential variables were mean annual precipitation, mean elevation, mean annual minimum temperature and mean annual maximum temperature. The most likely suitable range for S. parksii was the eastern portions of Leon and Madison Counties, the southern portion of Brazos County, a portion of northern Grimes County and along the borders between Burleson and Washington Counties. Our model can assist in the development of an integrated conservation strategy through: (i) focussing future survey and research efforts on areas with a high likelihood of occurrence, (ii) aiding in selection of areas for conservation and restoration and (iii) framing future research questions including those necessary for predicting responses to climate change. Our model could also

Spatial Scaling of Environmental Variables Improves Species-Habitat Models of Fishes in a Small, Sand-Bed Lowland River.

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Johannes Radinger

Full Text Available Habitat suitability and the distinct mobility of species depict fundamental keys for explaining and understanding the distribution of river fishes. In recent years, comprehensive data on river hydromorphology has been mapped at spatial scales down to 100 m, potentially serving high resolution species-habitat models, e.g., for fish. However, the relative importance of specific hydromorphological and in-stream habitat variables and their spatial scales of influence is poorly understood. Applying boosted regression trees, we developed species-habitat models for 13 fish species in a sand-bed lowland river based on river morphological and in-stream habitat data. First, we calculated mean values for the predictor variables in five distance classes (from the sampling site up to 4000 m up- and downstream to identify the spatial scale that best predicts the presence of fish species. Second, we compared the suitability of measured variables and assessment scores related to natural reference conditions. Third, we identified variables which best explained the presence of fish species. The mean model quality (AUC = 0.78, area under the receiver operating characteristic curve significantly increased when information on the habitat conditions up- and downstream of a sampling site (maximum AUC at 2500 m distance class, +0.049 and topological variables (e.g., stream order were included (AUC = +0.014. Both measured and assessed variables were similarly well suited to predict species' presence. Stream order variables and measured cross section features (e.g., width, depth, velocity were best-suited predictors. In addition, measured channel-bed characteristics (e.g., substrate types and assessed longitudinal channel features (e.g., naturalness of river planform were also good predictors. These findings demonstrate (i the applicability of high resolution river morphological and instream-habitat data (measured and assessed variables to predict fish presence, (ii the

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

Science.gov (United States)

Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

2011-01-01

Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

Solvable Catalyzed Birth-Death-Exchange Competition Model of Three Species

International Nuclear Information System (INIS)

Wang Haifeng; Gao Yan; Zhang Heng; Lin Zhenquan

2009-01-01

A competition model of three species in exchange-driven aggregation growth is proposed. In the model, three distinct aggregates grow by exchange of monomers and in parallel, birth of species A is catalyzed by species B and death of species A is catalyzed by species C. The rates for both catalysis processes are proportional to kj ν and kj ω respectively, where ν(Ω) is a parameter reflecting the dependence of the catalysis reaction rate of birth (death) on the catalyst aggregate's size. The kinetic evolution behaviors of the three species are investigated by the rate equation approach based on the mean-field theory. The form of the aggregate size distribution of A-species a k (t) is found to be dependent crucially on the two catalysis rate kernel parameters. The results show that (i) in case of μ ≤ 0, the form of a k (t) mainly depends on the competition between self-exchange of species A and species-C-catalyzed death of species A; (ii) in case of ν > 0, the form of a k (t) mainly depends on the competition between species-B-catalyzed birth of species A and species-C-catalyzed death of species A. (interdisciplinary physics and related areas of science and technology)

Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives.

Science.gov (United States)

Jung, Jaejoon; Park, Woojun

2015-03-01

Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.

Comparison of a species distribution model and a process model from a hierarchical perspective to quantify effects of projected climate change on tree species

Science.gov (United States)

Jeffrey E. Schneiderman; Hong S. He; Frank R. Thompson; William D. Dijak; Jacob S. Fraser

2015-01-01

Tree species distribution and abundance are affected by forces operating across a hierarchy of ecological scales. Process and species distribution models have been developed emphasizing forces at different scales. Understanding model agreement across hierarchical scales provides perspective on prediction uncertainty and ultimately enables policy makers and managers to...

Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models

Science.gov (United States)

Fieberg, John R.; Forester, James D.; Street, Garrett M.; Johnson, Douglas H.; ArchMiller, Althea A.; Matthiopoulos, Jason

2018-01-01

“Species distribution modeling” was recently ranked as one of the top five “research fronts” in ecology and the environmental sciences by ISI's Essential Science Indicators (Renner and Warton 2013), reflecting the importance of predicting how species distributions will respond to anthropogenic change. Unfortunately, species distribution models (SDMs) often perform poorly when applied to novel environments. Compounding on this problem is the shortage of methods for evaluating SDMs (hence, we may be getting our predictions wrong and not even know it). Traditional methods for validating SDMs quantify a model's ability to classify locations as used or unused. Instead, we propose to focus on how well SDMs can predict the characteristics of used locations. This subtle shift in viewpoint leads to a more natural and informative evaluation and validation of models across the entire spectrum of SDMs. Through a series of examples, we show how simple graphical methods can help with three fundamental challenges of habitat modeling: identifying missing covariates, non-linearity, and multicollinearity. Identifying habitat characteristics that are not well-predicted by the model can provide insights into variables affecting the distribution of species, suggest appropriate model modifications, and ultimately improve the reliability and generality of conservation and management recommendations.

Proximal Soil Sensing - A Contribution for Species Habitat Distribution Modelling of Earthworms in Agricultural Soils?

Science.gov (United States)

Schirrmann, Michael; Joschko, Monika; Gebbers, Robin; Kramer, Eckart; Zörner, Mirjam; Barkusky, Dietmar; Timmer, Jens

2016-01-01

Earthworms are important for maintaining soil ecosystem functioning and serve as indicators of soil fertility. However, detection of earthworms is time-consuming, which hinders the assessment of earthworm abundances with high sampling density over entire fields. Recent developments of mobile terrestrial sensor platforms for proximal soil sensing (PSS) provided new tools for collecting dense spatial information of soils using various sensing principles. Yet, the potential of PSS for assessing earthworm habitats is largely unexplored. This study investigates whether PSS data contribute to the spatial prediction of earthworm abundances in species distribution models of agricultural soils. Proximal soil sensing data, e.g., soil electrical conductivity (EC), pH, and near infrared absorbance (NIR), were collected in real-time in a field with two management strategies (reduced tillage / conventional tillage) and sandy to loam soils. PSS was related to observations from a long-term (11 years) earthworm observation study conducted at 42 plots. Earthworms were sampled from 0.5 x 0.5 x 0.2 m³ soil blocks and identified to species level. Sensor data were highly correlated with earthworm abundances observed in reduced tillage but less correlated with earthworm abundances observed in conventional tillage. This may indicate that management influences the sensor-earthworm relationship. Generalized additive models and state-space models showed that modelling based on data fusion from EC, pH, and NIR sensors produced better results than modelling without sensor data or data from just a single sensor. Regarding the individual earthworm species, particular sensor combinations were more appropriate than others due to the different habitat requirements of the earthworms. Earthworm species with soil-specific habitat preferences were spatially predicted with higher accuracy by PSS than more ubiquitous species. Our findings suggest that PSS contributes to the spatial modelling of

Proximal Soil Sensing - A Contribution for Species Habitat Distribution Modelling of Earthworms in Agricultural Soils?

Directory of Open Access Journals (Sweden)

Michael Schirrmann

Full Text Available Earthworms are important for maintaining soil ecosystem functioning and serve as indicators of soil fertility. However, detection of earthworms is time-consuming, which hinders the assessment of earthworm abundances with high sampling density over entire fields. Recent developments of mobile terrestrial sensor platforms for proximal soil sensing (PSS provided new tools for collecting dense spatial information of soils using various sensing principles. Yet, the potential of PSS for assessing earthworm habitats is largely unexplored. This study investigates whether PSS data contribute to the spatial prediction of earthworm abundances in species distribution models of agricultural soils.Proximal soil sensing data, e.g., soil electrical conductivity (EC, pH, and near infrared absorbance (NIR, were collected in real-time in a field with two management strategies (reduced tillage / conventional tillage and sandy to loam soils. PSS was related to observations from a long-term (11 years earthworm observation study conducted at 42 plots. Earthworms were sampled from 0.5 x 0.5 x 0.2 m³ soil blocks and identified to species level. Sensor data were highly correlated with earthworm abundances observed in reduced tillage but less correlated with earthworm abundances observed in conventional tillage. This may indicate that management influences the sensor-earthworm relationship. Generalized additive models and state-space models showed that modelling based on data fusion from EC, pH, and NIR sensors produced better results than modelling without sensor data or data from just a single sensor. Regarding the individual earthworm species, particular sensor combinations were more appropriate than others due to the different habitat requirements of the earthworms. Earthworm species with soil-specific habitat preferences were spatially predicted with higher accuracy by PSS than more ubiquitous species.Our findings suggest that PSS contributes to the spatial

Marmosets as model species in neuroscience and evolutionary anthropology.

Science.gov (United States)

Burkart, Judith M; Finkenwirth, Christa

2015-04-01

Marmosets are increasingly used as model species by both neuroscientists and evolutionary anthropologists, but with a different rationale for doing so. Whereas neuroscientists stress that marmosets share many cognitive traits with humans due to common descent, anthropologists stress those traits shared with marmosets - and callitrichid monkeys in general - due to convergent evolution, as a consequence of the cooperative breeding system that characterizes both humans and callitrichids. Similarities in socio-cognitive abilities due to convergence, rather than homology, raise the question whether these similarities also extend to the proximate regulatory mechanisms, which is particularly relevant for neuroscientific investigations. In this review, we first provide an overview of the convergent adaptations to cooperative breeding at the psychological and cognitive level in primates, which bear important implications for our understanding of human cognitive evolution. In the second part, we zoom in on two of these convergent adaptations, proactive prosociality and social learning, and compare their proximate regulation in marmosets and humans with regard to oxytocin and cognitive top down regulation. Our analysis suggests considerable similarity in these regulatory mechanisms presumably because the convergent traits emerged due to small motivational changes that define how pre-existing cognitive mechanisms are quantitatively combined. This finding reconciles the prima facie contradictory rationale for using marmosets as high priority model species in neuroscience and anthropology. Copyright © 2014 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

A real-time polymerase chain reaction method for the identification of four commercially important salmon and trout species.

Science.gov (United States)

Feng, Junli; Wu, Zhigang; Xie, Xiao; Dai, Zhiyuan; Liu, Shasha

2017-01-01

A duplex quantitative real-time PCR (qPCR) assay was developed for rapid and accurate identification of four commercially important salmon and trout species (Oncorhynchus keta, Oncorhynchus nerka, Oncorhynchus mykiss, and Salmo salar) commonly used for production process of fish in China. The assays targeting the mitochondrial control region (CR) and 16S rRNA gene were able to simultaneously discriminate four target species and the family Salmonidae from processed as well as fresh fish. The qPCR efficiency of each reaction was calculated according to the standard curve, and the method was validated by amplification DNA extracted from single or artificial mixtures prepared with the reference salmon and trout species. Testing of 11 commercial salmon and trout products by the established qPCR assay demonstrated that it was really a useful and academic technique to identify four commercially important salmon and trout species.

Selection bias in species distribution models: An econometric approach on forest trees based on structural modeling

Science.gov (United States)

Martin-StPaul, N. K.; Ay, J. S.; Guillemot, J.; Doyen, L.; Leadley, P.

2014-12-01

Species distribution models (SDMs) are widely used to study and predict the outcome of global changes on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of applications on forest trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8km). We also compared the outputs of the SSDM with outputs of a classical SDM (i.e. Biomod ensemble modelling) in terms of bioclimatic response curves and potential distributions under current climate and climate change scenarios. The shapes of the bioclimatic response curves and the modelled species distribution maps differed markedly between SSDM and classical SDMs, with contrasted patterns according to species and spatial resolutions. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents

Coupling Satellite Data with Species Distribution and Connectivity Models as a Tool for Environmental Management and Planning in Matrix-Sensitive Species

Science.gov (United States)

Rödder, Dennis; Nekum, Sven; Cord, Anna F.; Engler, Jan O.

2016-07-01

Climate change and anthropogenic habitat fragmentation are considered major threats for global biodiversity. As a direct consequence, connectivity is increasingly disrupted in many species, which might have serious consequences that could ultimately lead to the extinction of populations. Although a large number of reserves and conservation sites are designated and protected by law, potential habitats acting as inter-population connectivity corridors are, however, mostly ignored in the common practice of environmental planning. In most cases, this is mainly caused by a lack of quantitative measures of functional connectivity available for the planning process. In this study, we highlight the use of fine-scale potential connectivity models (PCMs) derived from multispectral satellite data for the quantification of spatially explicit habitat corridors for matrix-sensitive species of conservation concern. This framework couples a species distribution model with a connectivity model in a two-step framework, where suitability maps from step 1 are transformed into maps of landscape resistance in step 2 filtered by fragmentation thresholds. We illustrate the approach using the sand lizard ( Lacerta agilis L.) in the metropolitan area of Cologne, Germany, as a case study. Our model proved to be well suited to identify connected as well as completely isolated populations within the study area. Furthermore, due to its fine resolution, the PCM was also able to detect small linear structures known to be important for sand lizards' inter-population connectivity such as railroad embankments. We discuss the applicability and possible implementation of PCMs to overcome shortcomings in the common practice of environmental impact assessments.

The Bifurcation and Control of a Single-Species Fish Population Logistic Model with the Invasion of Alien Species

OpenAIRE

Zhang, Yi; Zhang, Qiaoling; Li, Jinghao; Zhang, Qingling

2014-01-01

The objective of this paper is to study systematically the bifurcation and control of a single-species fish population logistic model with the invasion of alien species based on the theory of singular system and bifurcation. It regards Spartina anglica as an invasive species, which invades the fisheries and aquaculture. Firstly, the stabilities of equilibria in this model are discussed. Moreover, the sufficient conditions for existence of the trans-critical bifurcation and the singularity ind...

Modelling for an improved integrated multi-trophic aquaculture system for the production of highly valued marine species

Directory of Open Access Journals (Sweden)

Luana Granada

2014-05-01

Full Text Available Integrated multi-trophic aquaculture (IMTA is regarded as a suitable approach to limit aquaculture nutrients and organic matter outputs through biomitigation. Here, species from different trophic or nutritional levels are connected through water transfer. The co-cultured species are used as biofilters, and each level has its own independent commercial value, providing both economic and environmental sustainability. In order to better understand and optimize aquaculture production systems, dynamic modelling has been developed towards the use of models for analysis and simulation of aquacultures. Several models available determine the carrying capacity of farms and the environmental effects of bivalve and fish aquaculture. Also, in the last two decades, modelling strategies have been designed in order to predict the dispersion and deposition of organic fish farm waste, usually using the mean settling velocity of faeces and feed pellets. Cultured organisms growth, effects of light and temperature on algae growth, retention of suspended solids, biodegradation of nitrogen and wastewater treatment are examples of other modelled parameters in aquaculture. Most modelling equations have been developed for monocultures, despite the increasing importance of multi-species systems, such as polyculture and IMTA systems. The main reason for the development of multi-species models is to maximize the production and optimize species combinations in order to reduce the environmental impacts of aquaculture. Some multi-species system models are available, including from the polyculture of different species of bivalves with fish to more complex systems with four trophic levels. These can incorporate ecosystem models and use dynamic energy budgets for each trophic group. In the proposed IMTA system, the bioremediation potential of the marine seaweed Gracilaria vermiculophylla (nutrient removal performance and the Mediterranean filter-feeding polychaete Sabella

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.

Science.gov (United States)

Richards, Christina L; Alonso, Conchita; Becker, Claude; Bossdorf, Oliver; Bucher, Etienne; Colomé-Tatché, Maria; Durka, Walter; Engelhardt, Jan; Gaspar, Bence; Gogol-Döring, Andreas; Grosse, Ivo; van Gurp, Thomas P; Heer, Katrin; Kronholm, Ilkka; Lampei, Christian; Latzel, Vít; Mirouze, Marie; Opgenoorth, Lars; Paun, Ovidiu; Prohaska, Sonja J; Rensing, Stefan A; Stadler, Peter F; Trucchi, Emiliano; Ullrich, Kristian; Verhoeven, Koen J F

2017-12-01

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Model uncertainties do not affect observed patterns of species richness in the Amazon

Science.gov (United States)

Sales, Lilian Patrícia; Neves, Olívia Viana; De Marco, Paulo

2017-01-01

Background Climate change is arguably a major threat to biodiversity conservation and there are several methods to assess its impacts on species potential distribution. Yet the extent to which different approaches on species distribution modeling affect species richness patterns at biogeographical scale is however unaddressed in literature. In this paper, we verified if the expected responses to climate change in biogeographical scale—patterns of species richness and species vulnerability to climate change—are affected by the inputs used to model and project species distribution. Methods We modeled the distribution of 288 vertebrate species (amphibians, birds and mammals), all endemic to the Amazon basin, using different combinations of the following inputs known to affect the outcome of species distribution models (SDMs): 1) biological data type, 2) modeling methods, 3) greenhouse gas emission scenarios and 4) climate forecasts. We calculated uncertainty with a hierarchical ANOVA in which those different inputs were considered factors. Results The greatest source of variation was the modeling method. Model performance interacted with data type and modeling method. Absolute values of variation on suitable climate area were not equal among predictions, but some biological patterns were still consistent. All models predicted losses on the area that is climatically suitable for species, especially for amphibians and primates. All models also indicated a current East-western gradient on endemic species richness, from the Andes foot downstream the Amazon river. Again, all models predicted future movements of species upwards the Andes mountains and overall species richness losses. Conclusions From a methodological perspective, our work highlights that SDMs are a useful tool for assessing impacts of climate change on biodiversity. Uncertainty exists but biological patterns are still evident at large spatial scales. As modeling methods are the greatest source of

Predicting Emergence of the Most Important Weed Species in Soybean (Glycine max L. under Different Management Operation

Directory of Open Access Journals (Sweden)

R. Khakzad

2017-12-01

Full Text Available Introduction: Summer annual weeds typically germinate in spring and early summer, grow throughout the summer, and set seeds by fall. Summer annual weeds are a persistent problem in summer annual row crops, competing directly for water, light, and nutrients, causing yield losses in quantity and quality. Although agriculture is increasingly relying on modern technology, knowledge of the biological systems in which these technologies are used is still critical for implementation of management strategies. Biological information about weeds is valuable and necessary for developing management strategies to minimize their impact. Scouting fields for pest problems are essential in any cropping system and knowledge of the timing and sequence of weed species emergence could increase the effectiveness of weed scouting trips and subsequent management practices. The success of any annual plant is directly correlated to its time of seedling emergence because it determines the ability of a plant to compete with its neighbors, survive biotic and abiotic stresses, and reproduce. The period and pattern of emergence of the weed community depend on the species present in the seed bank and their interaction with the environment. Therefore, knowledge of the weed species present in the soil seed bank and when these species are most likely to emerge is important in planning effective weed control programs. Temperature has been reported to be the main environmental factor regulating germination and emergence of weed species. Scientists have developed TT models to predict the emergence of weed species based on a daily accumulation of heat units or growing degree days (GDD above a minimum base threshold value (Tbase. The predictive models for weed emergence based on the accumulation of TT appear to be accurate enough for projections of weed emergence time (Grundy 2003. Moreover, soil temperature data are easily accessible, making this type of model practical and useful to

A multi-species exchange model for fully fluctuating polymer field theory simulations.

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Düchs, Dominik; Delaney, Kris T; Fredrickson, Glenn H

2014-11-07

Field-theoretic models have been used extensively to study the phase behavior of inhomogeneous polymer melts and solutions, both in self-consistent mean-field calculations and in numerical simulations of the full theory capturing composition fluctuations. The models commonly used can be grouped into two categories, namely, species models and exchange models. Species models involve integrations of functionals that explicitly depend on fields originating both from species density operators and their conjugate chemical potential fields. In contrast, exchange models retain only linear combinations of the chemical potential fields. In the two-component case, development of exchange models has been instrumental in enabling stable complex Langevin (CL) simulations of the full complex-valued theory. No comparable stable CL approach has yet been established for field theories of the species type. Here, we introduce an extension of the exchange model to an arbitrary number of components, namely, the multi-species exchange (MSE) model, which greatly expands the classes of soft material systems that can be accessed by the complex Langevin simulation technique. We demonstrate the stability and accuracy of the MSE-CL sampling approach using numerical simulations of triblock and tetrablock terpolymer melts, and tetrablock quaterpolymer melts. This method should enable studies of a wide range of fluctuation phenomena in multiblock/multi-species polymer blends and composites.

Characterization and identification of microRNA core promoters in four model species.

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Xuefeng Zhou

2007-03-01

Full Text Available MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well-understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize, in a genome scale, the promoters of intergenic microRNA genes in Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Oryza sativa. We show that most known microRNA genes in these four species have the same type of promoters as protein-coding genes have. To further characterize the promoters of microRNA genes, we developed a novel promoter prediction method, called common query voting (CoVote, which is more effective than available promoter prediction methods. Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species. We discover many significant, characteristic sequence motifs in these core promoters, several of which match or resemble the known cis-acting elements for transcription initiation. Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.

Using species abundance distribution models and diversity indices for biogeographical analyses

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Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.

2016-01-01

We examine whether Species Abundance Distribution models (SADs) and diversity indices can describe how species colonization status influences species community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic species restricted to only one island, should be represented by few rare species and consequently have abundance patterns that differ from those of more widespread species. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the species into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-abundance plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly abundant species and a lack of rare species, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted species; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for

Simplifying biochemical models with intermediate species

DEFF Research Database (Denmark)

Feliu, Elisenda; Wiuf, Carsten

2013-01-01

techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification...... systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple...... canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady...

Characterization of an Ar/O2 magnetron plasma by a multi-species Monte Carlo model

International Nuclear Information System (INIS)

Bultinck, E; Bogaerts, A

2011-01-01

A combined Monte Carlo (MC)/analytical surface model is developed to study the plasma processes occurring during the reactive sputter deposition of TiO x thin films. This model describes the important plasma species with a MC approach (i.e. electrons, Ar + ions, O 2 + ions, fast Ar atoms and sputtered Ti atoms). The deposition of the TiO x film is treated by an analytical surface model. The implementation of our so-called multi-species MC model is presented, and some typical calculation results are shown, such as densities, fluxes, energies and collision rates. The advantages and disadvantages of the multi-species MC model are illustrated by a comparison with a particle-in-cell/Monte Carlo collisions (PIC/MCC) model. Disadvantages include the fact that certain input values and assumptions are needed. However, when these are accounted for, the results are in good agreement with the PIC/MCC simulations, and the calculation time has drastically decreased, which enables us to simulate large and complicated reactor geometries. To illustrate this, the effect of larger target-substrate distances on the film properties is investigated. It is shown that a stoichiometric film is deposited at all investigated target-substrate distances (24, 40, 60 and 80 mm). Moreover, a larger target-substrate distance promotes film uniformity, but the deposition rate is much lower.

A cost minimisation and Bayesian inference model predicts startle reflex modulation across species.

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Bach, Dominik R

2015-04-07

In many species, rapid defensive reflexes are paramount to escaping acute danger. These reflexes are modulated by the state of the environment. This is exemplified in fear-potentiated startle, a more vigorous startle response during conditioned anticipation of an unrelated threatening event. Extant explanations of this phenomenon build on descriptive models of underlying psychological states, or neural processes. Yet, they fail to predict invigorated startle during reward anticipation and instructed attention, and do not explain why startle reflex modulation evolved. Here, we fill this lacuna by developing a normative cost minimisation model based on Bayesian optimality principles. This model predicts the observed pattern of startle modification by rewards, punishments, instructed attention, and several other states. Moreover, the mathematical formalism furnishes predictions that can be tested experimentally. Comparing the model with existing data suggests a specific neural implementation of the underlying computations which yields close approximations to the optimal solution under most circumstances. This analysis puts startle modification into the framework of Bayesian decision theory and predictive coding, and illustrates the importance of an adaptive perspective to interpret defensive behaviour across species. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

New species, hyper-diversity and potential importance of Calonectria spp. from Eucalyptus in South China.

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Lombard, L; Chen, S F; Mou, X; Zhou, X D; Crous, P W; Wingfield, M J

2015-03-01

Plantation forestry is expanding rapidly in China to meet an increasing demand for wood and pulp products globally. Fungal pathogens including species of Calonectria represent a serious threat to the growth and sustainability of this industry. Surveys were conducted in the Guangdong, Guangxi and Hainan Provinces of South China, where Eucalyptus trees in plantations or cuttings in nurseries displayed symptoms of leaf blight. Isolations from symptomatic leaves and soils collected close to infected trees resulted in a large collection of Calonectria isolates. These isolates were identified using the Consolidated Species Concept, employing morphological characters and DNA sequence comparisons for the β-tubulin, calmodulin, histone H3 and translation elongation factor 1-alpha gene regions. Twenty-one Calonectria species were identified of which 18 represented novel taxa. Of these, 12 novel taxa belonged to Sphaero-Naviculate Group and the remaining six to the Prolate Group. Southeast Asia appears to represent a centre of biodiversity for the Sphaero-Naviculate Group and this fact could be one of the important constraints to Eucalyptus forestry in China. The remarkable diversity of Calonectria species in a relatively small area of China and associated with a single tree species is surprising.

Mapping National Plant Biodiversity Patterns in South Korea with the MARS Species Distribution Model.

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Hyeyeong Choe

Full Text Available Accurate information on the distribution of existing species is crucial to assess regional biodiversity. However, data inventories are insufficient in many areas. We examine the ability of Multivariate Adaptive Regression Splines (MARS multi-response species distribution model to overcome species' data limitations and portray plant species distribution patterns for 199 South Korean plant species. The study models species with two or more observations, examines their contribution to national patterns of species richness, provides a sensitivity analysis of different range threshold cutoff approaches for modeling species' ranges, and presents considerations for species modeling at fine spatial resolution. We ran MARS models for each species and tested four threshold methods to transform occurrence probabilities into presence or absence range maps. Modeled occurrence probabilities were extracted at each species' presence points, and the mean, median, and one standard deviation (SD calculated to define data-driven thresholds. A maximum sum of sensitivity and specificity threshold was also calculated, and the range maps from the four cutoffs were tested using independent plant survey data. The single SD values were the best threshold tested for minimizing omission errors and limiting species ranges to areas where the associated occurrence data were correctly classed. Eight individual species range maps for rare plant species were identified that are potentially affected by resampling predictor variables to fine spatial scales. We portray spatial patterns of high species richness by assessing the combined range maps from three classes of species: all species, endangered and endemic species, and range-size rarity of all species, which could be used in conservation planning for South Korea. The MARS model is promising for addressing the common problem of few species occurrence records. However, projected species ranges are highly dependent on the

Assessing the importance of four sandfly species (Diptera: Psychodidae) as vectors of Leishmania mexicana in Campeche, Mexico.

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Pech-May, A; Peraza-Herrera, G; Moo-Llanes, D A; Escobedo-Ortegón, J; Berzunza-Cruz, M; Becker-Fauser, I; Montes DE Oca-Aguilar, A C; Rebollar-Téllez, E A

2016-09-01

Localized cutaneous leishmaniasis represents a public health problem in many areas of Mexico, especially in the Yucatan Peninsula. An understanding of vector ecology and bionomics is of great importance in evaluations of the transmission dynamics of Leishmania parasites. A field study was conducted in the county of Calakmul, state of Campeche, during the period from November 2006 to March 2007. Phlebotomine sandfly vectors were sampled using Centers for Disease Control light traps, baited Disney traps and Shannon traps. A total of 3374 specimens were captured in the two villages of Once de Mayo (93.8%) and Arroyo Negro (6.1%). In Once de Mayo, the most abundant species were Psathyromyia shannoni, Lutzomyia cruciata, Bichromomyia olmeca olmeca and Psychodopygus panamensis (all: Diptera: Psychodidae). The Shannon trap was by far the most efficient method of collection. The infection rate, as determined by Leishmania mexicana-specific polymerase chain reaction, was 0.3% in Once de Mayo and infected sandflies included Psy. panamensis, B. o. olmeca and Psa. shannoni. There were significant differences in human biting rates across sandfly species and month of sampling. Ecological niche modelling analyses showed an overall overlap of 39.1% for the four species in the whole state of Campeche. In addition, the finding of nine vector-reservoir pairs indicates a potential interaction. The roles of the various sandfly vectors in Calakmul are discussed. © 2016 The Royal Entomological Society.

Sensitivity to zinc of Mediterranean woody species important for restoration.

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Disante, Karen B; Fuentes, David; Cortina, Jordi

2010-04-15

Heavy metals have increased in natural woodlands and shrublands over the last several decades as a consequence of anthropogenic activities. However, our knowledge of the effects of these elements on woody species is scarce. In this study, we examined the responses of six Mediterranean woody species to increasing levels of zinc in hydroponic culture and discussed the possible implications for the restoration of contaminated sites. The species used, Pinus pinea L., Pinus pinaster Ait., Pinus halepensis Mill., Tetraclinis articulata (Vahl) Mast., Rhamnus alaternus L. and Quercus suber L. represent a climatic gradient from dry sub-humid to semi-arid conditions. Zinc concentrations in shoots ranged from 53 microg g(-1) in Q. suber to 382 microg g(-1) in T. articulata and were well below the levels found in roots. Zinc inhibited root elongation and root biomass and changed the root length distribution per diameter class, but the magnitude of the effects was species-specific. Only P. halepensis and Q. suber showed toxicity symptoms in aboveground parts. Species more characteristic from xeric environments (T. articulata, R. alaternus and P. halepensis) were more sensitive to zinc than species from mesic environments (Q. suber, P. pinaster and P. pinea). According to the Zn responses and bioaccumulation, Q. suber P. pinea and P. halepensis are the best candidates for field trials to test the value of woody species to restore contaminated sites. None of the species tested seemed suitable for phytoremediation. Copyright 2010 Elsevier B.V. All rights reserved.

Relative effects of disturbance on red imported fire ants and native ant species in a longleaf pine ecosystem

DEFF Research Database (Denmark)

Stuble, Katharine L.; Kirkman, L. Katherine; Carroll, C. Ronald

2011-01-01

and cases in which non-native species become established in intact (lacking extensive anthropogenic soil disturbance) communities and subsequently diminish the abundance and richness of native species is challenging on the basis of observation alone. The red imported fire ant (Solenopsis invicta......), an invasive species that occurs throughout much of the southeastern United States, is such an example. Rather than competitively displacing native species, fire ants may become established only in disturbed areas in which native species richness and abundance are already reduced. We used insecticide to reduce......, the abundance of native ants increased to levels comparable to those in control plots after 1 year. Our findings suggest that factors other than large reductions in ant abundance and species density (number of species per unit area) may affect the establishment of fire ants and that the response of native ants...

Species richness, area and climate correlates

DEFF Research Database (Denmark)

Nogues, David Bravo; Bastos Araujo, Miguel

2006-01-01

affects: (1) the selection of climate variables entering a species richness model; and (2) the accuracy of models in predicting species richness in unsampled grid cells. Location Western Europe. Methods Models are developed for European plant, breeding bird, mammal and herptile species richness using...... seven climate variables. Generalized additive models are used to relate species richness, climate and area. Results We found that variation in the grid cell area was large (50 × 50 km: 8-3311 km2; 220 × 220: 193-55,100 km2), but this did not affect the selection of variables in the models. Similarly...... support the assumption that variation in near-equal area cells may be of second-order importance for models explaining or predicting species richness in relation to climate, although there is a possibility that drops in accuracy might increase with grid cell size. The results are, however, contingent...

Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae.

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Aguilar, María; Lado, Carlos

2012-08-01

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.

The role of demography, intra-species variation, and species distribution models in species’ projections under climate change

DEFF Research Database (Denmark)

Swab, Rebecca Marie; Regan, Helen M.; Matthies, Diethart

2015-01-01

Organisms are projected to shift their distribution ranges under climate change. The typical way to assess range shifts is by species distribution models (SDMs), which predict species’ responses to climate based solely on projected climatic suitability. However, life history traits can impact...... species’ responses to shifting habitat suitability. Additionally, it remains unclear if differences in vital rates across populations within a species can offset or exacerbate the effects of predicted changes in climatic suitability on population viability. In order to obtain a fuller understanding...... of the response of one species to projected climatic changes, we coupled demographic processes with predicted changes in suitable habitat for the monocarpic thistle Carlina vulgaris across northern Europe. We first developed a life history model with species-specific average fecundity and survival rates...

Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia.

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Jens G Froese

Full Text Available Invasive wildlife often causes serious damage to the economy and agriculture as well as environmental, human and animal health. Habitat models can fill knowledge gaps about species distributions and assist planning to mitigate impacts. Yet, model accuracy and utility may be compromised by small study areas and limited integration of species ecology or temporal variability. Here we modelled seasonal habitat suitability for wild pigs, a widespread and harmful invader, in northern Australia. We developed a resource-based, spatially-explicit and regional-scale approach using Bayesian networks and spatial pattern suitability analysis. We integrated important ecological factors such as variability in environmental conditions, breeding requirements and home range movements. The habitat model was parameterized during a structured, iterative expert elicitation process and applied to a wet season and a dry season scenario. Model performance and uncertainty was evaluated against independent distributional data sets. Validation results showed that an expert-averaged model accurately predicted empirical wild pig presences in northern Australia for both seasonal scenarios. Model uncertainty was largely associated with different expert assumptions about wild pigs' resource-seeking home range movements. Habitat suitability varied considerably between seasons, retracting to resource-abundant rainforest, wetland and agricultural refuge areas during the dry season and expanding widely into surrounding grassland floodplains, savanna woodlands and coastal shrubs during the wet season. Overall, our model suggested that suitable wild pig habitat is less widely available in northern Australia than previously thought. Mapped results may be used to quantify impacts, assess risks, justify management investments and target control activities. Our methods are applicable to other wide-ranging species, especially in data-poor situations.

Modelling the growth of Populus species using Ecosystem Demography (ED) model

Science.gov (United States)

Wang, D.; Lebauer, D. S.; Feng, X.; Dietze, M. C.

2010-12-01

Hybrid poplar plantations are an important source being evaluated for biomass production. Effective management of such plantations requires adequate growth and yield models. The Ecosystem Demography model (ED) makes predictions about the large scales of interest in above- and belowground ecosystem structure and the fluxes of carbon and water from a description of the fine-scale physiological processes. In this study, we used a workflow management tool, the Predictive Ecophysiological Carbon flux Analyzer (PECAn), to integrate literature data, field measurement and the ED model to provide predictions of ecosystem functioning. Parameters for the ED ensemble runs were sampled from the posterior distribution of ecophysiological traits of Populus species compiled from the literature using a Bayesian meta-analysis approach. Sensitivity analysis was performed to identify the parameters which contribute the most to the uncertainties of the ED model output. Model emulation techniques were used to update parameter posterior distributions using field-observed data in northern Wisconsin hybrid poplar plantations. Model results were evaluated with 5-year field-observed data in a hybrid poplar plantation at New Franklin, MO. ED was then used to predict the spatial variability of poplar yield in the coterminous United States (United States minus Alaska and Hawaii). Sensitivity analysis showed that root respiration, dark respiration, growth respiration, stomatal slope and specific leaf area contribute the most to the uncertainty, which suggests that our field measurements and data collection should focus on these parameters. The ED model successfully captured the inter-annual and spatial variability of the yield of poplar. Analyses in progress with the ED model focus on evaluating the ecosystem services of short-rotation woody plantations, such as impacts on soil carbon storage, water use, and nutrient retention.

Direct Importance Estimation with Gaussian Mixture Models

Science.gov (United States)

Yamada, Makoto; Sugiyama, Masashi

The ratio of two probability densities is called the importance and its estimation has gathered a great deal of attention these days since the importance can be used for various data processing purposes. In this paper, we propose a new importance estimation method using Gaussian mixture models (GMMs). Our method is an extention of the Kullback-Leibler importance estimation procedure (KLIEP), an importance estimation method using linear or kernel models. An advantage of GMMs is that covariance matrices can also be learned through an expectation-maximization procedure, so the proposed method — which we call the Gaussian mixture KLIEP (GM-KLIEP) — is expected to work well when the true importance function has high correlation. Through experiments, we show the validity of the proposed approach.

Species distribution modeling based on the automated identification of citizen observations.

Science.gov (United States)

Botella, Christophe; Joly, Alexis; Bonnet, Pierre; Monestiez, Pascal; Munoz, François

2018-02-01

A species distribution model computed with automatically identified plant observations was developed and evaluated to contribute to future ecological studies. We used deep learning techniques to automatically identify opportunistic plant observations made by citizens through a popular mobile application. We compared species distribution modeling of invasive alien plants based on these data to inventories made by experts. The trained models have a reasonable predictive effectiveness for some species, but they are biased by the massive presence of cultivated specimens. The method proposed here allows for fine-grained and regular monitoring of some species of interest based on opportunistic observations. More in-depth investigation of the typology of the observations and the sampling bias should help improve the approach in the future.

Linking an ecosystem model and a landscape model to study forest species response to climate warming

Science.gov (United States)

Hong S. He; David J. Mladenoff; Thomas R. Crow

1999-01-01

No single model can address forest change from single tree to regional scales. We discuss a framework linking an ecosystem process model {LINKAGES) with a spatial landscape model (LANDIS) to examine forest species responses to climate warming for a large, heterogeneous landscape in northern Wisconsin, USA. Individual species response at the ecosystem scale was...

Keystone Species, Forest and Landscape: A Model to Select Protected Areas

Science.gov (United States)

Lins, Daniela Barbosa da Silva; Gardon, Fernando Ravanini; Meyer, João Frederico da Costa Azevedo; Santos, Rozely Ferreira dos

2017-06-01

The selection of forest fragments for conservation is usually based on spatial parameters as forest size and canopy integrity. This strategy assumes that chosen fragments present high conservation status, ensuring biodiversity and ecological functions. We argue that a well-preserved forest fragment that remains connected by the landscape structure, does not necessarily hold attributes that ensure the presence of keystone species. We also discuss that the presence of keystone species does not always mean that it has the best conditions for its occurrence and maintenance. We developed a model to select areas in forest landscapes to be prioritized for protection based on suitability curves that unify and compare spatial indicators of three categories: forest fragment quality, landscape quality, and environmental conditions for the occurrence of a keystone species. We use a case study to compare different suitability degrees for Euterpe edulis presence, considered an important functional element in Atlantic Forest (São Paulo, Brazil) landscapes and a forest resource for local people. The results show that the identification of medium or advanced stage fragments as singular indicator of forest quality does not guarantee the existence or maintenance of this keystone species. Even in some well-preserved forest fragments, connected to others and with palm presence, the reverse J-shaped distribution of the population size structure is not sustained and these forests continue to be threatened due to human disturbances.

Relative importance of current and past landscape structure and local habitat conditions for plant species richness in dry grassland-like forest openings.

Science.gov (United States)

Husáková, Iveta; Münzbergová, Zuzana

2014-01-01

In fragmented landscapes, plant species richness may depend not only on local habitat conditions but also on landscape structure. In addition, both present and past landscape structure may be important for species richness. There are, however, only a few studies that have investigated the relative importance of all of these factors. The aim of this study was to examine the effect of current and past landscape structures and habitat conditions on species richness at dry grassland-like forest openings in a forested landscape and to assess their relative importance for species richness. We analyzed information on past and present landscape structures using aerial photographs from 1938, 1973, 1988, 2000 and 2007. We calculated the area of each locality and its isolation in the present and in the past and the continuity of localities in GIS. At each locality, we recorded all vascular plant species (296 species in 110 forest openings) and information on abiotic conditions of the localities. We found that the current species richness of the forest openings was significantly determined by local habitat conditions as well as by landscape structure in the present and in the past. The highest species richness was observed on larger and more heterogeneous localities with rocks and shallow soils, which were already large and well connected to other localities in 1938. The changes in the landscape structure in the past can thus have strong effects on current species richness. Future studies attempting to understand determinants of species diversity in fragmented landscapes should also include data on past landscape structure, as it may in fact be more important than the present structure.

Modeling Rare Species Distribution at the Edge: The Case for the Vulnerable Endemic Pyrenean Desman in France

Directory of Open Access Journals (Sweden)

M. Williams-Tripp

2012-01-01

Full Text Available The endemic Pyrenean Desman (Galemys pyrenaicus is an elusive, rare, and vulnerable species declining over its entire and narrow range (Spain, Portugal, France, and Andorra. The principal set of conservation measures in France is a 5-years National Action Plan based on 25 conservation actions. Priority is given to update its present distribution and develop tools for predictive distribution models. We aim at building the first species distribution model and map for the northern edge of the range of the Desman and confronting the outputs of the model to target conservation efforts in the context of environmental change. Contrasting to former comparable studies, we derive a simpler model emphasizing the importance of factors linked to precipitation and not to the temperature. If temperature is one of the climate change key factors, depicted shrinkage in Desman distribution could be lower or null at the northern (French edge suggesting thus a major role for this northern population in terms of conservation of the species. Finally, we question the applied issue of temporal and spatial transferability for such environmental favourability models when it is made at the edge of the distribution range.

Do laboratory species protect endangered species? Interspecies variation in responses to 17β-estradiol, a model endocrine active compound

Science.gov (United States)

Jorgenson, Zachary G.; Buhl, Kevin J.; Bartell, Stephen E.; Schoenfuss, Heiko L.

2015-01-01

Although the effects of estrogens on model laboratory species are well documented, their utility as surrogates for other species, including those listed as endangered, are less clear. Traditionally, conservation policies are evaluated based on model organism responses but are intended to protect all species in an environment. We tested the hypothesis that the endangered Rio Grande silvery minnow (Hybognathus amarus) is more vulnerable to endocrine disruption—as assessed through its larval predator-escape performance, survival, juvenile sex ratios, and whole-body vitellogenin concentration—than the commonly used toxicological model species fathead minnow (Pimephales promelas) and the bluegill sunfish (Lepomis macrochirus). Fish were exposed concurrently for 21 days to the model endocrine active compound (EAC) 17ß-estradiol (E2) at 10 ng E2/L and 30 ng E2/L in a flow-through system using reconstituted water that simulated the physicochemical conditions of the Middle Rio Grande in New Mexico, USA. No significant differences were observed between the fathead and silvery minnow in larval predator-escape response or juvenile sex ratio. Rio Grande silvery minnow survival decreased significantly at day 14 compared with the other two species; by day 21, both cyprinid species (silvery minnow and fathead minnow) exhibited a significant decrease in survival compared with bluegill sunfish, a member of the family Centrarchidae. Male Rio Grande silvery minnow showed a significant increase in whole-body vitellogenin concentration in the 10 ng/L treatment, whereas fathead minnow and bluegill sunfish showed no significant increases in vitellogenin concentrations across treatments. Our study showed response differences to estrogen exposures between the two cyprinid species and further divergence in responses between the families Cyprinidae and Centrarchidae. These results suggest that commonly used laboratory model organisms may be less sensitive to EACs than the endangered

Do laboratory species protect endangered species? Interspecies variation in responses to 17β-estradiol, a model endocrine active compound.

Science.gov (United States)

Jorgenson, Z G; Buhl, K; Bartell, S E; Schoenfuss, H L

2015-01-01

Although the effects of estrogens on model laboratory species are well documented, their utility as surrogates for other species, including those listed as endangered, are less clear. Traditionally, conservation policies are evaluated based on model organism responses but are intended to protect all species in an environment. We tested the hypothesis that the endangered Rio Grande silvery minnow (Hybognathus amarus) is more vulnerable to endocrine disruption-as assessed through its larval predator-escape performance, survival, juvenile sex ratios, and whole-body vitellogenin concentration-than the commonly used toxicological model species fathead minnow (Pimephales promelas) and the bluegill sunfish (Lepomis macrochirus). Fish were exposed concurrently for 21 days to the model endocrine active compound (EAC) 17ß-estradiol (E2) at 10 ng E2/L and 30 ng E2/L in a flow-through system using reconstituted water that simulated the physicochemical conditions of the Middle Rio Grande in New Mexico, USA. No significant differences were observed between the fathead and silvery minnow in larval predator-escape response or juvenile sex ratio. Rio Grande silvery minnow survival decreased significantly at day 14 compared with the other two species; by day 21, both cyprinid species (silvery minnow and fathead minnow) exhibited a significant decrease in survival compared with bluegill sunfish, a member of the family Centrarchidae. Male Rio Grande silvery minnow showed a significant increase in whole-body vitellogenin concentration in the 10 ng/L treatment, whereas fathead minnow and bluegill sunfish showed no significant increases in vitellogenin concentrations across treatments. Our study showed response differences to estrogen exposures between the two cyprinid species and further divergence in responses between the families Cyprinidae and Centrarchidae. These results suggest that commonly used laboratory model organisms may be less sensitive to EACs than the endangered Rio

Heavy Metal Concentrations in an Important Mangrove Species, Sonneratia caseolaris, in Peninsular Malaysia

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Mohd Fazlin Nazli

2010-01-01

Full Text Available Mangrove forests in Peninsular Malaysia are increasingly threatened by heavy metal pollution. Due to their unique location, mangroves receive heavy metal pollution from upstream areas and the sea. However, little is known about the capacity of mangrove plants to take up and store heavy metals. In this study, the concentrations of cadmium (Cd, chromium (Cr, copper (Cu, lead (Pb and zinc (Zn in an important mangrove species, Sonneratia caseolaris, were measured. It was found that the total concentrations of Cd, Cr, Cu, Pb, and Zn in the sediments were below the general critical soil concentrations. However, the total concentrations of Cu and Pb in both the roots and leaves of Sonneratia caseolaris exceeded the general normal upper range in plants. This study has therefore shown the potential of Sonneratia caseolaris as a phytoremediation species for selected heavy metals in Malaysian mangrove ecosystem.

Modeling the Distribution of Rare or Cryptic Bird Species of Taiwan

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Tsai-Yu Wu

2012-12-01

Full Text Available For the study of the macroecology and conservation of Taiwan’s birds, there was an urgent need to develop distribution models of bird species whose distribution had never before been modeled. Therefore, we here model the distributions of 27 mostly rare and cryptic breeding bird species using a statistical approach which has been shown to be especially reliable for modeling species with a low sample size of presence localities, namely the maximum entropy (Maxent modeling technique. For this purpose, we began with a dedicated attempt to collate as much high-quality distributional data as possible, assembling databases from several scientific reports, contacting individual data recorders and searching publicly accessible database, the internet and the available literature. This effort resulted in 2022 grid cells of 1 × 1 km size being associated with a presence record for one of the 27 species. These records and 10 pre-selected environmental variables were then used to model each species’ probability distribution which we show here with all grid cells below the lowest presence threshold being converted to zeros. We then in detail discuss the interpretation and applicability of these distributions, whereby we pay close attention to habitat requirements, the intactness and fragmentation of their habitat, the general detectability of the species and data reliability. This study is another one in an ongoing series of studies which highlight the usefulness of using large electronic databases and modern analytical methods to help with the monitoring and assessment of Taiwan’s bird species.

Cross-scale modelling of alien and native vascular plant species richness in Great Britain: where is geodiversity information most relevant?

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Bailey, Joseph; Field, Richard; Boyd, Doreen

2016-04-01

We assess the scale-dependency of the relationship between biodiversity and novel geodiversity information by studying spatial patterns of native and alien (archaeophytes and neophytes) vascular plant species richness at varying spatial scales across Great Britain. Instead of using a compound geodiversity metric, we study individual geodiversity components (GDCs) to advance our understanding of which aspects of 'geodiversity' are most important and at what scale. Terrestrial native (n = 1,490) and alien (n = 1,331) vascular plant species richness was modelled across the island of Great Britain at two grain sizes and several extent radii. Various GDCs (landforms, hydrology, geology) were compiled from existing national datasets and automatically extracted landform coverage information (e.g. hollows, valleys, peaks), the latter using a digital elevation model (DEM) and geomorphometric techniques. More traditional predictors of species richness (climate, widely-used topography metrics, land cover diversity, and human population) were also incorporated. Boosted Regression Tree (BRT) models were produced at all grain sizes and extents for each species group and the dominant predictors were assessed. Models with and without geodiversity data were compared. Overarching patterns indicated a clear dominance of geodiversity information at the smallest study extent (12.5km radius) and finest grain size (1x1km), which substantially decreased for each increase in extent as the contribution of climatic variables increased. The contribution of GDCs to biodiversity models was chiefly driven by landform information from geomorphometry, but hydrology (rivers and lakes), and to a lesser extent materials (soil, superficial deposits, and geology), were important, also. GDCs added significantly to vascular plant biodiversity models in Great Britain, independently of widely-used topographic metrics, particularly for native species. The wider consideration of geodiversity alongside

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

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De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

2016-01-01

Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.

Science.gov (United States)

De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

2016-05-01

Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Use of Occupancy Models to Evaluate Expert Knowledge-based Species-Habitat Relationships

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Monica N. Iglecia

2012-12-01

Full Text Available Expert knowledge-based species-habitat relationships are used extensively to guide conservation planning, particularly when data are scarce. Purported relationships describe the initial state of knowledge, but are rarely tested. We assessed support in the data for suitability rankings of vegetation types based on expert knowledge for three terrestrial avian species in the South Atlantic Coastal Plain of the United States. Experts used published studies, natural history, survey data, and field experience to rank vegetation types as optimal, suitable, and marginal. We used single-season occupancy models, coupled with land cover and Breeding Bird Survey data, to examine the hypothesis that patterns of occupancy conformed to species-habitat suitability rankings purported by experts. Purported habitat suitability was validated for two of three species. As predicted for the Eastern Wood-Pewee (Contopus virens and Brown-headed Nuthatch (Sitta pusilla, occupancy was strongly influenced by vegetation types classified as "optimal habitat" by the species suitability rankings for nuthatches and wood-pewees. Contrary to predictions, Red-headed Woodpecker (Melanerpes erythrocephalus models that included vegetation types as covariates received similar support by the data as models without vegetation types. For all three species, occupancy was also related to sampling latitude. Our results suggest that covariates representing other habitat requirements might be necessary to model occurrence of generalist species like the woodpecker. The modeling approach described herein provides a means to test expert knowledge-based species-habitat relationships, and hence, help guide conservation planning.

Functional importance of GLP-1 receptor species and expression levels in cell lines.

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Knudsen, Lotte Bjerre; Hastrup, Sven; Underwood, Christina Rye; Wulff, Birgitte Schjellerup; Fleckner, Jan

2012-04-10

Of the mammalian species, only the GLP-1 receptors of rat and human origin have been described and characterized. Here, we report the cloning of the homologous GLP-1 receptors from mouse, rabbit, pig, cynomolgus monkey and chimp. The GLP-1 receptor is highly conserved across species, thus underlining the physiological importance of the peptide hormone and its receptor across a wide range of mammals. We expressed the receptors by stable transfection of BHK cells, both in cell lines with high expression levels of the cloned receptors, as well as in cell lines with lower expression levels, more comparable to endogenous expression of these receptors. High expression levels of cloned GLP-1 receptors markedly increased the potency of GLP-1 and other high affinity ligands, whereas the K(d) values were not affected. For a low affinity ligand like the ago-allosteric modulator Compound 2, expression levels of the human GLP-1 receptor were important for maximal efficacy as well as potency. The two natural metabolites of GLP-1, GLP-1(9-37) and GLP-1(9-36)amide were agonists when tested on a cell line with high expression of the recombinant human GLP-1 receptor, whereas they behaved as (low potent) antagonists on a cell line that expressed the receptor endogenously, as well as cells expressing a moderate level of the recombinant human GLP-1 receptor. The amide form was a more potent agonist than the free acid from. In conclusion, receptor expression level is an important parametre for selecting cell lines with cloned GLP-1 receptors for functional characterization of physiological and pharmaceutical ligands. Copyright © 2011 Elsevier B.V. All rights reserved.

An updated checklist of the Culicidae (Diptera) of Morocco, with notes on species of historical and current medical importance.

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Trari, Bouchra; Dakki, Mohamed; Harbach, Ralph E

2017-06-01

An updated checklist of the mosquito species (Diptera: Culicidae) recorded in Morocco from 1916 to 2016 is provided, including synonyms and synonymous usage for each species. Forty-three species belonging to seven genera are recorded so far: Anopheles (9), Aedes (12) Coquillettidia (2), Culex (12), Culiseta (5), Orthopodomyia (1) and Uranotaenia (2). Traditional and equivalent names in the polyphyletic concept of Aedes are provided for the aedine species. The historical importance and current potential threat of mosquitoes to human health in Morocco is reviewed. © 2017 The Society for Vector Ecology.

An empirical probability model of detecting species at low densities.

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Delaney, David G; Leung, Brian

2010-06-01

False negatives, not detecting things that are actually present, are an important but understudied problem. False negatives are the result of our inability to perfectly detect species, especially those at low density such as endangered species or newly arriving introduced species. They reduce our ability to interpret presence-absence survey data and make sound management decisions (e.g., rapid response). To reduce the probability of false negatives, we need to compare the efficacy and sensitivity of different sampling approaches and quantify an unbiased estimate of the probability of detection. We conducted field experiments in the intertidal zone of New England and New York to test the sensitivity of two sampling approaches (quadrat vs. total area search, TAS), given different target characteristics (mobile vs. sessile). Using logistic regression we built detection curves for each sampling approach that related the sampling intensity and the density of targets to the probability of detection. The TAS approach reduced the probability of false negatives and detected targets faster than the quadrat approach. Mobility of targets increased the time to detection but did not affect detection success. Finally, we interpreted two years of presence-absence data on the distribution of the Asian shore crab (Hemigrapsus sanguineus) in New England and New York, using our probability model for false negatives. The type of experimental approach in this paper can help to reduce false negatives and increase our ability to detect species at low densities by refining sampling approaches, which can guide conservation strategies and management decisions in various areas of ecology such as conservation biology and invasion ecology.

The importance of distance to resources in the spatial modelling of bat foraging habitat.

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Ana Rainho

Full Text Available Many bats are threatened by habitat loss, but opportunities to manage their habitats are now increasing. Success of management depends greatly on the capacity to determine where and how interventions should take place, so models predicting how animals use landscapes are important to plan them. Bats are quite distinctive in the way they use space for foraging because (i most are colonial central-place foragers and (ii exploit scattered and distant resources, although this increases flying costs. To evaluate how important distances to resources are in modelling foraging bat habitat suitability, we radio-tracked two cave-dwelling species of conservation concern (Rhinolophus mehelyi and Miniopterus schreibersii in a Mediterranean landscape. Habitat and distance variables were evaluated using logistic regression modelling. Distance variables greatly increased the performance of models, and distance to roost and to drinking water could alone explain 86 and 73% of the use of space by M. schreibersii and R. mehelyi, respectively. Land-cover and soil productivity also provided a significant contribution to the final models. Habitat suitability maps generated by models with and without distance variables differed substantially, confirming the shortcomings of maps generated without distance variables. Indeed, areas shown as highly suitable in maps generated without distance variables proved poorly suitable when distance variables were also considered. We concluded that distances to resources are determinant in the way bats forage across the landscape, and that using distance variables substantially improves the accuracy of suitability maps generated with spatially explicit models. Consequently, modelling with these variables is important to guide habitat management in bats and similarly mobile animals, particularly if they are central-place foragers or depend on spatially scarce resources.

Effects of storage on microbial loads of two commercially important shellfish species, Crassostrea virginica and Mercenaria campechiensis.

OpenAIRE

Hood, M A; Ness, G E; Rodrick, G E; Blake, N J

1983-01-01

The effects of storage on the microbial load in two commercially important species of shellfish were examined. Oysters (Crassostrea virginica) were stored as shellstock, shucked meats, and fully processed meats at four temperatures for up to 21 days, and clams (Mercenaria campechiensis) were stored only as shellstock. The concentrations of most microbiological groups of organisms increased with the duration and temperature of storage in both shellfish species, although the increases were sign...

Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

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Wemheuer, Franziska; Kaiser, Kristin; Karlovsky, Petr; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

2017-01-01

Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.

Temporal distribution of ten calyptrate dipteran species of medicolegal importance in Rio de Janeiro, Brazil

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Rodrigo Rocha Barbosa

2010-03-01

Full Text Available Brazilian studies involving entomological succession patterns in carcasses have been used to describe the necrophagous entomofauna of a determined municipality or region with forensic objectives. Following the same objectives, an ecological study with 10 calyptrate dipterans was carried out during the winter of 2007 and the summer of 2008 in the metropolitan region of the municipality of Rio de Janeiro. The aim of this study was to describe several aspects of the phenology of these species in three neighbouring areas. Carcasses of three domestic pigs (Sus scrofa L. were used in each season as models for forensic and legal medicine investigations in the region. Temperature, relative humidity and rainfall were measured daily and their relations with population abundance of the colonising species and the decomposition stages were analysed. Ten fly species were recorded to be colonising the carcasses, five of which belonged to the Calliphoridae family, three to the Muscidae, one to the Fanniidae and one to the Sarcophagidae family. Data show preferences of these species for climatic season and decomposition stage, as well as for the studied area and suggest that short distances can significantly influence the abundance of some species.

Modeling the role and impact of alien species and fisheries on the Israeli marine continental shelf ecosystem

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Corrales, X.; Ofir, E.; Coll, M.; Goren, M.; Edelist, D.; Heymans, J. J.; Gal, G.

2017-06-01

The ecosystems of the Israeli Mediterranean coast have undergone significant changes in recent decades mainly due to species invasions and fishing. In order to characterize the structure and functioning of the marine continental shelf of the Israeli Mediterranean coast and assess temporal changes, we developed a food web model representing two time periods: 1990-1994 and 2008-2012. The 1990-1994 and 2008-2012 food web models were composed of 39 and 41 functional groups, respectively. Functional groups ranged from primary producers to top predators, and included six and eight alien functional groups, respectively, encompassing several crustacean and fish species. Input data included local surveys and fishery statistics, published data on stomach content analyses, and the application of empirical equations to estimate consumption and production rates. Results of the competitive interactions between alien and native species and changes in trophic flows between food web components highlight the increasing impact of alien species over time. Fishing had noticeable impacts in both time periods and played an important role in the ecosystem. Despite different productivity rates and other environmental differences, the Israeli marine ecosystem shared common structural and functional traits with other Mediterranean marine ecosystems. This is the first attempt to study the ecosystem of the Levant region using mass-balance models and to integrate such a large amount of alien species into food web analyses.

Establishing endangered species recovery criteria using predictive simulation modeling

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McGowan, Conor P.; Catlin, Daniel H.; Shaffer, Terry L.; Gratto-Trevor, Cheri L.; Aron, Carol

2014-01-01

Listing a species under the Endangered Species Act (ESA) and developing a recovery plan requires U.S. Fish and Wildlife Service to establish specific and measurable criteria for delisting. Generally, species are listed because they face (or are perceived to face) elevated risk of extinction due to issues such as habitat loss, invasive species, or other factors. Recovery plans identify recovery criteria that reduce extinction risk to an acceptable level. It logically follows that the recovery criteria, the defined conditions for removing a species from ESA protections, need to be closely related to extinction risk. Extinction probability is a population parameter estimated with a model that uses current demographic information to project the population into the future over a number of replicates, calculating the proportion of replicated populations that go extinct. We simulated extinction probabilities of piping plovers in the Great Plains and estimated the relationship between extinction probability and various demographic parameters. We tested the fit of regression models linking initial abundance, productivity, or population growth rate to extinction risk, and then, using the regression parameter estimates, determined the conditions required to reduce extinction probability to some pre-defined acceptable threshold. Binomial regression models with mean population growth rate and the natural log of initial abundance were the best predictors of extinction probability 50 years into the future. For example, based on our regression models, an initial abundance of approximately 2400 females with an expected mean population growth rate of 1.0 will limit extinction risk for piping plovers in the Great Plains to less than 0.048. Our method provides a straightforward way of developing specific and measurable recovery criteria linked directly to the core issue of extinction risk. Published by Elsevier Ltd.

Estimating species – area relationships by modeling abundance and frequency subject to incomplete sampling

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Yamaura, Yuichi; Connor, Edward F.; Royle, Andy; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

2016-01-01

Models and data used to describe species–area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species–area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species–area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density–area relationships and occurrence probability–area relationships can alter the form of species–area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied

Combining state-and-transition simulations and species distribution models to anticipate the effects of climate change

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Miller, Brian W.; Frid, Leonardo; Chang, Tony; Piekielek, N. B.; Hansen, Andrew J.; Morisette, Jeffrey T.

2015-01-01

State-and-transition simulation models (STSMs) are known for their ability to explore the combined effects of multiple disturbances, ecological dynamics, and management actions on vegetation. However, integrating the additional impacts of climate change into STSMs remains a challenge. We address this challenge by combining an STSM with species distribution modeling (SDM). SDMs estimate the probability of occurrence of a given species based on observed presence and absence locations as well as environmental and climatic covariates. Thus, in order to account for changes in habitat suitability due to climate change, we used SDM to generate continuous surfaces of species occurrence probabilities. These data were imported into ST-Sim, an STSM platform, where they dictated the probability of each cell transitioning between alternate potential vegetation types at each time step. The STSM was parameterized to capture additional processes of vegetation growth and disturbance that are relevant to a keystone species in the Greater Yellowstone Ecosystem—whitebark pine (Pinus albicaulis). We compared historical model runs against historical observations of whitebark pine and a key disturbance agent (mountain pine beetle, Dendroctonus ponderosae), and then projected the simulation into the future. Using this combination of correlative and stochastic simulation models, we were able to reproduce historical observations and identify key data gaps. Results indicated that SDMs and STSMs are complementary tools, and combining them is an effective way to account for the anticipated impacts of climate change, biotic interactions, and disturbances, while also allowing for the exploration of management options.

Conditions Promoting Mycorrhizal Parasitism Are of Minor Importance for Competitive Interactions in Two Differentially Mycotrophic Species

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Friede, Martina; Unger, Stephan; Hellmann, Christine; Beyschlag, Wolfram

2016-01-01

Interactions of plants with arbuscular mycorrhizal fungi (AMF) may range along a broad continuum from strong mutualism to parasitism, with mycorrhizal benefits received by the plant being determined by climatic and edaphic conditions affecting the balance between carbon costs vs. nutritional benefits. Thus, environmental conditions promoting either parasitism or mutualism can influence the mycorrhizal growth dependency (MGD) of a plant and in consequence may play an important role in plant-plant interactions. In a multifactorial field experiment we aimed at disentangling the effects of environmental and edaphic conditions, namely the availability of light, phosphorus and nitrogen, and the implications for competitive interactions between Hieracium pilosella and Corynephorus canescens for the outcome of the AMF symbiosis. Both species were planted in single, intraspecific and interspecific combinations using a target-neighbor approach with six treatments distributed along a gradient simulating conditions for the interaction between plants and AMF ranking from mutualistic to parasitic. Across all treatments we found mycorrhizal association of H. pilosella being consistently mutualistic, while pronounced parasitism was observed in C. canescens, indicating that environmental and edaphic conditions did not markedly affect the cost:benefit ratio of the mycorrhizal symbiosis in both species. Competitive interactions between both species were strongly affected by AMF, with the impact of AMF on competition being modulated by colonization. Biomass in both species was lowest when grown in interspecific competition, with colonization being increased in the less mycotrophic C. canescens, while decreased in the obligate mycotrophic H. pilosella. Although parasitism-promoting conditions negatively affected MGD in C. canescens, these effects were small as compared to growth decreases related to increased colonization levels in this species. Thus, the lack of plant control over

Conditions Promoting Mycorrhizal Parasitism are of Minor Importance for Competitive Interactions in Two Differentially Mycotrophic Species

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Martina Friede

2016-09-01

Full Text Available Interactions of plants with arbuscular mycorrhizal fungi (AMF may range along a broad continuum from strong mutualism to parasitism, with mycorrhizal benefits received by the plant being determined by climatic and edaphic conditions affecting the balance between carbon costs vs. nutritional benefits. Thus, environmental conditions promoting either parasitism or mutualism can influence the mycorrhizal growth dependency (MGD of a plant and in consequence may play an important role in plant-plant interactions.In a multifactorial field experiment we aimed at disentangling the effects of environmental and edaphic conditions, namely the availability of light, phosphorus and nitrogen, and the implications for competitive interactions between Hieracium pilosella and Corynephorus canescens for the outcome of the AMF symbiosis. Both species were planted in single, intraspecific and interspecific combinations using a target-neighbor approach with six treatments distributed along a gradient simulating conditions for the interaction between plants and AMF ranking from mutualistic to parasitic.Across all treatments we found mycorrhizal association of H. pilosella being consistently mutualistic, while pronounced parasitism was observed in C. canescens, indicating that environmental and edaphic conditions did not markedly affect the cost:benefit ratio of the mycorrhizal symbiosis in both species. Competitive interactions between both species were strongly affected by AMF, with the impact of AMF on competition being modulated by colonization. Biomass in both species was lowest when grown in interspecific competition, with colonization being increased in the less mycotrophic C. canescens, while decreased in the obligate mycotrophic H. pilosella. Although parasitism-promoting conditions negatively affected MGD in C. canescens, these effects were small as compared to growth decreases related to increased colonization levels in this species. Thus, the lack of plant

Landscape-scale evaluation of asymmetric interactions between Brown Trout and Brook Trout using two-species occupancy models

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Wagner, Tyler; Jefferson T. Deweber,; Jason Detar,; John A. Sweka,

2013-01-01

Predicting the distribution of native stream fishes is fundamental to the management and conservation of many species. Modeling species distributions often consists of quantifying relationships between species occurrence and abundance data at known locations with environmental data at those locations. However, it is well documented that native stream fish distributions can be altered as a result of asymmetric interactions between dominant exotic and subordinate native species. For example, the naturalized exotic Brown Trout Salmo trutta has been identified as a threat to native Brook Trout Salvelinus fontinalis in the eastern United States. To evaluate large-scale patterns of co-occurrence and to quantify the potential effects of Brown Trout presence on Brook Trout occupancy, we used data from 624 stream sites to fit two-species occupancy models. These models assumed that asymmetric interactions occurred between the two species. In addition, we examined natural and anthropogenic landscape characteristics we hypothesized would be important predictors of occurrence of both species. Estimated occupancy for Brook Trout, from a co-occurrence model with no landscape covariates, at sites with Brown Trout present was substantially lower than sites where Brown Trout were absent. We also observed opposing patterns for Brook and Brown Trout occurrence in relation to percentage forest, impervious surface, and agriculture within the network catchment. Our results are consistent with other studies and suggest that alterations to the landscape, and specifically the transition from a forested catchment to one that contains impervious surface or agriculture, reduces the occurrence probability of wild Brook Trout. Our results, however, also suggest that the presence of Brown Trout results in lower occurrence probability of Brook Trout over a range of anthropogenic landscape characteristics, compared with streams where Brown Trout were absent.

Presence-only Species Distribution Modeling for King Mackerel (Scomberomorus cavalla) and its 31 Prey Species in the Gulf of Mexico

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Cai, X.; Simons, J.; Carollo, C.; Sterba-Boatwright, B.; Sadovski, A.

2016-02-01

Ecosystem based fisheries management has been broadly recognized throughout the world as a way to achieve better conservation. Therefore, there is a strong need for mapping of multi-species interactions or spatial distributions. Species distribution models are widely applied since information regarding the presence of species is usually only available for limited locations due to the high cost of fisheries surveys. Instead of regular presence and absence records, a large proportion of the fisheries survey data have only presence records. This makes the modeling problem one of one-class classification (presence only), which is much more complex than the regular two-class classification (presence/absence). In this study, four different presence-only species distribution algorithms (Bioclim, Domain, Mahal and Maxent) were applied using 13 environmental parameters (e.g., depth, DO, bottom types) as predictors to model the distribution of king mackerel (Scomberomorus cavalla) and its 31 prey species in the Gulf of Mexico (a total of 13625 georeferenced presence records from OBIS and GBIF were used). Five-fold cross validations were applied for each of the 128 (4 algorithms × 32 species) models. Area under curve (AUC) and correlation coefficient (R) were used to evaluate the model performances. The AUC of the models based on these four algorithms were 0.83±0.14, 0.77±0.16, 0.94±0.06 and 0.94±0.06, respectively; while R for the models were 0.47±0.27, 0.43±0.24, 0.27±0.16 and 0.76±0.16, respectively. Post hoc with Tukey's test showed that AUC for the Maxent-based models were significantly (pMexico to help managers better manage related fisheries resources.

The Atmospheric Tomography Mission (ATom): Comparing the Chemical Climatology of Reactive Species and Air Parcels from Measurements and Global Models

Science.gov (United States)

Prather, M. J.; Flynn, C.; Wennberg, P. O.; Kim, M. J.; Ryerson, T. B.; Hanisco, T. F.; Diskin, G. S.; Daube, B. C.; Commane, R.; McKain, K.; Apel, E. C.; Blake, N. J.; Blake, D. R.; Elkins, J. W.; Hall, S.; Steenrod, S.; Strahan, S. E.; Lamarque, J. F.; Fiore, A. M.; Horowitz, L. W.; Murray, L. T.; Mao, J.; Shindell, D. T.; Wofsy, S. C.

2017-12-01

The NASA Atmospheric Tomography Mission (ATom) is building a photochemical climatology of the remote troposphere based on objective sampling and profiling transects over the Pacific and Atlantic Oceans. These statistics provide direct tests of chemistry-climate models. The choice of species focuses on those controlling primary reactivity (a.k.a. oxidative state) of the troposphere, specifically chemical tendencies of O3 and CH4. These key species include, inter alia, O3, CH4, CO, C2H6, other alkanes, alkenes, aromatics, NOx, HNO3, HO2NO2, PAN, other organic nitrates, H2O, HCHO, H2O2, CH3OOH. Three of the four ATom deployments are now complete, and data from the first two (ATom-1 & -2) have been released as of this talk (see espoarchive.nasa.gov/archive/browse/atom). The statistical distributions of key species are presented as 1D and 2D probability densities (PDs) and we focus here on the tropical and mid-latitude regions of the Pacific during ATom-1 (Aug) and -2 (Feb). PDs are computed from ATom observations and 6 global chemistry models over the tropospheric depth (0-12 km) and longitudinal extent of the observations. All data are weighted to achieve equal mass-weighting by latitude regimes to account for spatial sampling biases. The models are used to calculate the reactivity in each ATom air parcel. Reweighting parcels with loss of CH4 or production of O3, for example, allows us to identify which air parcels are most influential, including assessment of the importance of fine pollution layers in the most remote troposphere. Another photochemical climatology developed from ATom, and used to test models, includes the effect of clouds on photolysis rates. The PDs and reactivity-weighted PDs reveal important seasonal differences and similarities between the two campaigns and also show which species may be most important in controlling reactivities. They clearly identify some very specific failings in the modeled climatologies and help us evaluate the chemical

Habitat Modeling of Alien Plant Species at Varying Levels of Occupancy

Directory of Open Access Journals (Sweden)

Jennifer A. Brown

2012-09-01

Full Text Available Distribution models of invasive plants are very useful tools for conservation management. There are challenges in modeling expanding populations, especially in a dynamic environment, and when data are limited. In this paper, predictive habitat models were assessed for three invasive plant species, at differing levels of occurrence, using two different habitat modeling techniques: logistic regression and maximum entropy. The influence of disturbance, spatial and temporal heterogeneity, and other landscape characteristics is assessed by creating regional level models based on occurrence records from the USDA Forest Service’s Forest Inventory and Analysis database. Logistic regression and maximum entropy models were assessed independently. Ensemble models were developed to combine the predictions of the two analysis approaches to obtain a more robust prediction estimate. All species had strong models with Area Under the receiver operator Curve (AUC of >0.75. The species with the highest occurrence, Ligustrum spp., had the greatest agreement between the models (93%. Lolium arundinaceum had the most disagreement between models at 33% and the lowest AUC values. Overall, the strength of integrative modeling in assessing and understanding habitat modeling was demonstrated.

VisTrails SAHM: visualization and workflow management for species habitat modeling

Science.gov (United States)

Morisette, Jeffrey T.; Jarnevich, Catherine S.; Holcombe, Tracy R.; Talbert, Colin B.; Ignizio, Drew A.; Talbert, Marian; Silva, Claudio; Koop, David; Swanson, Alan; Young, Nicholas E.

2013-01-01

The Software for Assisted Habitat Modeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre- and post-processing steps and modeling options incorporated in the construction of a species distribution model through the established workflow management and visualization VisTrails software. This paper provides an overview of the VisTrails:SAHM software including a link to the open source code, a table detailing the current SAHM modules, and a simple example modeling an invasive weed species in Rocky Mountain National Park, USA.

Cross-Species Extrapolation of Models for Predicting Lead Transfer from Soil to Wheat Grain.

Directory of Open Access Journals (Sweden)

Ke Liu

Full Text Available The transfer of Pb from the soil to crops is a serious food hygiene security problem in China because of industrial, agricultural, and historical contamination. In this study, the characteristics of exogenous Pb transfer from 17 Chinese soils to a popular wheat variety (Xiaoyan 22 were investigated. In addition, bioaccumulation prediction models of Pb in grain were obtained based on soil properties. The results of the analysis showed that pH and OC were the most important factors contributing to Pb uptake by wheat grain. Using a cross-species extrapolation approach, the Pb uptake prediction models for cultivar Xiaoyan 22 in different soil Pb levels were satisfactorily applied to six additional non-modeled wheat varieties to develop a prediction model for each variety. Normalization of the bioaccumulation factor (BAF to specific soil physico-chemistry is essential, because doing so could significantly reduce the intra-species variation of different wheat cultivars in predicted Pb transfer and eliminate the influence of soil properties on ecotoxicity parameters for organisms of interest. Finally, the prediction models were successfully verified against published data (including other wheat varieties and crops and used to evaluate the ecological risk of Pb for wheat in contaminated agricultural soils.

What do we gain from simplicity versus complexity in species distribution models?

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Merow, Cory; Smith, Matthew J.; Edwards, Thomas C.; Guisan, Antoine; McMahon, Sean M.; Normand, Signe; Thuiller, Wilfried; Wuest, Rafael O.; Zimmermann, Niklaus E.; Elith, Jane

2014-01-01

Species distribution models (SDMs) are widely used to explain and predict species ranges and environmental niches. They are most commonly constructed by inferring species' occurrence–environment relationships using statistical and machine-learning methods. The variety of methods that can be used to construct SDMs (e.g. generalized linear/additive models, tree-based models, maximum entropy, etc.), and the variety of ways that such models can be implemented, permits substantial flexibility in SDM complexity. Building models with an appropriate amount of complexity for the study objectives is critical for robust inference. We characterize complexity as the shape of the inferred occurrence–environment relationships and the number of parameters used to describe them, and search for insights into whether additional complexity is informative or superfluous. By building ‘under fit’ models, having insufficient flexibility to describe observed occurrence–environment relationships, we risk misunderstanding the factors shaping species distributions. By building ‘over fit’ models, with excessive flexibility, we risk inadvertently ascribing pattern to noise or building opaque models. However, model selection can be challenging, especially when comparing models constructed under different modeling approaches. Here we argue for a more pragmatic approach: researchers should constrain the complexity of their models based on study objective, attributes of the data, and an understanding of how these interact with the underlying biological processes. We discuss guidelines for balancing under fitting with over fitting and consequently how complexity affects decisions made during model building. Although some generalities are possible, our discussion reflects differences in opinions that favor simpler versus more complex models. We conclude that combining insights from both simple and complex SDM building approaches best advances our knowledge of current and future species

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

OpenAIRE

DeBiasse, Melissa B; Hellberg, Michael E

2015-01-01

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach...

Transferability of species distribution models for the detection of an invasive alien bryophyte using imaging spectroscopy data

Science.gov (United States)

Skowronek, Sandra; Van De Kerchove, Ruben; Rombouts, Bjorn; Aerts, Raf; Ewald, Michael; Warrie, Jens; Schiefer, Felix; Garzon-Lopez, Carol; Hattab, Tarek; Honnay, Olivier; Lenoir, Jonathan; Rocchini, Duccio; Schmidtlein, Sebastian; Somers, Ben; Feilhauer, Hannes

2018-06-01

Remote sensing is a promising tool for detecting invasive alien plant species. Mapping and monitoring those species requires accurate detection. So far, most studies relied on models that are locally calibrated and validated against available field data. Consequently, detecting invasive alien species at new study areas requires the acquisition of additional field data which can be expensive and time-consuming. Model transfer might thus provide a viable alternative. Here, we mapped the distribution of the invasive alien bryophyte Campylopus introflexus to i) assess the feasibility of spatially transferring locally calibrated models for species detection between four different heathland areas in Germany and Belgium and ii) test the potential of combining calibration data from different sites in one species distribution model (SDM). In a first step, four different SDMs were locally calibrated and validated by combining field data and airborne imaging spectroscopy data with a spatial resolution ranging from 1.8 m to 4 m and a spectral resolution of about 10 nm (244 bands). A one-class classifier, Maxent, which is based on the comparison of probability densities, was used to generate all SDMs. In a second step, each model was transferred to the three other study areas and the performance of the models for predicting C. introflexus occurrences was assessed. Finally, models combining calibration data from three study areas were built and tested on the remaining fourth site. In this step, different combinations of Maxent modelling parameters were tested. For the local models, the area under the curve for a test dataset (test AUC) was between 0.57-0.78, while the test AUC for the single transfer models ranged between 0.45-0.89. For the combined models the test AUC was between 0.54-0.9. The success of transferring models calibrated in one site to another site highly depended on the respective study site; the combined models provided higher test AUC values than the locally

Morphology of immature stages of blow fly, Lucilia sinensis Aubertin (Diptera: Calliphoridae), a potential species of forensic importance.

Science.gov (United States)

Sanit, Sangob; Sukontason, Kom; Kurahashi, Hiromu; Tomberlin, Jeffery K; Wannasan, Anchalee; Kraisittipanit, Rungroj; Sukontason, Kabkaew L

2017-12-01

Lucilia sinensis Aubertin (Diptera: Calliphoridae) is a blow fly species of potential forensic importance since adults are attracted to, and colonize, decomposing vertebrate remains. Blow fly larvae associated with human corpses can be useful evidence in forensic investigations; however, their use is dependent in most cases on proper species identification and availability of developmental data. For identification, morphological information on each life stage is traditionally used. We used scanning electron microscopy (SEM) to examine the ultrastructure of eggs, all instars, and puparia, of L. sinensis. The important characteristics used to differentiate L. sinensis from other species are provided. Distinctive features of the eggs are the slight widening median area extending almost the entire length. The last abdominal segment of the first instar bears elongated outer ventral tubercles along the rim of the last abdominal segment. These tubercles, as well as the well developed median and outer dorsal tubercles, are more prominent in the second and third instars. The surface integument of the tubercles is equipped with circular rows of microtrichia. Pairs of inner dorsal tubercle are absent. Each anterior spiracle is comprised of 9-12 papillae arrange in a single row in the second and third instars. As for the third instar, the dorsal spines between the first and second thoracic segments are delicate, narrow, small, and close together (as row or set). The peristigmatic tufts adjacent to the posterior spiracle of the third instar are moderately branches of short, fine hairs, but minute in puparia. In conclusion, the prominent outer ventral tubercle in all instars and puparia is a new diagnostic feature of L. sinensis and helpful in differentiating it from other Lucilia species that are forensically important. The description of immature L. sinensis in this study will be useful for forensic entomologists in countries where this species exists. Copyright © 2017

Assessment of oil content and fatty acid composition variability in two economically important Hibiscus species.

Science.gov (United States)

Wang, Ming Li; Morris, Brad; Tonnis, Brandon; Davis, Jerry; Pederson, Gary A

2012-07-04

The Hibiscus genus encompasses more than 300 species, but kenaf (Hibiscus cannabinus L.) and roselle (Hibiscus sabdariffa L.) are the two most economically important species within the genus. Seeds from these two Hibiscus species contain a relatively high amount of oil with two unusual fatty acids: dihydrosterculic and vernolic acids. The fatty acid composition in the oil can directly affect oil quality and its utilization. However, the variability in oil content and fatty acid composition for these two species is unclear. For these two species, 329 available accessions were acquired from the USDA germplasm collection. Their oil content and fatty acid composition were determined by nuclear magnetic resonance (NMR) and gas chromatography (GC), respectively. Using NMR and GC analyses, we found that Hibiscus seeds on average contained 18% oil and seed oil was composed of six major fatty acids (each >1%) and seven minor fatty acids (each Hibiscus cannabinus seeds contained significantly higher amounts of oil (18.14%), palmitic (20.75%), oleic (28.91%), vernolic acids (VA, 4.16%), and significantly lower amounts of stearic (3.96%), linoleic (39.49%), and dihydrosterculic acids (DHSA, 1.08%) than H. sabdariffa seeds (17.35%, 18.52%, 25.16%, 3.52%, 4.31%, 44.72%, and 1.57%, respectively). For edible oils, a higher oleic/linoleic (O/L) ratio and lower level of DHSA are preferred, and for industrial oils a high level of VA is preferred. Our results indicate that seeds from H. cannabinus may be of higher quality than H. sabdariffa seeds for these reasons. Significant variability in oil content and major fatty acids was also detected within both species. The variability in oil content and fatty acid composition revealed from this study will be useful for exploring seed utilization and developing new cultivars in these Hibiscus species.

Insects associated with hospital environment in Egypt with special reference to the medically important species.

Science.gov (United States)

Kenawy, Mohamed A; Amer, Hanan S; Lotfy, Nadia M; Khamis, Nagwa; Abdel-Hamid, Yousrya M

2014-12-01

A study was planned to examine the insect fauna associated with two hospitals: urban (A) in Cairo and rural (B) in Banha, Egypt with varying hygienic levels and their adjacent residential areas (AC) and (BC), respectively and to investigate the effect of hygienic level on species composition and relative abundance. A total of 22 species belonging to 7 orders and 15 families were reported in the four study areas of which, Dipterous flies were the most common (8/22, 36.36% species). A total of 5257 adults were collected of which Dipterous flies were the abundant (3800, 72.28% insect) and Musca domestica was the most abundant species (3535, 67.24% insect) which was present in all areas where it was more common / predominant species (21.94%-90.91% insect). Moreover, higher densities of M domestica were in (B) and BC than in (A) or (AC). The heavily infested area was AC (54.55% species) followed by (A), (BC) and (B) however, the total number of the collected insects was higher in (BC) and (B) than in (AC) and (A). This was confirmed by finding maximum diversity indices in (AC) and minimum ones in B. In all areas, means of M domestica was more common during summer/autumn and spring than in the winter. Periplaneta americana collected oily during autumn in AC and was more common in autumn in (BC) while Blatella germanica collected only during summer in (AC) and was more common in autumn in (B). The prevalence and higher abundance of the medically important species mainly M domestica, P. americana and B. germanica in rural hospital than in urban one attribute mainly to the lower hygienic level of rural hospital This require a control program based mainly on sanitation supplemented by other measures to overcome the risk of disease transmission by such insects

Fate modeling of mercury species and fluxes estimation in an urban river

International Nuclear Information System (INIS)

Tong, Yindong; Zhang, Wei; Chen, Cen; Chen, Long; Wang, Wentao; Hu, Xindi; Wang, Huanhuan; Hu, Dan; Ou, Langbo; Wang, Xuejun; Wang, Qiguang

2014-01-01

The fate and transfer of mercury in urban river is an important environmental concern. In this study, QWASI (Quantitative Water–Air–Sediment Interaction) model was selected to estimate the levels of total mercury and three mercury species in water and sediment, and was used to quantify the fluxes of mercury at water/air and sediment/water interfaces of an urban river. The predicted mercury levels in water and sediments were closed to the measured values. Water inflow, re-suspension of sediment and diffusion from sediment to water are major input sources of mercury in water. The net mercury transfer flux from water to air was 0.16 ng/(m 2 h). At the sediment/water interface, a net total mercury transfer of 1.32 ng/(m 2 h) from water to sediment was seen. In addition to the existing dynamic flux chambers measurement, this model method could provide a new perspective to identify the distribution and transfer of mercury in the urban river. -- Highlights: • QWASI could be a good tool to quantify transfer and fate of mercury in environment. • Distribution and flux of mercury species in an urban river was modeled. • Mercury in water mainly came from water inflow, sediment re-suspension and diffusion. • Net mercury transfer from water to air and sediment were 0.16 and 1.32 ng/(m 2 h). -- Quantitative Water–Air–Sediment Interaction model was used to quantify the transfer and fate of mercury in an urban river

Choice of baseline climate data impacts projected species' responses to climate change.

Science.gov (United States)

Baker, David J; Hartley, Andrew J; Butchart, Stuart H M; Willis, Stephen G

2016-07-01

Climate data created from historic climate observations are integral to most assessments of potential climate change impacts, and frequently comprise the baseline period used to infer species-climate relationships. They are often also central to downscaling coarse resolution climate simulations from General Circulation Models (GCMs) to project future climate scenarios at ecologically relevant spatial scales. Uncertainty in these baseline data can be large, particularly where weather observations are sparse and climate dynamics are complex (e.g. over mountainous or coastal regions). Yet, importantly, this uncertainty is almost universally overlooked when assessing potential responses of species to climate change. Here, we assessed the importance of historic baseline climate uncertainty for projections of species' responses to future climate change. We built species distribution models (SDMs) for 895 African bird species of conservation concern, using six different climate baselines. We projected these models to two future periods (2040-2069, 2070-2099), using downscaled climate projections, and calculated species turnover and changes in species-specific climate suitability. We found that the choice of baseline climate data constituted an important source of uncertainty in projections of both species turnover and species-specific climate suitability, often comparable with, or more important than, uncertainty arising from the choice of GCM. Importantly, the relative contribution of these factors to projection uncertainty varied spatially. Moreover, when projecting SDMs to sites of biodiversity importance (Important Bird and Biodiversity Areas), these uncertainties altered site-level impacts, which could affect conservation prioritization. Our results highlight that projections of species' responses to climate change are sensitive to uncertainty in the baseline climatology. We recommend that this should be considered routinely in such analyses. © 2016 John Wiley

Fish species of greatest conservation need in wadeable Iowa streams: current status and effectiveness of Aquatic Gap Program distribution models

Science.gov (United States)

Sindt, Anthony R.; Pierce, Clay; Quist, Michael C.

2012-01-01

Effective conservation of fish species of greatest conservation need (SGCN) requires an understanding of species–habitat relationships and distributional trends. Thus, modeling the distribution of fish species across large spatial scales may be a valuable tool for conservation planning. Our goals were to evaluate the status of 10 fish SGCN in wadeable Iowa streams and to test the effectiveness of Iowa Aquatic Gap Analysis Project (IAGAP) species distribution models. We sampled fish assemblages from 86 wadeable stream segments in the Mississippi River drainage of Iowa during 2009 and 2010 to provide contemporary, independent fish species presence–absence data. The frequencies of occurrence in stream segments where species were historically documented varied from 0.0% for redfin shiner Lythrurus umbratilis to 100.0% for American brook lampreyLampetra appendix, with a mean of 53.0%, suggesting that the status of Iowa fish SGCN is highly variable. Cohen's kappa values and other model performance measures were calculated by comparing field-collected presence–absence data with IAGAP model–predicted presences and absences for 12 fish SGCN. Kappa values varied from 0.00 to 0.50, with a mean of 0.15. The models only predicted the occurrences of banded darterEtheostoma zonale, southern redbelly dace Phoxinus erythrogaster, and longnose daceRhinichthys cataractae more accurately than would be expected by chance. Overall, the accuracy of the twelve models was low, with a mean correct classification rate of 58.3%. Poor model performance probably reflects the difficulties associated with modeling the distribution of rare species and the inability of the large-scale habitat variables used in IAGAP models to explain the variation in fish species occurrences. Our results highlight the importance of quantifying the confidence in species distribution model predictions with an independent data set and the need for long-term monitoring to better understand the

Implications of movement for species distribution models - Rethinking environmental data tools.

Science.gov (United States)

Bruneel, Stijn; Gobeyn, Sacha; Verhelst, Pieterjan; Reubens, Jan; Moens, Tom; Goethals, Peter

2018-07-01

Movement is considered an essential process in shaping the distributions of species. Nevertheless, most species distribution models (SDMs) still focus solely on environment-species relationships to predict the occurrence of species. Furthermore, the currently used indirect estimates of movement allow to assess habitat accessibility, but do not provide an accurate description of movement. Better proxies of movement are needed to assess the dispersal potential of individual species and to gain a more practical insight in the interconnectivity of communities. Telemetry techniques are rapidly evolving and highly capable to provide explicit descriptions of movement, but their usefulness for SDMs will mainly depend on the ability of these models to deal with hitherto unconsidered ecological processes. More specifically, the integration of movement is likely to affect the environmental data requirements as the connection between environmental and biological data is crucial to provide reliable results. Mobility implies the occupancy of a continuum of space, hence an adequate representation of both geographical and environmental space is paramount to study mobile species distributions. In this context, environmental models, remote sensing techniques and animal-borne environmental sensors are discussed as potential techniques to obtain suitable environmental data. In order to provide an in-depth review of the aforementioned methods, we have chosen to use the modelling of fish distributions as a case study. The high mobility of fish and the often highly variable nature of the aquatic environment generally complicate model development, making it an adequate subject for research. Furthermore, insight into the distribution of fish is of great interest for fish stock assessments and water management worldwide, underlining its practical relevance. Copyright © 2018 Elsevier B.V. All rights reserved.

Using economic instruments to develop effective management of invasive species: insights from a bioeconomic model.

Science.gov (United States)

McDermott, Shana M; Irwin, Rebecca E; Taylor, Brad W

2013-07-01

Economic growth is recognized as an important factor associated with species invasions. Consequently, there is increasing need to develop solutions that combine economics and ecology to inform invasive species management. We developed a model combining economic, ecological, and sociological factors to assess the degree to which economic policies can be used to control invasive plants. Because invasive plants often spread across numerous properties, we explored whether property owners should manage invaders cooperatively as a group by incorporating the negative effects of invader spread in management decisions (collective management) or independently, whereby the negative effects of invasive plant spread are ignored (independent management). Our modeling approach used a dynamic optimization framework, and we applied the model to invader spread using Linaria vulgaris. Model simulations allowed us to determine the optimal management strategy based on net benefits for a range of invader densities. We found that optimal management strategies varied as a function of initial plant densities. At low densities, net benefits were high for both collective and independent management to eradicate the invader, suggesting the importance of early detection and eradication. At moderate densities, collective management led to faster and more frequent invader eradication compared to independent management. When we used a financial penalty to ensure that independent properties were managed collectively, we found that the penalty would be most feasible when levied on a property's perimeter boundary to control spread among properties. At the highest densities, the optimal management strategy was "do nothing" because the economic costs of removal were too high relative to the benefits of removal. Spatial variation in L. vulgaris densities resulted in different optimal management strategies for neighboring properties, making a formal economic policy to encourage invasive species removal

Addressing potential local adaptation in species distribution models: implications for conservation under climate change

Science.gov (United States)

Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason D. K.; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C.; Hellmann, Jessica J.

2016-01-01

Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

Environmental species sorting dominates forest-bird community assembly across scales

DEFF Research Database (Denmark)

Özkan, Korhan; Svenning, J.-C.; Jeppesen, Erik

2013-01-01

species richness and composition within the metacommunity. Second, we analysed species' abundance–occupancy relationship across the metacommunity and used null models to assess whether occupancy is determined by species' environmental niches. Third, we used generalized linear models to test for links...... between species' metacommunity-wide occupancy and their broader WP regional populations and assessed whether these links are consistent with environmental species sorting. There was strong environmental control on local species richness and composition patterns within the metacommunity, but non......-environmental spatial factors had also an important joint role. Null model analyses on randomized communities showed that species' occupancy across the metacommunity was strongly determined by species' environmental niches, with occupancy being related to niche position marginality. Species' metacommunity...

Woody-Herbaceous Species Coexistence in Mulga Hillslopes: Modelling Structure and Function

Science.gov (United States)

Soltanjalili, M. J.; Saco, P. M.; Willgoose, G. R.

2016-12-01

The fundamental processes underlying the coexistence of woody and herbaceous species in arid and semi-arid areas have been a topic of intense research during the last few decades. Experimental and modelling studies have both supported and disputed alternative hypotheses explaining this phenomenon. Vegetation models including the key processes that drive coexistence can be used to understand vegetation pattern dynamics and structure under current climate conditions, and to predict changes under future conditions. Here we present work done towards linking the observations to modelling. The model captures woody-herbaceous coexistence along a rainfall gradient characteristic of typical conditions on Mulga ecosystems in Australia. The dynamic vegetation model simulates the spatial dynamics of overland flow, soil moisture and vegetation growth of two species. It incorporates key mechanisms for coexistence and pattern formation, including facilitation by evaporation reduction through shading, and infiltration feedbacks, local and non-local seed dispersal, competition for water uptake. Model outcomes, obtained including diflerent mechanisms, are qualitatively compared to typical vegetation cover patterns in the Australian Mulga bioregion where bush fire is very infrequent and the fate of vegetation cover is mostly determined by intra- and interspecies interactions. Through these comparisons, and by drawing on the large number of recent studies that have delivered new insights into the dynamics of such ecosystems, we identify main mechanisms that need an improved representation in the dynamic vegetation models. We show that a realistic parameterization of the model leads to results which are aligned with the observations reported in the literature. At the lower end of the rainfall gradient woody species coexist with herbaceous species within a sparse banded pattern, while at higher rainfall woody species tend to dominate the landscape.

Analysis of a Fishery Model with two competing prey species in the presence of a predator species for Optimal Harvesting

Science.gov (United States)

Sutimin; Khabibah, Siti; Munawwaroh, Dita Anis

2018-02-01

A harvesting fishery model is proposed to analyze the effects of the presence of red devil fish population, as a predator in an ecosystem. In this paper, we consider an ecological model of three species by taking into account two competing species and presence of a predator (red devil), the third species, which incorporates the harvesting efforts of each fish species. The stability of the dynamical system is discussed and the existence of biological and bionomic equilibrium is examined. The optimal harvest policy is studied and the solution is derived in the equilibrium case applying Pontryagin's maximal principle. The simulation results is presented to simulate the dynamical behavior of the model and show that the optimal equilibrium solution is globally asymptotically stable. The results show that the optimal harvesting effort is obtained regarding to bionomic and biological equilibrium.

Accounting for selection bias in species distribution models: An econometric approach on forested trees based on structural modeling

Science.gov (United States)

Ay, Jean-Sauveur; Guillemot, Joannès; Martin-StPaul, Nicolas K.; Doyen, Luc; Leadley, Paul

2015-04-01

Species distribution models (SDMs) are widely used to study and predict the outcome of global change on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of application on forested trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8 km). We also compared the output of the SSDM with outputs of a classical SDM in term of bioclimatic response curves and potential distribution under current climate. According to the species and the spatial resolution of the calibration dataset, shapes of bioclimatic response curves the modelled species distribution maps differed markedly between the SSDM and classical SDMs. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents a crucial step to account for economic constraints on tree

Mechanistic species distribution modeling reveals a niche shift during invasion.

Science.gov (United States)

Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M

2017-06-01

Niche shifts of nonnative 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 reanalyzing 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 northward 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

Using multi-species occupancy models in structured decision making on managed lands

Science.gov (United States)

Sauer, John R.; Blank, Peter J.; Zipkin, Elise F.; Fallon, Jane E.; Fallon, Frederick W.

2013-01-01

Land managers must balance the needs of a variety of species when manipulating habitats. Structured decision making provides a systematic means of defining choices and choosing among alternative management options; implementation of a structured decision requires quantitative approaches to predicting consequences of management on the relevant species. Multi-species occupancy models provide a convenient framework for making structured decisions when the management objective is focused on a collection of species. These models use replicate survey data that are often collected on managed lands. Occupancy can be modeled for each species as a function of habitat and other environmental features, and Bayesian methods allow for estimation and prediction of collective responses of groups of species to alternative scenarios of habitat management. We provide an example of this approach using data from breeding bird surveys conducted in 2008 at the Patuxent Research Refuge in Laurel, Maryland, evaluating the effects of eliminating meadow and wetland habitats on scrub-successional and woodland-breeding bird species using summed total occupancy of species as an objective function. Removal of meadows and wetlands decreased value of an objective function based on scrub-successional species by 23.3% (95% CI: 20.3–26.5), but caused only a 2% (0.5, 3.5) increase in value of an objective function based on woodland species, documenting differential effects of elimination of meadows and wetlands on these groups of breeding birds. This approach provides a useful quantitative tool for managers interested in structured decision making.

Not to put too fine a point on it - does increasing precision of geographic referencing improve species distribution models for a wide-ranging migratory bat?

Science.gov (United States)

Hayes, Mark A.; Ozenberger, Katharine; Cryan, Paul M.; Wunder, Michael B.

2015-01-01

Bat specimens held in natural history museum collections can provide insights into the distribution of species. However, there are several important sources of spatial error associated with natural history specimens that may influence the analysis and mapping of bat species distributions. We analyzed the importance of geographic referencing and error correction in species distribution modeling (SDM) using occurrence records of hoary bats (Lasiurus cinereus). This species is known to migrate long distances and is a species of increasing concern due to fatalities documented at wind energy facilities in North America. We used 3,215 museum occurrence records collected from 1950–2000 for hoary bats in North America. We compared SDM performance using five approaches: generalized linear models, multivariate adaptive regression splines, boosted regression trees, random forest, and maximum entropy models. We evaluated results using three SDM performance metrics (AUC, sensitivity, and specificity) and two data sets: one comprised of the original occurrence data, and a second data set consisting of these same records after the locations were adjusted to correct for identifiable spatial errors. The increase in precision improved the mean estimated spatial error associated with hoary bat records from 5.11 km to 1.58 km, and this reduction in error resulted in a slight increase in all three SDM performance metrics. These results provide insights into the importance of geographic referencing and the value of correcting spatial errors in modeling the distribution of a wide-ranging bat species. We conclude that the considerable time and effort invested in carefully increasing the precision of the occurrence locations in this data set was not worth the marginal gains in improved SDM performance, and it seems likely that gains would be similar for other bat species that range across large areas of the continent, migrate, and are habitat generalists.

Incorporating interspecific competition into species-distribution mapping by upward scaling of small-scale model projections to the landscape.

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Mark Baah-Acheamfour

Full Text Available There are a number of overarching questions and debate in the scientific community concerning the importance of biotic interactions in species distribution models at large spatial scales. In this paper, we present a framework for revising the potential distribution of tree species native to the Western Ecoregion of Nova Scotia, Canada, by integrating the long-term effects of interspecific competition into an existing abiotic-factor-based definition of potential species distribution (PSD. The PSD model is developed by combining spatially explicit data of individualistic species' response to normalized incident photosynthetically active radiation, soil water content, and growing degree days. A revised PSD model adds biomass output simulated over a 100-year timeframe with a robust forest gap model and scaled up to the landscape using a forestland classification technique. To demonstrate the method, we applied the calculation to the natural range of 16 target tree species as found in 1,240 provincial forest-inventory plots. The revised PSD model, with the long-term effects of interspecific competition accounted for, predicted that eastern hemlock (Tsuga canadensis, American beech (Fagus grandifolia, white birch (Betula papyrifera, red oak (Quercus rubra, sugar maple (Acer saccharum, and trembling aspen (Populus tremuloides would experience a significant decline in their original distribution compared with balsam fir (Abies balsamea, black spruce (Picea mariana, red spruce (Picea rubens, red maple (Acer rubrum L., and yellow birch (Betula alleghaniensis. True model accuracy improved from 64.2% with original PSD evaluations to 81.7% with revised PSD. Kappa statistics slightly increased from 0.26 (fair to 0.41 (moderate for original and revised PSDs, respectively.

Model of Peatland Vegetation Species using HyMap Image and Machine Learning

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Dayuf Jusuf, Muhammad; Danoedoro, Projo; Muljo Sukojo, Bangun; Hartono

2017-12-01

Species Tumih / Parepat (Combretocarpus-rotundatus Mig. Dancer) family Anisophylleaceae and Meranti (Shorea Belangerang, Shorea Teysmanniana Dyer ex Brandis) family Dipterocarpaceae is a group of vegetation species distribution model. Species pioneer is predicted as an indicator of the succession of ecosystem restoration of tropical peatland characteristics and extremely fragile (unique) in the endemic hot spot of Sundaland. Climate change projections and conservation planning are hot topics of current discussion, analysis of alternative approaches and the development of combinations of species projection modelling algorithms through geospatial information systems technology. Approach model to find out the research problem of vegetation level based on the machine learning hybrid method, wavelet and artificial neural networks. Field data are used as a reference collection of natural resource field sample objects and biodiversity assessment. The testing and training ANN data set iterations times 28, achieve a performance value of 0.0867 MSE value is smaller than the ANN training data, above 50%, and spectral accuracy 82.1 %. Identify the location of the sample point position of the Tumih / Parepat vegetation species using HyMap Image is good enough, at least the modelling, design of the species distribution can reach the target in this study. The computation validation rate above 90% proves the calculation can be considered.

Development of Solar Drying Model for Selected Cambodian Fish Species

Science.gov (United States)

Hubackova, Anna; Kucerova, Iva; Chrun, Rithy; Chaloupkova, Petra; Banout, Jan

2014-01-01

A solar drying was investigated as one of perspective techniques for fish processing in Cambodia. The solar drying was compared to conventional drying in electric oven. Five typical Cambodian fish species were selected for this study. Mean solar drying temperature and drying air relative humidity were 55.6°C and 19.9%, respectively. The overall solar dryer efficiency was 12.37%, which is typical for natural convection solar dryers. An average evaporative capacity of solar dryer was 0.049 kg·h−1. Based on coefficient of determination (R 2), chi-square (χ 2) test, and root-mean-square error (RMSE), the most suitable models describing natural convection solar drying kinetics were Logarithmic model, Diffusion approximate model, and Two-term model for climbing perch and Nile tilapia, swamp eel and walking catfish and Channa fish, respectively. In case of electric oven drying, the Modified Page 1 model shows the best results for all investigated fish species except Channa fish where the two-term model is the best one. Sensory evaluation shows that most preferable fish is climbing perch, followed by Nile tilapia and walking catfish. This study brings new knowledge about drying kinetics of fresh water fish species in Cambodia and confirms the solar drying as acceptable technology for fish processing. PMID:25250381

The importance of assessing climate change vulnerability to address species conservation

Science.gov (United States)

Karen E. Bagne; Megan M. Friggens; Sharon J. Coe; Deborah M. Finch

2014-01-01

Species conservation often prioritizes attention on a small subset of "special status" species at high risk of extinction, but actions based on current lists of special status species may not effectively moderate biodiversity loss if climate change alters threats. Assessments of climate change vulnerability may provide a method to enhance identification of...

Postglacial migration supplements climate in determining plant species ranges in Europe

Science.gov (United States)

Normand, Signe; Ricklefs, Robert E.; Skov, Flemming; Bladt, Jesper; Tackenberg, Oliver; Svenning, Jens-Christian

2011-01-01

The influence of dispersal limitation on species ranges remains controversial. Considering the dramatic impacts of the last glaciation in Europe, species might not have tracked climate changes through time and, as a consequence, their present-day ranges might be in disequilibrium with current climate. For 1016 European plant species, we assessed the relative importance of current climate and limited postglacial migration in determining species ranges using regression modelling and explanatory variables representing climate, and a novel species-specific hind-casting-based measure of accessibility to postglacial colonization. Climate was important for all species, while postglacial colonization also constrained the ranges of more than 50 per cent of the species. On average, climate explained five times more variation in species ranges than accessibility, but accessibility was the strongest determinant for one-sixth of the species. Accessibility was particularly important for species with limited long-distance dispersal ability, with southern glacial ranges, seed plants compared with ferns, and small-range species in southern Europe. In addition, accessibility explained one-third of the variation in species' disequilibrium with climate as measured by the realized/potential range size ratio computed with niche modelling. In conclusion, we show that although climate is the dominant broad-scale determinant of European plant species ranges, constrained dispersal plays an important supplementary role. PMID:21543356

Combining state-and-transition simulations and species distribution models to anticipate the effects of climate change

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Brian W. Miller

2015-05-01

Full Text Available State-and-transition simulation models (STSMs are known for their ability to explore the combined effects of multiple disturbances, ecological dynamics, and management actions on vegetation. However, integrating the additional impacts of climate change into STSMs remains a challenge. We address this challenge by combining an STSM with species distribution modeling (SDM. SDMs estimate the probability of occurrence of a given species based on observed presence and absence locations as well as environmental and climatic covariates. Thus, in order to account for changes in habitat suitability due to climate change, we used SDM to generate continuous surfaces of species occurrence probabilities. These data were imported into ST-Sim, an STSM platform, where they dictated the probability of each cell transitioning between alternate potential vegetation types at each time step. The STSM was parameterized to capture additional processes of vegetation growth and disturbance that are relevant to a keystone species in the Greater Yellowstone Ecosystem—whitebark pine (Pinus albicaulis. We compared historical model runs against historical observations of whitebark pine and a key disturbance agent (mountain pine beetle, Dendroctonus ponderosae, and then projected the simulation into the future. Using this combination of correlative and stochastic simulation models, we were able to reproduce historical observations and identify key data gaps. Results indicated that SDMs and STSMs are complementary tools, and combining them is an effective way to account for the anticipated impacts of climate change, biotic interactions, and disturbances, while also allowing for the exploration of management options.

Malaria in Africa: vector species' niche models and relative risk maps.

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Alexander Moffett

2007-09-01

Full Text Available A central theoretical goal of epidemiology is the construction of spatial models of disease prevalence and risk, including maps for the potential spread of infectious disease. We provide three continent-wide maps representing the relative risk of malaria in Africa based on ecological niche models of vector species and risk analysis at a spatial resolution of 1 arc-minute (9 185 275 cells of approximately 4 sq km. Using a maximum entropy method we construct niche models for 10 malaria vector species based on species occurrence records since 1980, 19 climatic variables, altitude, and land cover data (in 14 classes. For seven vectors (Anopheles coustani, A. funestus, A. melas, A. merus, A. moucheti, A. nili, and A. paludis these are the first published niche models. We predict that Central Africa has poor habitat for both A. arabiensis and A. gambiae, and that A. quadriannulatus and A. arabiensis have restricted habitats in Southern Africa as claimed by field experts in criticism of previous models. The results of the niche models are incorporated into three relative risk models which assume different ecological interactions between vector species. The "additive" model assumes no interaction; the "minimax" model assumes maximum relative risk due to any vector in a cell; and the "competitive exclusion" model assumes the relative risk that arises from the most suitable vector for a cell. All models include variable anthrophilicity of vectors and spatial variation in human population density. Relative risk maps are produced from these models. All models predict that human population density is the critical factor determining malaria risk. Our method of constructing relative risk maps is equally general. We discuss the limits of the relative risk maps reported here, and the additional data that are required for their improvement. The protocol developed here can be used for any other vector-borne disease.

Alpha proteobacteria of genus Anaplasma (Rickettsiales: Anaplasmataceae): Epidemiology and characteristics of Anaplasma species related to veterinary and public health importance.

Science.gov (United States)

Atif, Farhan Ahmad

2016-05-01

The Anaplasma species are important globally distributed tick-transmitted bacteria of veterinary and public health importance. These pathogens, cause anaplasmosis in domestic and wild animal species including humans. Rhipicephalus, Ixodes, Dermacentor and Amblyomma genera of ticks are the important vectors of Anaplasma. Acute anaplasmosis is usually diagnosed upon blood smear examination followed by antibodies and nucleic acid detection. All age groups are susceptible but prevalence increases with age. Serological cross-reactivity is one of the important issues among Anaplasma species. They co-exist and concurrent infections occur in animals and ticks in same geographic area. These are closely related bacteria and share various common attributes which should be considered while developing vaccines and diagnostic assays. Movement of susceptible animals from non-endemic to endemic regions is the major risk factor of bovine/ovine anaplasmosis and tick-borne fever. Tetracyclines are currently available drugs for clearance of infection and treatment in humans and animals. Worldwide vaccine is not yet available. Identification, elimination of reservoirs, vector control (chemical and biological), endemic stability, habitat modification, rearing of tick resistant breeds, chemotherapy and tick vaccination are major control measures of animal anaplasmosis. Identification of reservoirs and minimizing the high-risk tick exposure activities are important control strategies for human granulocytic anaplasmosis.

Formation of hydrothermal tin deposits: Raman spectroscopic evidence for an important role of aqueous Sn(IV) species

Science.gov (United States)

Schmidt, Christian

2018-01-01

The speciation of tin and the solubility of cassiterite in H2O + HCl were determined at temperatures to 600 °C using in situ Raman spectroscopy. In addition, information on the fluid-melt partition of Sn was obtained at 700 °C and indicated a preference of the fluid only at HCl concentrations that are much higher than in fluids exsolved from natural felsic melts. Dissolution of cassiterite generally resulted in formation of Sn(IV) species unless reduced conditions were generated by hydrogen permeation or carbohydrates in the starting material. The prevalent aqueous Sn(IV) species was [SnCl4(H2O)2]0, with additional [SnCl3(H2O)3]+ and [SnCl5(H2O)]-. The only detectable Sn(II) species was very likely [Sn(II)Cl3]-. Cassiterite solubility increased with HCl concentration and was generally high in H2O+HCl fluids, with no strong dependencies on temperature, pressure, or the oxidation state of tin in the fluid. The Sn(IV) concentrations at 500 and 600 °C determined from the integrated ν1[Sn(IV)sbnd Cl] band intensity are in good agreement with literature data on the cassiterite solubility in H2O + HCl at oxygen fugacities along the hematite-magnetite buffer. The combined results from previous experimental studies and this study demonstrate that HCl molality is a crucial parameter for hydrothermal mobilization and transport of tin and for cassiterite precipitation, and that pH, pressure and temperature are less important. Current models on hydrothermal tin deposit formation need to be augmented to include Sn(IV)sbnd Cl complexes as significant tin-transporting species. Irrespective of the oxidation state of tin in the fluid, cassiterite precipitates due to reaction of the hydrothermal fluid with the wall rock (greisen or skarn formation), dilution (mixing with meteoric water) or a decrease in the HCl activity in the aqueous liquid by boiling. A redox reaction is only required for tin transported as Sn(II) to be converted to Sn(IV).

Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae

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Johannes Bergsten

2017-06-01

Full Text Available The species status of Hyphydrus anatolicus Guignot, 1957 and H. sanctus Sharp, 1882, previously often confused with the widespread H. ovatus (Linnaeus, 1760, are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1 was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the three species with no other than the three species solution included in the confidence interval. A likelihood ratio test rejected the one-species null model. Important morphological characters distinguishing the species are provided and illustrated. New distributional data are given for the following species: Hyphydrus anatolicus from Slovakia and Ukraine, and H. aubei Ganglbauer, 1891, and H. sanctus from Turkey.

Species Distribution Modelling: Contrasting presence-only models with plot abundance data

NARCIS (Netherlands)

Gomes, Vitor H.F.; Ijff, Stéphanie D.; Raes, Niels; Amaral, Iêda Leão; Salomão, Rafael P.; Coelho, Luiz De Souza; Matos, Francisca Dionízia De Almeida; Castilho, Carolina V.; Filho, Diogenes De Andrade Lima; López, Dairon Cárdenas; Guevara, Juan Ernesto; Magnusson, William E.; Phillips, Oliver L.; Wittmann, Florian; Carim, Marcelo De Jesus Veiga; Martins, Maria Pires; Irume, Mariana Victória; Sabatier, Daniel; Molino, Jean François; Bánki, Olaf S.; Guimarães, José Renan Da Silva; Pitman, Nigel C.A.; Piedade, Maria Teresa Fernandez; Mendoza, Abel Monteagudo; Luize, Bruno Garcia; Venticinque, Eduardo Martins; Novo, Evlyn Márcia Moraes De Leão; Vargas, Percy Núñez; Silva, Thiago Sanna Freire; Manzatto, Angelo Gilberto; Terborgh, John; Reis, Neidiane Farias Costa; Montero, Juan Carlos; Casula, Katia Regina; Marimon, Beatriz S.; Marimon, Ben Hur; Coronado, Euridice N.Honorio; Feldpausch, Ted R.; Duque, Alvaro; Zartman, Charles Eugene; Arboleda, Nicolás Castaño; Killeen, Timothy J.; Mostacedo, Bonifacio; Vasquez, Rodolfo; Schöngart, Jochen; Assis, Rafael L.; Medeiros, Marcelo Brilhante; Simon, Marcelo Fragomeni; Andrade, Ana; Laurance, William F.; Camargo, José Luís; Demarchi, Layon O.; Laurance, Susan G.W.; Farias, Emanuelle De Sousa; Nascimento, Henrique Eduardo Mendonça; Revilla, Juan David Cardenas; Quaresma, Adriano; Costa, Flavia R.C.; Vieira, Ima Célia Guimarães; Cintra, Bruno Barçante Ladvocat; Castellanos, Hernán; Brienen, Roel; Stevenson, Pablo R.; Feitosa, Yuri; Duivenvoorden, Joost F.; Aymard, Gerardo A.C.; Mogollón, Hugo F.; Targhetta, Natalia; Comiskey, James A.; Vicentini, Alberto; Lopes, Aline; Damasco, Gabriel; Dávila, Nállarett; García-Villacorta, Roosevelt; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Emilio, Thaise; Alonso, Alfonso; Neill, David; Dallmeier, Francisco; Ferreira, Leandro Valle; Araujo-Murakami, Alejandro; Praia, Daniel; Do Amaral, Dário Dantas; Carvalho, Fernanda Antunes; De Souza, Fernanda Coelho; Feeley, Kenneth; Arroyo, Luzmila; Pansonato, Marcelo Petratti; Gribel, Rogerio; Villa, Boris; Licona, Juan Carlos; Fine, Paul V.A.; Cerón, Carlos; Baraloto, Chris; Jimenez, Eliana M.; Stropp, Juliana; Engel, Julien; Silveira, Marcos; Mora, Maria Cristina Peñuela; Petronelli, Pascal; Maas, Paul; Thomas-Caesar, Raquel; Henkel, Terry W.; Daly, Doug; Paredes, Marcos Ríos; Baker, Tim R.; Fuentes, Alfredo; Peres, Carlos A.; Chave, Jerome; Pena, Jose Luis Marcelo; Dexter, Kyle G.; Silman, Miles R.; Jørgensen, Peter Møller; Pennington, Toby; Di Fiore, Anthony; Valverde, Fernando Cornejo; Phillips, Juan Fernando; Rivas-Torres, Gonzalo; Von Hildebrand, Patricio; Van Andel, Tinde R.; Ruschel, Ademir R.; Prieto, Adriana; Rudas, Agustín; Hoffman, Bruce; Vela, César I.A.; Barbosa, Edelcilio Marques; Zent, Egleé L.; Gonzales, George Pepe Gallardo; Doza, Hilda Paulette Dávila; Miranda, Ires Paula De Andrade; Guillaumet, Jean Louis; Pinto, Linder Felipe Mozombite; Bonates, Luiz Carlos De Matos; Silva, Natalino; Gómez, Ricardo Zárate; Zent, Stanford; Gonzales, Therany; Vos, Vincent A.; Malhi, Yadvinder; Oliveira, Alexandre A.; Cano, Angela; Albuquerque, Bianca Weiss; Vriesendorp, Corine; Correa, Diego Felipe; Torre, Emilio Vilanova; Van Der Heijden, Geertje; Ramirez-Angulo, Hirma; Ramos, José Ferreira; Young, Kenneth R.; Rocha, Maira; Nascimento, Marcelo Trindade; Medina, Maria Natalia Umaña; Tirado, Milton; Wang, Ophelia; Sierra, Rodrigo; Torres-Lezama, Armando; Mendoza, Casimiro; Ferreira, Cid; Baider, Cláudia; Villarroel, Daniel; Balslev, Henrik; Mesones, Italo; Giraldo, Ligia Estela Urrego; Casas, Luisa Fernanda; Reategui, Manuel Augusto Ahuite; Linares-Palomino, Reynaldo; Zagt, Roderick; Cárdenas, Sasha; Farfan-Rios, William; Sampaio, Adeilza Felipe; Pauletto, Daniela; Sandoval, Elvis H.Valderrama; Arevalo, Freddy Ramirez; Huamantupa-Chuquimaco, Isau; Garcia-Cabrera, Karina; Hernandez, Lionel; Gamarra, Luis Valenzuela; Alexiades, Miguel N.; Pansini, Susamar; Cuenca, Walter Palacios; Milliken, William; Ricardo, Joana; Lopez-Gonzalez, Gabriela; Pos, Edwin; Ter Steege, Hans

2018-01-01

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs.

A development of multi-Species mass transport model considering thermodynamic phase equilibrium

DEFF Research Database (Denmark)

Hosokawa, Yoshifumi; Yamada, Kazuo; Johannesson, Björn

2008-01-01

) variation in solid-phase composition when using different types of cement, (ii) physicochemical evaluation of steel corrosion initiation behaviour by calculating the molar ratio of chloride ion to hydroxide ion [Cl]/[OH] in pore solution, (iii) complicated changes of solid-phase composition caused......In this paper, a multi-species mass transport model, which can predict time dependent variation of pore solution and solid-phase composition due to the mass transport into the hardened cement paste, has been developed. Since most of the multi-species models established previously, based...... on the Poisson-Nernst-Planck theory, did not involve the modeling of chemical process, it has been coupled to thermodynamic equilibrium model in this study. By the coupling of thermodynamic equilibrium model, the multi-species model could simulate many different behaviours in hardened cement paste such as: (i...

Effects of environmental temperature on oviposition behavior in three blow fly species of forensic importance.

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Ody, Helen; Bulling, Mark T; Barnes, Kate M

2017-06-01

A number of factors are known to affect blow fly behavior with respect to oviposition. Current research indicates that temperature is the most significant factor. However temperature thresholds for oviposition in forensically important blow flies have not been well studied. Here, the oviposition behavior of three species of forensically important blow fly species (Calliphora vicina, Calliphora vomitoria and Lucilia sericata,) was studied under controlled laboratory conditions over a range of temperatures (10-40°C). Lower temperature thresholds for oviposition of 16°C and 17.5°C were established for C. vomitoria and L. sericata respectively, whilst C. vicina continued to lay eggs at 10°C. C. vomitoria and L. sericata both continued to lay eggs at 40°C, whilst the highest temperature at which oviposition occurred in C. vicina was 35°C. Within these thresholds there was considerable variation in the number of surviving pupae, with a general pattern of a single peak within the range of temperatures at which eggs were laid, but with the pattern being much less distinct for L. sericata. Copyright © 2017 Elsevier B.V. All rights reserved.

Expertly validated models and phylogenetically-controlled analysis suggests responses to climate change are related to species traits in the order lagomorpha.

Directory of Open Access Journals (Sweden)

Katie Leach

Full Text Available Climate change during the past five decades has impacted significantly on natural ecosystems, and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs have been used widely to project changes in species' bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical, and habitat variables for all 87 lagomorph species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current models and only those deemed 'modellable' within our framework were projected under future climate scenarios (58 species. Phylogenetically-controlled regressions were used to test whether species traits correlated with predicted responses to climate change. Climate change is likely to impact more than two-thirds of lagomorph species, with leporids (rabbits, hares, and jackrabbits likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov's Pika (Ochotona koslowi. Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management. We strongly advocate studies minimising data gaps in our knowledge of

The factors controlling species density in herbaceous plant communities: An assessment

Science.gov (United States)

Grace, J.B.

1999-01-01

This paper evaluates both the ideas and empirical evidence pertaining to the control of species density in herbaceous plant communities. While most theoretical discussions of species density have emphasized the importance of habitat productivity and disturbance regimes, many other factors (e.g. species pools, plant litter accumulation, plant morphology) have been proposed to be important. A review of literature presenting observations on the density of species in small plots (in the vicinity of a few square meters or less), as well as experimental studies, suggests several generalizations: (1) Available data are consistent with an underlying unimodal relationship between species density and total community biomass. While variance in species density is often poorly explained by predictor variables, there is strong evidence that high levels of community biomass are antagonistic to high species density. (2) Community biomass is just one of several factors affecting variations in species density. Multivariate analyses typically explain more than twice as much variance in species density as can be explained by community biomass alone. (3) Disturbance has important and sometimes complex effects on species density. In general, the evidence is consistent with the intermediate disturbance hypothesis but exceptions exist and effects can be complex. (4) Gradients in the species pool can have important influences on patterns of species density. Evidence is mounting that a considerable amount of the observed variability in species density within a landscape or region may result from environmental effects on the species pool. (5) Several additional factors deserve greater consideration, including time lags, species composition, plant morphology, plant density and soil microbial effects. Based on the available evidence, a conceptual model of the primary factors controlling species density is presented here. This model suggests that species density is controlled by the effects of

A survey of mosquitoes breeding in used tires in Spain for the detection of imported potential vector species.

Science.gov (United States)

Roiz, D; Eritja, R; Escosa, R; Lucientes, J; Marquès, E; Melero-Alcíbar, R; Ruiz, S; Molina, R

2007-06-01

The used tire trade has facilitated the introduction, spread, and establishment of the Asian tiger mosquito, Aedes albopictus, and other mosquito species in several countries of America, Africa, Oceania, and Europe. A strategy for detecting these imported mosquito vectors was developed in Spain during 2003-2004 by EVITAR (multidisciplinary network for the study of viruses transmitted by arthropods and rodents). A survey in 45 locations found no invasive species. Eight autochthonous species of mosquitoes were detected in used tires, including Culex pipiens, Cx. hortensis, Cx. modestus, Anopheles atroparvus, An. claviger, Culiseta longiareolata, Cs. annulata, and Aedes caspius. Dominant species were Cx. pipiens and Cs. longiareolata. Aedes caspius was found in only once, near its natural breeding habitat. Considering the recent discovery of an established population of Ae. albopictus in Catalonia, the increasing commerce of used tires in Spain for recycling, storage, and recapping might greatly contribute to the rapid spread of this species across the Iberian Peninsula.

Mechanistic species distribution modelling as a link between physiology and conservation.

Science.gov (United States)

Evans, Tyler G; Diamond, Sarah E; Kelly, Morgan W

2015-01-01

Climate change conservation planning relies heavily on correlative species distribution models that estimate future areas of occupancy based on environmental conditions encountered in present-day ranges. The approach benefits from rapid assessment of vulnerability over a large number of organisms, but can have poor predictive power when transposed to novel environments and reveals little in the way of causal mechanisms that define changes in species distribution or abundance. Having conservation planning rely largely on this single approach also increases the risk of policy failure. Mechanistic models that are parameterized with physiological information are expected to be more robust when extrapolating distributions to future environmental conditions and can identify physiological processes that set range boundaries. Implementation of mechanistic species distribution models requires knowledge of how environmental change influences physiological performance, and because this information is currently restricted to a comparatively small number of well-studied organisms, use of mechanistic modelling in the context of climate change conservation is limited. In this review, we propose that the need to develop mechanistic models that incorporate physiological data presents an opportunity for physiologists to contribute more directly to climate change conservation and advance the field of conservation physiology. We begin by describing the prevalence of species distribution modelling in climate change conservation, highlighting the benefits and drawbacks of both mechanistic and correlative approaches. Next, we emphasize the need to expand mechanistic models and discuss potential metrics of physiological performance suitable for integration into mechanistic models. We conclude by summarizing other factors, such as the need to consider demography, limiting broader application of mechanistic models in climate change conservation. Ideally, modellers, physiologists and

Species distribution modeling for the invasive raccoon dog (Nyctereutes procyonoides in Austria and first range predictions for alpine environments

Directory of Open Access Journals (Sweden)

Duscher Tanja

2017-01-01

Full Text Available Species distribution models are important tools for wildlife management planning, particularly in the case of invasive species. We employed a recent framework for niche-based invasive species distribution modeling to predict the probability of presence for the invasive raccoon dog (Nyctereutes procyonoides in Austria. The raccoon dog is an adaptive, mobile and highly reproductive Asiatic canid that has successfully invaded many parts of Europe. It is known to occur in Austria since 1963 and is now widespread in the northern and eastern parts of the country, but its population density remains low. With the help of a species distribution model we identified focal areas for future monitoring and management actions, and we address some management implications for the raccoon dog in Austria. We also determined the environmental predictors of raccoon dog distribution in this alpine country. Its distribution seems to be mainly limited by climatic factors (snow depth, duration of snow cover, winter precipitation and mean annual temperature and is thus linked to elevation. Consequently, we assumed the Alps to be a barrier for the spread of the invasive raccoon dog in Europe; however, its ecological permeability is expected to increase with ongoing climate change.

Predicting plant invasions under climate change: are species distribution models validated by field trials?

Science.gov (United States)

Sheppard, Christine S; Burns, Bruce R; Stanley, Margaret C

2014-09-01

Climate change may facilitate alien species invasion into new areas, particularly for species from warm native ranges introduced into areas currently marginal for temperature. Although conclusions from modelling approaches and experimental studies are generally similar, combining the two approaches has rarely occurred. The aim of this study was to validate species distribution models by conducting field trials in sites of differing suitability as predicted by the models, thus increasing confidence in their ability to assess invasion risk. Three recently naturalized alien plants in New Zealand were used as study species (Archontophoenix cunninghamiana, Psidium guajava and Schefflera actinophylla): they originate from warm native ranges, are woody bird-dispersed species and of concern as potential weeds. Seedlings were grown in six sites across the country, differing both in climate and suitability (as predicted by the species distribution models). Seedling growth and survival were recorded over two summers and one or two winter seasons, and temperature and precipitation were monitored hourly at each site. Additionally, alien seedling performances were compared to those of closely related native species (Rhopalostylis sapida, Lophomyrtus bullata and Schefflera digitata). Furthermore, half of the seedlings were sprayed with pesticide, to investigate whether enemy release may influence performance. The results showed large differences in growth and survival of the alien species among the six sites. In the more suitable sites, performance was frequently higher compared to the native species. Leaf damage from invertebrate herbivory was low for both alien and native seedlings, with little evidence that the alien species should have an advantage over the native species because of enemy release. Correlations between performance in the field and predicted suitability of species distribution models were generally high. The projected increase in minimum temperature and reduced

Development of Solar Drying Model for Selected Cambodian Fish Species

Directory of Open Access Journals (Sweden)

Anna Hubackova

2014-01-01

Full Text Available A solar drying was investigated as one of perspective techniques for fish processing in Cambodia. The solar drying was compared to conventional drying in electric oven. Five typical Cambodian fish species were selected for this study. Mean solar drying temperature and drying air relative humidity were 55.6°C and 19.9%, respectively. The overall solar dryer efficiency was 12.37%, which is typical for natural convection solar dryers. An average evaporative capacity of solar dryer was 0.049 kg·h−1. Based on coefficient of determination (R2, chi-square (χ2 test, and root-mean-square error (RMSE, the most suitable models describing natural convection solar drying kinetics were Logarithmic model, Diffusion approximate model, and Two-term model for climbing perch and Nile tilapia, swamp eel and walking catfish and Channa fish, respectively. In case of electric oven drying, the Modified Page 1 model shows the best results for all investigated fish species except Channa fish where the two-term model is the best one. Sensory evaluation shows that most preferable fish is climbing perch, followed by Nile tilapia and walking catfish. This study brings new knowledge about drying kinetics of fresh water fish species in Cambodia and confirms the solar drying as acceptable technology for fish processing.

The ecological importance of cephalopods in multi- species ...

African Journals Online (AJOL)

spamer

of commercial fish species in years of abundance of squid. ... landed in several different EU countries and cephalopod catches do not ... Using data from research vessel surveys, there seems to be a peak in feeding intensity in the early ... MATERIAL AND METHODS ... averaged to calculate daily catch per unit effort (cpue).

Balancing energy development and conservation: A method utilizing species distribution models

Science.gov (United States)

Jarnevich, C.S.; Laubhan, M.K.

2011-01-01

Alternative energy development is increasing, potentially leading to negative impacts on wildlife populations already stressed by other factors. Resource managers require a scientifically based methodology to balance energy development and species conservation, so we investigated modeling habitat suitability using Maximum Entropy to develop maps that could be used with other information to help site energy developments. We selected one species of concern, the Lesser Prairie-Chicken (LPCH; Tympanuchus pallidicinctus) found on the southern Great Plains of North America, as our case study. LPCH populations have been declining and are potentially further impacted by energy development. We used LPCH lek locations in the state of Kansas along with several environmental and anthropogenic parameters to develop models that predict the probability of lek occurrence across the landscape. The models all performed well as indicated by the high test area under the curve (AUC) scores (all >0.9). The inclusion of anthropogenic parameters in models resulted in slightly better performance based on AUC values, indicating that anthropogenic features may impact LPCH lek habitat suitability. Given the positive model results, this methodology may provide additional guidance in designing future survey protocols, as well as siting of energy development in areas of marginal or unsuitable habitat for species of concern. This technique could help to standardize and quantify the impacts various developments have upon at-risk species. ?? 2011 Springer Science+Business Media, LLC (outside the USA).

Assessing environmental attributes and effects of climate change on Sphagnum peatland distributions in North America using single- and multi-species models.

Science.gov (United States)

Oke, Tobi A; Hager, Heather A

2017-01-01

The fate of Northern peatlands under climate change is important because of their contribution to global carbon (C) storage. Peatlands are maintained via greater plant productivity (especially of Sphagnum species) than decomposition, and the processes involved are strongly mediated by climate. Although some studies predict that warming will relax constraints on decomposition, leading to decreased C sequestration, others predict increases in productivity and thus increases in C sequestration. We explored the lack of congruence between these predictions using single-species and integrated species distribution models as proxies for understanding the environmental correlates of North American Sphagnum peatland occurrence and how projected changes to the environment might influence these peatlands under climate change. Using Maximum entropy and BIOMOD modelling platforms, we generated single and integrated species distribution models for four common Sphagnum species in North America under current climate and a 2050 climate scenario projected by three general circulation models. We evaluated the environmental correlates of the models and explored the disparities in niche breadth, niche overlap, and climate suitability among current and future models. The models consistently show that Sphagnum peatland distribution is influenced by the balance between soil moisture deficit and temperature of the driest quarter-year. The models identify the east and west coasts of North America as the core climate space for Sphagnum peatland distribution. The models show that, at least in the immediate future, the area of suitable climate for Sphagnum peatland could expand. This result suggests that projected warming would be balanced effectively by the anticipated increase in precipitation, which would increase Sphagnum productivity.

Interspecific shared collective decision-making in two forensically important species.

Science.gov (United States)

Boulay, Julien; Deneubourg, Jean-Louis; Hédouin, Valéry; Charabidzé, Damien

2016-02-10

To date, the study of collective behaviour has mainly focused on intraspecific situations: the collective decision-making of mixed-species groups involving interspecific aggregation-segregation has received little attention. Here, we show that, in both conspecific and heterospecific groups, the larvae of two species (Lucilia sericata and Calliphora vomitoria, calliphorid carrion-feeding flies) were able to make a collective choice. In all groups, the choice was made within a few minutes and persisted throughout the period of the experiment. The monitoring of a focal individual within a group showed that these aggregations were governed by attractive and retentive effects of the group. Furthermore, the similarity observed between the conspecific and heterospecific groups suggested the existence of shared aggregation signals. The group size was found to have a stronger influence than the species of necrophagous larvae. These results should be viewed in relation to the well-known correlation between group size and heat generation. This study provides the first experimental examination of the dynamics of collective decision-making in mixed-species groups of invertebrates, contributing to our understanding of the cooperation-competition phenomenon in animal social groups. © 2016 The Author(s).

Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change.

Science.gov (United States)

Wang, Wen J; He, Hong S; Thompson, Frank R; Spetich, Martin A; Fraser, Jacob S

2018-09-01

Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are not well represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts. We investigate how species biological traits and environmental heterogeneity affect species distribution shifts. We used a species-specific, spatially explicit forest dynamic model LANDIS PRO, which incorporates site-scale tree species demography and competition, landscape-scale dispersal and disturbances, and regional-scale abiotic controls, to simulate the distribution shifts of four representative tree species with distinct biological traits in the central hardwood forest region of United States. Our results suggested that biological traits (e.g., dispersal capacity, maturation age) were important for determining tree species distribution shifts. Environmental heterogeneity, on average, reduced shift rates by 8% compared to perfect environmental conditions. The average distribution shift rates ranged from 24 to 200myear -1 under climate change scenarios, implying that many tree species may not able to keep up with climate change because of limited dispersal capacity, long generation time, and environmental heterogeneity. We suggest that climate-distribution models should include species demographic processes (e.g., fecundity, dispersal, colonization), biological traits (e.g., dispersal capacity, maturation age), and environmental heterogeneity (e.g., habitat fragmentation) to improve future predictions of species distribution shifts in response to changing climates. Copyright © 2018 Elsevier B.V. All rights reserved.

A HIERARCHICAL SET OF MODELS FOR SPECIES RESPONSE ANALYSIS

NARCIS (Netherlands)

HUISMAN, J; OLFF, H; FRESCO, LFM

Variation in the abundance of species in space and/or time can be caused by a wide range of underlying processes. Before such causes can be analysed we need simple mathematical models which can describe the observed response patterns. For this purpose a hierarchical set of models is presented. These

A hierarchical set of models for species response analysis

NARCIS (Netherlands)

Huisman, J.; Olff, H.; Fresco, L.F.M.

1993-01-01

Variation in the abundance of species in space and/or time can be caused by a wide range of underlying processes. Before such causes can be analysed we need simple mathematical models which can describe the observed response patterns. For this purpose a hierarchical set of models is presented. These

Climate change velocity since the Last Glacial Maximum and its importance for patterns of species richness and range size

DEFF Research Database (Denmark)

Sandel, Brody Steven; Arge, Lars Allan; Svenning, J.-C.

to fully occupy suitable habitat, or when local diversification rates are depressed by local population extinctions and changing selective regimes. Locations with long-term climate instability should therefore show reduced species richness with small-ranged species particularly missing from the community...... these predictions using global data on mammal and amphibian distributions. Consistent with our predictions, richness of small-ranged species of both groups was negatively associated with velocity. Velocity generally explained more variation in richness than did the simple climate anomaly. Climate velocity appears...... to capture an important historical signal on current mammal and amphibian distributions....

Patterns and causes of species richness: a general simulation model for macroecology

DEFF Research Database (Denmark)

Gotelli, Nicholas J; Anderson, Marti J; Arita, Hector T

2009-01-01

to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non-linearity. However, curve-fitting approaches are problematic because most theoretical models...... in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species' geographical ranges...... in an environmentally heterogeneous, gridded domain and describe progress to date regarding their implementation. The output from such a general simulation model (GSM) would, at a minimum, consist of the simulated distribution of species ranges on a map, yielding the predicted number of species in each grid cell...

Phylogeny of economically important insect pests that infesting several crops species in Malaysia

Science.gov (United States)

Ghazali, Siti Zafirah; Zain, Badrul Munir Md.; Yaakop, Salmah

2014-09-01

This paper reported molecular data on insect pests of commercial crops in Peninsular Malaysia. Fifteen insect pests (Metisa plana, Calliteara horsefeldii, Cotesia vestalis, Bactrocera papayae, Bactrocera carambolae, Bactrocera latifrons, Conopomorpha cramella, Sesamia inferens, Chilo polychrysa, Rhynchophorus vulneratus, and Rhynchophorus ferrugineus) of nine crops were sampled (oil palm, coconut, paddy, cocoa, starfruit, angled loofah, guava, chili and mustard) and also four species that belong to the fern's pest (Herpetogramma platycapna) and storage and rice pests (Tribolium castaneum, Oryzaephilus surinamensis and Cadra cautella). The presented phylogeny summarized the initial phylogenetic hypothesis, which concerning by implementation of the economically important insect pests. In this paper, phylogenetic relationships among 39 individuals of 15 species that belonging to three orders under 12 genera were inferred from DNA sequences of mitochondrial marker, cytochrome oxidase subunit I (COI) and nuclear marker, ribosomal DNA 28S D2 region. The phylogenies resulted from the phylogenetic analyses of both genes are relatively similar, but differ in the sequence of evolution. Interestingly, this most recent molecular data of COI sequences data by using Bayesian Inference analysis resulted a more-resolved phylogeny that corroborated with traditional hypotheses of holometabolan relationships based on traditional hypotheses of holometabolan relationships and most of recently molecular study compared to 28S sequences. This finding provides the information on relationships of pests species, which infested several crops in Malaysia and also estimation on Holometabola's order relationships. The identification of the larval stages of insect pests could be done accurately, without waiting the emergence of adults and supported by the phylogenetic tree.

New models for estimating the carbon sink capacity of Spanish softwood species

Energy Technology Data Exchange (ETDEWEB)

Ruiz-Peinado, R.; Rio, M. del; Montero, G.

2011-07-01

Quantifying the carbon balance in forests is one of the main challenges in forest management. Forest carbon stocks are usually estimated indirectly through biomass equations applied to forest inventories, frequently considering different tree biomass components. The aim of this study is to develop systems of equations for predicting tree biomass components for the main forest softwood species in Spain: Abies alba Mill., A. pinsapo Boiss., Juniperus thurifera L., Pinus canariensis Sweet ex Spreng., P. halepensis Mill., P. nigra Arn., P. pinaster Ait., P. pinea L., P. sylvestris L., P. uncinata Mill. For each species, a system of additive biomass models was fitted using seemingly unrelated regression. Diameter at the breast height and total height were used as independent variables. Diameter appears in all component models, while tree height was included in the stem component model of all species and in some branch component equations. Total height was included in order to improve biomass estimations at different sites. These biomass models were compared to previously available equations in order to test their accuracy and it was found that they yielded better fitting statistics in all cases. Moreover, the models fulfil the additivity property. We also developed root:shoot ratios in order to determine the partitioning into aboveground and belowground biomass. A number of differences were found between species, with a minimum of 0.183 for A. alba and a maximum of 0.385 for P. uncinata. The mean value for the softwood species studied was 0.265. Since the Spanish National Forest Inventory (NFI) records species, tree diameter and height of sample trees, these biomass models and ratios can be used to accurately estimate carbon stocks from NFI data. (Author) 55 refs.

New models for estimating the carbon sink capacity of Spanish softwood species

International Nuclear Information System (INIS)

Ruiz-Peinado, R.; Rio, M. del; Montero, G.

2011-01-01

Quantifying the carbon balance in forests is one of the main challenges in forest management. Forest carbon stocks are usually estimated indirectly through biomass equations applied to forest inventories, frequently considering different tree biomass components. The aim of this study is to develop systems of equations for predicting tree biomass components for the main forest softwood species in Spain: Abies alba Mill., A. pinsapo Boiss., Juniperus thurifera L., Pinus canariensis Sweet ex Spreng., P. halepensis Mill., P. nigra Arn., P. pinaster Ait., P. pinea L., P. sylvestris L., P. uncinata Mill. For each species, a system of additive biomass models was fitted using seemingly unrelated regression. Diameter at the breast height and total height were used as independent variables. Diameter appears in all component models, while tree height was included in the stem component model of all species and in some branch component equations. Total height was included in order to improve biomass estimations at different sites. These biomass models were compared to previously available equations in order to test their accuracy and it was found that they yielded better fitting statistics in all cases. Moreover, the models fulfil the additivity property. We also developed root:shoot ratios in order to determine the partitioning into aboveground and belowground biomass. A number of differences were found between species, with a minimum of 0.183 for A. alba and a maximum of 0.385 for P. uncinata. The mean value for the softwood species studied was 0.265. Since the Spanish National Forest Inventory (NFI) records species, tree diameter and height of sample trees, these biomass models and ratios can be used to accurately estimate carbon stocks from NFI data. (Author) 55 refs.

Early Engagement of Stakeholders with Individual-Based Modeling Can Inform Research for Improving Invasive Species Management: The Round Goby as a Case Study

Directory of Open Access Journals (Sweden)

Emma Samson

2017-11-01

Full Text Available Individual-based models (IBMs incorporating realistic representations of key range-front processes such as dispersal can be used as tools to investigate the dynamics of invasive species. Managers can apply insights from these models to take effective action to prevent further spread and prioritize measures preventing establishment of invasive species. We highlight here how early-stage IBMs (constructed under constraints of time and data availability can also play an important role in defining key research priorities for providing key information on the biology of an invasive species in order that subsequent models can provide robust insight into potential management interventions. The round goby, Neogobius melanostomus, is currently spreading through the Baltic Sea, with major negative effects being reported in the wake of its invasion. Together with stakeholders, we parameterize an IBM to investigate the goby's potential spread pattern throughout the Gulf of Gdansk and the Baltic Sea. Model parameters were assigned by integrating information obtained through stakeholder interaction, from scientific literature, or estimated using an inverse modeling approach when not available. IBMs can provide valuable direction to research on invasive species even when there is limited data and/or time available to parameterize/fit them to the degree to which we might aspire in an ideal world. Co-development of models with stakeholders can be used to recognize important invasion patterns, in addition to identifying and estimating unknown environmental parameters, thereby guiding the direction of future research. Well-parameterized and validated models are not required in the earlier stages of the modeling cycle where their main utility is as a tool for thought.

Testing species distribution models across space and time: high latitude butterflies and recent warming

DEFF Research Database (Denmark)

Eskildsen, Anne; LeRoux, Peter C.; Heikkinen, Risto K.

2013-01-01

changes at expanding range margins can be predicted accurately. Location. Finland. Methods. Using 10-km resolution butterfly atlas data from two periods, 1992–1999 (t1) and 2002–2009 (t2), with a significant between-period temperature increase, we modelled the effects of climatic warming on butterfly...... butterfly distributions under climate change. Model performance was lower with independent compared to non-independent validation and improved when land cover and soil type variables were included, compared to climate-only models. SDMs performed less well for highly mobile species and for species with long......Aim. To quantify whether species distribution models (SDMs) can reliably forecast species distributions under observed climate change. In particular, to test whether the predictive ability of SDMs depends on species traits or the inclusion of land cover and soil type, and whether distributional...

Predicting occupancy for pygmy rabbits in Wyoming: an independent evaluation of two species distribution models

Science.gov (United States)

Germaine, Stephen S.; Ignizio, Drew; Keinath, Doug; Copeland, Holly

2014-01-01

Species distribution models are an important component of natural-resource conservation planning efforts. Independent, external evaluation of their accuracy is important before they are used in management contexts. We evaluated the classification accuracy of two species distribution models designed to predict the distribution of pygmy rabbit Brachylagus idahoensis habitat in southwestern Wyoming, USA. The Nature Conservancy model was deductive and based on published information and expert opinion, whereas the Wyoming Natural Diversity Database model was statistically derived using historical observation data. We randomly selected 187 evaluation survey points throughout southwestern Wyoming in areas predicted to be habitat and areas predicted to be nonhabitat for each model. The Nature Conservancy model correctly classified 39 of 77 (50.6%) unoccupied evaluation plots and 65 of 88 (73.9%) occupied plots for an overall classification success of 63.3%. The Wyoming Natural Diversity Database model correctly classified 53 of 95 (55.8%) unoccupied plots and 59 of 88 (67.0%) occupied plots for an overall classification success of 61.2%. Based on 95% asymptotic confidence intervals, classification success of the two models did not differ. The models jointly classified 10.8% of the area as habitat and 47.4% of the area as nonhabitat, but were discordant in classifying the remaining 41.9% of the area. To evaluate how anthropogenic development affected model predictive success, we surveyed 120 additional plots among three density levels of gas-field road networks. Classification success declined sharply for both models as road-density level increased beyond 5 km of roads per km-squared area. Both models were more effective at predicting habitat than nonhabitat in relatively undeveloped areas, and neither was effective at accounting for the effects of gas-energy-development road networks. Resource managers who wish to know the amount of pygmy rabbit habitat present in an

From species to trait evolution in Aethionema (Brassicaceae)

NARCIS (Netherlands)

Mohammadin, Setareh

2017-01-01

The plant family Brassicaceae (or crucifers) is an economically important group that includes many food crops (e.g. cabbages and radishes), horticultural species (e.g. Draba, Iberis, Lunaria), and model plant species (particularly Arabidopsis thaliana). Because of the

Importance of Triticosecale Wittmack ex A.Camus varieties in the formation of species diversity of agro-ecosystems

Directory of Open Access Journals (Sweden)

В. В. Москалець

2015-12-01

Full Text Available Purpose. To find out the ecological importance of winter triticale varieties in the formation of species diversity of agro-ecosystems. Methods. Field, laboratoryones and mathematical and statistical analysis. Results. The authors studied ecological importance of winter triticale varieties of forest-steppe and Polissia ecotopes as determinants of agrobiocenosis in the structural and functional organization of species diversity. It was found that less favourable ecological niche for pests-phytophags is such winter triticale varieties and lines as ‘Slavetne’, ‘AD 256’, ‘Chaian’, ‘DAU 5’, for epiphytoparasites – ‘Vivate Nosivske’, ‘Pshenychne’, ‘Slavetne polipshene’, ‘Slavetne’, ‘Yaguar’, respectively. It is determined that varieties and lines of winter triticale such as ‘AD 256’, ‘Vivate Nosivske’, ‘Pshenychne’, ‘Slavetne polipshene’, ‘Slavetne’ show high biological ability to compete with synanthropic vegetation and form distinct associations of segetal plants. Conclusions. It was found that agrophytocenoses of the studied varieties of winter triticale under the conditions of forest-steppe, Polissia-forest-steppe and Polissia ecotops determined in movements structural and functional organization of species diversity of agroecosystems.

Economic indicators of the production of important fruit-specific species in Vojvodina

Directory of Open Access Journals (Sweden)

Lukač-Bulatović Mirjana

2017-01-01

Full Text Available The paper discusses the basic economic and production results of important fruit species (apple, pear, peach, sour cherry and plum on agricultural farms of Vojvodina. The aim of the research is to evaluate the most important parameters of cost-effectiveness of these productions, and propose measures to improve the existing situation. Comparative analysis clearly shows that the most cost-effective is pears production, followed by apple, cherry, peach and plum. Pear production gives the largest coverage margin per unit capacity (1,261,786 din /ha, which is 16.5% better than in apple production (1,083,160 din /ha, or about 7.8 times better in relation to plums production (161,796 din /ha. The highest coefficient of economy (3.19 is, also, recorded in the production of pear (for apples 2.94, cherry 2.27, peach 2.17 and plum 1.44. Further development of fruit production in Vojvodina involves raising intensive farms with quality fruit varieties, firmer vertical linking of producers and processors, ensurement of economic safety of producers in the long run, making of fruit producing regions, etc.

Importance-truncated shell model for multi-shell valence spaces

Energy Technology Data Exchange (ETDEWEB)

Stumpf, Christina; Vobig, Klaus; Roth, Robert [Institut fuer Kernphysik, TU Darmstadt (Germany)

2016-07-01

The valence-space shell model is one of the work horses in nuclear structure theory. In traditional applications, shell-model calculations are carried out using effective interactions constructed in a phenomenological framework for rather small valence spaces, typically spanned by one major shell. We improve on this traditional approach addressing two main aspects. First, we use new effective interactions derived in an ab initio approach and, thus, establish a connection to the underlying nuclear interaction providing access to single- and multi-shell valence spaces. Second, we extend the shell model to larger valence spaces by applying an importance-truncation scheme based on a perturbative importance measure. In this way, we reduce the model space to the relevant basis states for the description of a few target eigenstates and solve the eigenvalue problem in this physics-driven truncated model space. In particular multi-shell valence spaces are not tractable otherwise. We combine the importance-truncated shell model with refined extrapolation schemes to approximately recover the exact result. We present first results obtained in the importance-truncated shell model with the newly derived ab initio effective interactions for multi-shell valence spaces, e.g., the sdpf shell.

The Bifurcation and Control of a Single-Species Fish Population Logistic Model with the Invasion of Alien Species

Directory of Open Access Journals (Sweden)

Yi Zhang

2014-01-01

Full Text Available The objective of this paper is to study systematically the bifurcation and control of a single-species fish population logistic model with the invasion of alien species based on the theory of singular system and bifurcation. It regards Spartina anglica as an invasive species, which invades the fisheries and aquaculture. Firstly, the stabilities of equilibria in this model are discussed. Moreover, the sufficient conditions for existence of the trans-critical bifurcation and the singularity induced bifurcation are obtained. Secondly, the state feedback controller is designed to eliminate the unexpected singularity induced bifurcation by combining harvested effort with the purification capacity. It obviously inhibits the switch of population and makes the system stable. Finally, the numerical simulation is proposed to show the practical significance of the bifurcation and control from the biological point of view.

Analysis Monthly Import of Palm Oil Products Using Box-Jenkins Model

Science.gov (United States)

Ahmad, Nurul F. Y.; Khalid, Kamil; Saifullah Rusiman, Mohd; Ghazali Kamardan, M.; Roslan, Rozaini; Che-Him, Norziha

2018-04-01

The palm oil industry has been an important component of the national economy especially the agriculture sector. The aim of this study is to identify the pattern of import of palm oil products, to model the time series using Box-Jenkins model and to forecast the monthly import of palm oil products. The method approach is included in the statistical test for verifying the equivalence model and statistical measurement of three models, namely Autoregressive (AR) model, Moving Average (MA) model and Autoregressive Moving Average (ARMA) model. The model identification of all product import palm oil is different in which the AR(1) was found to be the best model for product import palm oil while MA(3) was found to be the best model for products import palm kernel oil. For the palm kernel, MA(4) was found to be the best model. The results forecast for the next four months for products import palm oil, palm kernel oil and palm kernel showed the most significant decrease compared to the actual data.

Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae.

Directory of Open Access Journals (Sweden)

Justin C Bagley

Full Text Available Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the

Generation of risk importance information from severe accident PSA model

International Nuclear Information System (INIS)

Seo, Mi Ro; Kim, Hyeong Taek; Moon, Chan Kook

2012-01-01

One of the important objects conducting Probabilistic Safety Assessment (PSA) is the relative evaluation of importance of the component or function that is greatly affected to the plant safety. This evaluation is performed by the importance assessment methods such as Risk Reduction Worth, Risk Achievement Worth, and Fuss el Vessley method from the aspect of core damage frequency (CDF). In the Level 1 PSA model, the importance of each component can be evaluated since the CDF is calculated by the combination of the branch probability of event tree and the component failure probability in the fault tree. But, the Level 2 PSA model in order to assess the containment integrity cannot evaluate the risk importance by the above methods because the model is consisted of 3 parts, plant damage status, containment event tree, and source term category. So, in the field that the Level 2 PSA risk importance information should be reflected, such as maintenance rule program, risk importance has been determined by the subjective judgment of the model developer. This study was performed in order to generate the risk importance information more objectively and systematically in the Level 2 PSA model, focused on the containment event tree in the domain PHWR Level 2 PSA model

Current state of the art for statistical modeling of species distributions [Chapter 16

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Troy M. Hegel; Samuel A. Cushman; Jeffrey Evans; Falk Huettmann

2010-01-01

Over the past decade the number of statistical modelling tools available to ecologists to model species' distributions has increased at a rapid pace (e.g. Elith et al. 2006; Austin 2007), as have the number of species distribution models (SDM) published in the literature (e.g. Scott et al. 2002). Ten years ago, basic logistic regression (Hosmer and Lemeshow 2000)...

Weather, not climate, defines distributions of vagile bird species.

Directory of Open Access Journals (Sweden)

April E Reside

Full Text Available BACKGROUND: Accurate predictions of species distributions are essential for climate change impact assessments. However the standard practice of using long-term climate averages to train species distribution models might mute important temporal patterns of species distribution. The benefit of using temporally explicit weather and distribution data has not been assessed. We hypothesized that short-term weather associated with the time a species was recorded should be superior to long-term climate measures for predicting distributions of mobile species. METHODOLOGY: We tested our hypothesis by generating distribution models for 157 bird species found in Australian tropical savannas (ATS using modelling algorithm Maxent. The variable weather of the ATS supports a bird assemblage with variable movement patterns and a high incidence of nomadism. We developed "weather" models by relating climatic variables (mean temperature, rainfall, rainfall seasonality and temperature seasonality from the three month, six month and one year period preceding each bird record over a 58 year period (1950-2008. These weather models were compared against models built using long-term (30 year averages of the same climatic variables. CONCLUSIONS: Weather models consistently achieved higher model scores than climate models, particularly for wide-ranging, nomadic and desert species. Climate models predicted larger range areas for species, whereas weather models quantified fluctuations in habitat suitability across months, seasons and years. Models based on long-term climate averages over-estimate availability of suitable habitat and species' climatic tolerances, masking species potential vulnerability to climate change. Our results demonstrate that dynamic approaches to distribution modelling, such as incorporating organism-appropriate temporal scales, improves understanding of species distributions.

Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution.

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Melkikh, Alexey V; Khrennikov, Andrei

2017-11-01

A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs.

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Scholz, Holger C; Mühldorfer, Kristin; Shilton, Cathy; Benedict, Suresh; Whatmore, Adrian M; Blom, Jochen; Eisenberg, Tobias

2016-01-01

The genus Brucella comprises various species of both veterinary and human medical importance. All species are genetically highly related to each other, sharing intra-species average nucleotide identities (ANI) of > 99%. Infections occur among various warm-blooded animal species, marine mammals, and humans. Until recently, amphibians had not been recognized as a host for Brucella. In this study, however, we show that novel Brucella species are distributed among exotic frogs worldwide. Comparative recA gene analysis of 36 frog isolates from various continents and different frog species revealed an unexpected high genetic diversity, not observed among classical Brucella species. In phylogenetic reconstructions the isolates consequently formed various clusters and grouped together with atypical more distantly related brucellae, like B. inopinata, strain BO2, and Australian isolates from rodents, some of which were isolated as human pathogens. Of one frog isolate (10RB9215) the genome sequence was determined. Comparative genome analysis of this isolate and the classical Brucella species revealed additional genetic material, absent from classical Brucella species but present in Ochrobactrum, the closest genetic neighbor of Brucella, and in other soil associated genera of the Alphaproteobacteria. The presence of gene clusters encoding for additional metabolic functions, flanked by tRNAs and mobile genetic elements, as well as by bacteriophages is suggestive for a different ecology compared to classical Brucella species. Furthermore it suggests that amphibian isolates may represent a link between free living soil saprophytes and the pathogenic Brucella with a preferred intracellular habitat. We therefore assume that brucellae from frogs have a reservoir in soil and, in contrast to classical brucellae, undergo extensive horizontal gene transfer.

Post-discharge evolution of reactive species in the water activated by a surface air plasma: a modeling study

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Liu, Z. C.; Liu, D. X.; Chen, C.; Liu, Z. J.; Yang, A. J.; Rong, M. Z.; Chen, H. L.; Kong, M. G.

2018-05-01

Plasma-activated water (PAW) has been reported to sustain a bactericidal ability for months. However, many reactive species regarded as the main antibacterial agents in PAW have short lifetimes of less than one second. In order to explain the prolonged antibacterial ability of PAW and predict how to extend its effective time, we studied the post-discharge evolution of reactive species in PAW based on a system-level model reported previously. Three common storage conditions for PAW were considered within the post-discharge time of 14 d: (I) leaving the residual gas and PAW in the sealed reactor; (II) leaving PAW in the open air; (III) sealing the container of PAW. In comparison, storage condition III was the best condition to preserve the long-lived species including H2O2 and HNO2/, whereas storage condition I was the best method to preserve the short-lived species including OH, HO2 and ONOOH/ONOO‑. It suggests that the gas–liquid mass transfer plays an important role in the evolution of reactive species. We also found that O2NOOH/O2NOO‑ had an almost one order of magnitude higher concentration and a longer residue time than those of ONOOH/ONOO‑. This distinction suggests that the biological effect of O2NOOH/O2NOO‑ may be important.

Maxent modeling for predicting the potential geographical distribution of two peony species under climate change.

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Zhang, Keliang; Yao, Linjun; Meng, Jiasong; Tao, Jun

2018-09-01

Paeonia (Paeoniaceae), an economically important plant genus, includes many popular ornamentals and medicinal plant species used in traditional Chinese medicine. Little is known about the properties of the habitat distribution and the important eco-environmental factors shaping the suitability. Based on high-resolution environmental data for current and future climate scenarios, we modeled the present and future suitable habitat for P. delavayi and P. rockii by Maxent, evaluated the importance of environmental factors in shaping their distribution, and identified distribution shifts under climate change scenarios. The results showed that the moderate and high suitable areas for P. delavayi and P. rockii encompassed ca. 4.46×10 5 km 2 and 1.89×10 5 km 2 , respectively. Temperature seasonality and isothermality were identified as the most critical factors shaping P. delavayi distribution, and UVB-4 and annual precipitation were identified as the most critical for shaping P. rockii distribution. Under the scenario with a low concentration of greenhouse gas emissions (RCP2.6), the range of both species increased as global warming intensified; however, under the scenario with higher concentrations of emissions (RCP8.5), the suitable habitat range of P. delavayi decreased while P. rockii increased. Overall, our prediction showed that a shift in distribution of suitable habitat to higher elevations would gradually become more significant. The information gained from this study should provide a useful reference for implementing long-term conservation and management strategies for these species. Copyright © 2018. Published by Elsevier B.V.

Controlled comparison of species- and community-level models across novel climates and communities

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Maguire, Kaitlin C.; Blois, Jessica L.; Fitzpatrick, Matthew C.; Williams, John W.; Ferrier, Simon; Lorenz, David J.

2016-01-01

Species distribution models (SDMs) assume species exist in isolation and do not influence one another's distributions, thus potentially limiting their ability to predict biodiversity patterns. Community-level models (CLMs) capitalize on species co-occurrences to fit shared environmental responses of species and communities, and therefore may result in more robust and transferable models. Here, we conduct a controlled comparison of five paired SDMs and CLMs across changing climates, using palaeoclimatic simulations and fossil-pollen records of eastern North America for the past 21 000 years. Both SDMs and CLMs performed poorly when projected to time periods that are temporally distant and climatically dissimilar from those in which they were fit; however, CLMs generally outperformed SDMs in these instances, especially when models were fit with sparse calibration datasets. Additionally, CLMs did not over-fit training data, unlike SDMs. The expected emergence of novel climates presents a major forecasting challenge for all models, but CLMs may better rise to this challenge by borrowing information from co-occurring taxa. PMID:26962143

Optimal allocation of conservation effort among subpopulations of a threatened species: how important is patch quality?

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Chauvenet, Aliénor L M; Baxter, Peter W J; McDonald-Madden, Eve; Possingham, Hugh P

2010-04-01

Money is often a limiting factor in conservation, and attempting to conserve endangered species can be costly. Consequently, a framework for optimizing fiscally constrained conservation decisions for a single species is needed. In this paper we find the optimal budget allocation among isolated subpopulations of a threatened species to minimize local extinction probability. We solve the problem using stochastic dynamic programming, derive a useful and simple alternative guideline for allocating funds, and test its performance using forward simulation. The model considers subpopulations that persist in habitat patches of differing quality, which in our model is reflected in different relationships between money invested and extinction risk. We discover that, in most cases, subpopulations that are less efficient to manage should receive more money than those that are more efficient to manage, due to higher investment needed to reduce extinction risk. Our simple investment guideline performs almost as well as the exact optimal strategy. We illustrate our approach with a case study of the management of the Sumatran tiger, Panthera tigris sumatrae, in Kerinci Seblat National Park (KSNP), Indonesia. We find that different budgets should be allocated to the separate tiger subpopulations in KSNP. The subpopulation that is not at risk of extinction does not require any management investment. Based on the combination of risks of extinction and habitat quality, the optimal allocation for these particular tiger subpopulations is an unusual case: subpopulations that occur in higher-quality habitat (more efficient to manage) should receive more funds than the remaining subpopulation that is in lower-quality habitat. Because the yearly budget allocated to the KSNP for tiger conservation is small, to guarantee the persistence of all the subpopulations that are currently under threat we need to prioritize those that are easier to save. When allocating resources among subpopulations

Solution of the spatial neutral model yields new bounds on the Amazonian species richness

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Shem-Tov, Yahav; Danino, Matan; Shnerb, Nadav M.

2017-02-01

Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with spatial structure, but the analytic results presented so far are limited to well-mixed or mainland-island scenarios. Here we combine analytic results and numerics to obtain an approximate solution for the species abundance distribution and the species richness for the neutral model on continuous landscape. We show how the regional diversity increases when the recruitment length decreases and the spatial segregation of species grows. Our results are supported by extensive numerical simulations and allow one to probe the numerically inaccessible regime of large-scale systems with extremely small mutation/speciation rates. Model predictions are compared with the findings of recent large-scale surveys of tropical trees across the Amazon basin, yielding new bounds for the species richness (between 13100 and 15000) and the number of singleton species (between 455 and 690).

Species abundance distributions in neutral models with immigration or mutation and general lifetimes.

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Lambert, Amaury

2011-07-01

We consider a general, neutral, dynamical model of biodiversity. Individuals have i.i.d. lifetime durations, which are not necessarily exponentially distributed, and each individual gives birth independently at constant rate λ. Thus, the population size is a homogeneous, binary Crump-Mode-Jagers process (which is not necessarily a Markov process). We assume that types are clonally inherited. We consider two classes of speciation models in this setting. In the immigration model, new individuals of an entirely new species singly enter the population at constant rate μ (e.g., from the mainland into the island). In the mutation model, each individual independently experiences point mutations in its germ line, at constant rate θ. We are interested in the species abundance distribution, i.e., in the numbers, denoted I(n)(k) in the immigration model and A(n)(k) in the mutation model, of species represented by k individuals, k = 1, 2, . . . , n, when there are n individuals in the total population. In the immigration model, we prove that the numbers (I(t)(k); k ≥ 1) of species represented by k individuals at time t, are independent Poisson variables with parameters as in Fisher's log-series. When conditioning on the total size of the population to equal n, this results in species abundance distributions given by Ewens' sampling formula. In particular, I(n)(k) converges as n → ∞ to a Poisson r.v. with mean γ/k, where γ : = μ/λ. In the mutation model, as n → ∞, we obtain the almost sure convergence of n (-1) A(n)(k) to a nonrandom explicit constant. In the case of a critical, linear birth-death process, this constant is given by Fisher's log-series, namely n(-1) A(n)(k) converges to α(k)/k, where α : = λ/(λ + θ). In both models, the abundances of the most abundant species are briefly discussed.

Wet thermal accumulation modeling of germination of western U.S. rangeland species

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Jennifer K. Rawlins

2009-01-01

The key to stopping high-frequency or catastrophic wildfires in the western U.S. is the successful restoration of burned lands to native plant communities. Developing models of establishment for invasive and native species will help in the selection of species for restoration projects that are able to establish and compete with invasive species given the abiotic...

To eat and not be eaten: modelling resources and safety in multi-species animal groups.

Directory of Open Access Journals (Sweden)

Umesh Srinivasan

Full Text Available Using mixed-species bird flocks as an example, we model the payoffs for two types of species from participating in multi-species animal groups. Salliers feed on mobile prey, are good sentinels and do not affect prey capture rates of gleaners; gleaners feed on prey on substrates and can enhance the prey capture rate of salliers by flushing prey, but are poor sentinels. These functional types are known from various animal taxa that form multi-species associations. We model costs and benefits of joining groups for a wide range of group compositions under varying abundances of two types of prey-prey on substrates and mobile prey. Our model predicts that gleaners and salliers show a conflict of interest in multi-species groups, because gleaners benefit from increasing numbers of salliers in the group, whereas salliers benefit from increasing gleaner numbers. The model also predicts that the limits to size and variability in composition of multi-species groups are driven by the relative abundance of different types of prey, independent of predation pressure. Our model emphasises resources as a primary driver of temporal and spatial group dynamics, rather than reproductive activity or predation per se, which have hitherto been thought to explain patterns of multi-species group formation and cohesion. The qualitative predictions of the model are supported by empirical patterns from both terrestrial and marine multi-species groups, suggesting that similar mechanisms might underlie group dynamics in a range of taxa. The model also makes novel predictions about group dynamics that can be tested using variation across space and time.

Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics.

Science.gov (United States)

Schunter, Celia; Vollmer, Steven V; Macpherson, Enrique; Pascual, Marta

2014-02-28

Social dominance is important for the reproductive success of males in many species. In the black-faced blenny (Tripterygion delaisi) during the reproductive season, some males change color and invest in nest making and defending a territory, whereas others do not change color and 'sneak' reproductions when females lay their eggs. Using RNAseq, we profiled differential gene expression between the brains of territorial males, sneaker males, and females to study the molecular signatures of male dimorphism. We found that more genes were differentially expressed between the two male phenotypes than between males and females, suggesting that during the reproductive period phenotypic plasticity is a more important factor in differential gene expression than sexual dimorphism. The territorial male overexpresses genes related to synaptic plasticity and the sneaker male overexpresses genes involved in differentiation and development. Previously suggested candidate genes for social dominance in the context of alternative mating strategies seem to be predominantly species-specific. We present a list of novel genes which are differentially expressed in Tripterygion delaisi. This is the first genome-wide study for a molecular non-model species in the context of alternative mating strategies and provides essential information for further studies investigating the molecular basis of social dominance.

Diversity-interaction modeling: estimating contributions of species identities and interactions to ecosystem function

DEFF Research Database (Denmark)

Kirwan, L; Connolly, J; Finn, J A

2009-01-01

to the roles of evenness, functional groups, and functional redundancy. These more parsimonious descriptions can be especially useful in identifying general diversity-function relationships in communities with large numbers of species. We provide an example of the application of the modeling framework......We develop a modeling framework that estimates the effects of species identity and diversity on ecosystem function and permits prediction of the diversity-function relationship across different types of community composition. Rather than just measure an overall effect of diversity, we separately....... These models describe community-level performance and thus do not require separate measurement of the performance of individual species. This flexible modeling approach can be tailored to test many hypotheses in biodiversity research and can suggest the interaction mechanisms that may be acting....

Predicting habitat suitability for rare plants at local spatial scales using a species distribution model.

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Gogol-Prokurat, Melanie

2011-01-01

If species distribution models (SDMs) can rank habitat suitability at a local scale, they may be a valuable conservation planning tool for rare, patchily distributed species. This study assessed the ability of Maxent, an SDM reported to be appropriate for modeling rare species, to rank habitat suitability at a local scale for four edaphic endemic rare plants of gabbroic soils in El Dorado County, California, and examined the effects of grain size, spatial extent, and fine-grain environmental predictors on local-scale model accuracy. Models were developed using species occurrence data mapped on public lands and were evaluated using an independent data set of presence and absence locations on surrounding lands, mimicking a typical conservation-planning scenario that prioritizes potential habitat on unsurveyed lands surrounding known occurrences. Maxent produced models that were successful at discriminating between suitable and unsuitable habitat at the local scale for all four species, and predicted habitat suitability values were proportional to likelihood of occurrence or population abundance for three of four species. Unfortunately, models with the best discrimination (i.e., AUC) were not always the most useful for ranking habitat suitability. The use of independent test data showed metrics that were valuable for evaluating which variables and model choices (e.g., grain, extent) to use in guiding habitat prioritization for conservation of these species. A goodness-of-fit test was used to determine whether habitat suitability values ranked habitat suitability on a continuous scale. If they did not, a minimum acceptable error predicted area criterion was used to determine the threshold for classifying habitat as suitable or unsuitable. I found a trade-off between model extent and the use of fine-grain environmental variables: goodness of fit was improved at larger extents, and fine-grain environmental variables improved local-scale accuracy, but fine-grain variables

Modelling planktic foraminifer growth and distribution using an ecophysiological multi-species approach

Directory of Open Access Journals (Sweden)

F. Lombard

2011-04-01

Full Text Available We present an eco-physiological model reproducing the growth of eight foraminifer species (Neogloboquadrina pachyderma, Neogloboquadrina incompta, Neogloboquadrina dutertrei, Globigerina bulloides, Globigerinoides ruber, Globigerinoides sacculifer, Globigerinella siphonifera and Orbulina universa. By using the main physiological rates of foraminifers (nutrition, respiration, symbiotic photosynthesis, this model estimates their growth as a function of temperature, light availability, and food concentration. Model parameters are directly derived or calibrated from experimental observations and only the influence of food concentration (estimated via Chlorophyll-a concentration was calibrated against field observations. Growth rates estimated from the model show positive correlation with observed abundance from plankton net data suggesting close coupling between individual growth and population abundance. This observation was used to directly estimate potential abundance from the model-derived growth. Using satellite data, the model simulate the dominant foraminifer species with a 70.5% efficiency when compared to a data set of 576 field observations worldwide. Using outputs of a biogeochemical model of the global ocean (PISCES instead of satellite images as forcing variables gives also good results, but with lower efficiency (58.9%. Compared to core tops observations, the model also correctly reproduces the relative worldwide abundance and the diversity of the eight species when using either satellite data either PISCES results. This model allows prediction of the season and water depth at which each species has its maximum abundance potential. This offers promising perspectives for both an improved quantification of paleoceanographic reconstructions and for a better understanding of the foraminiferal role in the marine carbon cycle.

Modeling for Endangered-Species Recovery: Gray Wolves in the Western Great Lakes Region

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Jean Fitts Cochrane; Robert G. Haight; Anthony M. Starfield

2003-01-01

The Federal Endangered Species Act is intended to conserve endangered and threatened species and their habitats and to improve the species' status so that they no longer need protection under the Act. In the process of planning the recovery of threatened or endangered species, the U.S. Fish and Wildlife Service increasingly uses demographic models to predict...

The role of advection in a two-species competition model

CERN Document Server

Averill, Isabel; Lou, Yuan

2017-01-01

The effects of weak and strong advection on the dynamics of reaction-diffusion models have long been studied. In contrast, the role of intermediate advection remains poorly understood. For example, concentration phenomena can occur when advection is strong, providing a mechanism for the coexistence of multiple populations, in contrast with the situation of weak advection where coexistence may not be possible. The transition of the dynamics from weak to strong advection is generally difficult to determine. In this work the authors consider a mathematical model of two competing populations in a spatially varying but temporally constant environment, where both species have the same population dynamics but different dispersal strategies: one species adopts random dispersal, while the dispersal strategy for the other species is a combination of random dispersal and advection upward along the resource gradient. For any given diffusion rates the authors consider the bifurcation diagram of positive steady states by u...

Species climate range influences hydraulic and stomatal traits in Eucalyptus species.

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Bourne, Aimee E; Creek, Danielle; Peters, Jennifer M R; Ellsworth, David S; Choat, Brendan

2017-07-01

Plant hydraulic traits influence the capacity of species to grow and survive in water-limited environments, but their comparative study at a common site has been limited. The primary aim of this study was to determine whether selective pressures on species originating in drought-prone environments constrain hydraulic traits among related species grown under common conditions. Leaf tissue water relations, xylem anatomy, stomatal behaviour and vulnerability to drought-induced embolism were measured on six Eucalyptus species growing in a common garden to determine whether these traits were related to current species climate range and to understand linkages between the traits. Hydraulically weighted xylem vessel diameter, leaf turgor loss point, the water potential at stomatal closure and vulnerability to drought-induced embolism were significantly ( P Eucalyptus trees has important implications for the limits of species responses to changing environmental conditions and thus for species survival and distribution into the future, and yields new information for physiological models. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Detection of four important Eimeria species by multiplex PCR in a single assay.

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You, Myung-Jo

2014-06-01

The oocysts of some of the recognized species of chicken coccidiosis are difficult to distinguish morphologically. Diagnostic laboratories are increasingly utilizing DNA-based technologies for the specific identification of Eimeria species. This study reports a multiplex polymerase chain reaction (PCR) assay based on internal transcribed spacer-1 (ITS-1) for the simultaneous diagnosis of the Eimeria tenella, Eimeria acervulina, Eimeria maxima, and Eimeria necatrix species, which infect domestic fowl. Primer pairs specific to each species were designed in order to generate a ladder of amplification products ranging from 20 to 25 bp, and a common optimum annealing temperature for these species was determined to be 52.5 °C. Sensitivity tests were performed for each species, showing a detection threshold of 1-5 pg. All the species were amplified homogeneously, and a homogenous band ladder was observed, indicating that the assay permitted the simultaneous detection of all the species in a single-tube reaction. In the phylogenic study, there was a clear species clustering, which was irrespective of geographical location, for all the ITS-1 sequences used. This multiplex PCR assay represents a rapid and potential cost-effective diagnostic method for the detection of some key Eimeria species that infect domestic fowl. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Moving Towards Dynamic Ocean Management: How Well Do Modeled Ocean Products Predict Species Distributions?

Directory of Open Access Journals (Sweden)

Elizabeth A. Becker

2016-02-01

Full Text Available Species distribution models are now widely used in conservation and management to predict suitable habitat for protected marine species. The primary sources of dynamic habitat data have been in situ and remotely sensed oceanic variables (both are considered “measured data”, but now ocean models can provide historical estimates and forecast predictions of relevant habitat variables such as temperature, salinity, and mixed layer depth. To assess the performance of modeled ocean data in species distribution models, we present a case study for cetaceans that compares models based on output from a data assimilative implementation of the Regional Ocean Modeling System (ROMS to those based on measured data. Specifically, we used seven years of cetacean line-transect survey data collected between 1991 and 2009 to develop predictive habitat-based models of cetacean density for 11 species in the California Current Ecosystem. Two different generalized additive models were compared: one built with a full suite of ROMS output and another built with a full suite of measured data. Model performance was assessed using the percentage of explained deviance, root mean squared error (RMSE, observed to predicted density ratios, and visual inspection of predicted and observed distributions. Predicted distribution patterns were similar for models using ROMS output and measured data, and showed good concordance between observed sightings and model predictions. Quantitative measures of predictive ability were also similar between model types, and RMSE values were almost identical. The overall demonstrated success of the ROMS-based models opens new opportunities for dynamic species management and biodiversity monitoring because ROMS output is available in near real time and can be forecast.

Modeling of the spatial distribution of ten endangered bird species in jurisdiction of Corantioquia

International Nuclear Information System (INIS)

Gomez M, Ana Maria; Alvarez, Esteban

2006-01-01

Recently, thanks to advances made in Geographic Information Systems (GIS), techniques have been developed for the construction of models that predict the spatial distribution of species and other attributes of biodiversity. These methods have allowed for the development of objective criteria that are fundamental for making decisions regarding the creation of protected areas systems throughout the world. In this research, the spatial distribution of ten endangered species of birds found within the jurisdiction of CORANTIOQUIA (JDC from here on) was modelled, using GIS techniques. The JDC was divided into 177 squares of 15 x 10 Km and the following variables were quantified within each one: presence or absence of endangered species of birds, rainfall, temperature, sun brightness, relative humidity, day duration, altitude, vegetal cover, slope and primary net productivity. With the help of logistic regression were made predictive models. Based on logistic regressions techniques predictive models were made. These models allow to explain a percentage between 24% and 80% of spatial distribution variability of these species. Those results can help in the identification of valuable zones for the biodiversity conservation. In places where there are neither the time or the economic resources to carry out exhaustive analyses of biodiversity, the models can predict the probable presence of this endangered species

On the well posedness and further regularity of a diffusive three species aquatic model

KAUST Repository

Parshad, R.D.; Upadhyay, R.K.; Thakur, N.K.

2012-01-01

We consider Upadhay's three species aquatic food chain model, with the inclusion of spatial spread. This is a well established food chain model for the interaction of three given aquatic species. It exhibits rich dynamical behavior, including chaos

Quantifying the Relative Importance of Climate and Habitat on Structuring the Species and Taxonomic Diversity of Aquatic Plants in a Biodiversity Hotspot of Tropical Asia

International Nuclear Information System (INIS)

Chen, Y.

2015-01-01

It has not been well known how climate and habitat variables will influence the distribution of plant species to some extents at mesoscale. In this report, by using the distribution of aquatic plants in Western Ghats, a biodiversity hotspot in tropical Asian region, I quantify the relative importance of climate and habitat variables on structuring spatially species richness and taxonomic diversity patterns using structural equation modeling. All the sampling qudrats in the region used for the study has a spatial resolution of 0.5 latitude x 0.5 longitude. The results showed that species richness is high in both northern and southern part of the region, while low in the middle part. In contrast, taxonomic distinctiveness is relatively homogeneous over all the sampling quadrats in the region. Structural equation modeling suggested that taxonomic distinctiveness patterns of aquatic plants in the region follow temperature (partial regression coefficient=0.31, p<0.05) and elevational (partial regression coefficient=0.31, p<0.05) gradients, while richness patterns cannot be explained by any of the currently used variables. In conclusion, environmental variables that are related to taxonomic distinctiveness would not be related to richness, given the fact that these two quantities are orthogonal more or less. Both climate and habitat are equally influential on taxonomic distinctiveness patterns for aquatic plants in Western Ghats of India. (author)

Scenario-Led Habitat Modelling of Land Use Change Impacts on Key Species.

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Matthew Geary

Full Text Available Accurate predictions of the impacts of future land use change on species of conservation concern can help to inform policy-makers and improve conservation measures. If predictions are spatially explicit, predicted consequences of likely land use changes could be accessible to land managers at a scale relevant to their working landscape. We introduce a method, based on open source software, which integrates habitat suitability modelling with scenario-building, and illustrate its use by investigating the effects of alternative land use change scenarios on landscape suitability for black grouse Tetrao tetrix. Expert opinion was used to construct five near-future (twenty years scenarios for the 800 km2 study site in upland Scotland. For each scenario, the cover of different land use types was altered by 5-30% from 20 random starting locations and changes in habitat suitability assessed by projecting a MaxEnt suitability model onto each simulated landscape. A scenario converting grazed land to moorland and open forestry was the most beneficial for black grouse, and 'increased grazing' (the opposite conversion the most detrimental. Positioning of new landscape blocks was shown to be important in some situations. Increasing the area of open-canopy forestry caused a proportional decrease in suitability, but suitability gains for the 'reduced grazing' scenario were nonlinear. 'Scenario-led' landscape simulation models can be applied in assessments of the impacts of land use change both on individual species and also on diversity and community measures, or ecosystem services. A next step would be to include landscape configuration more explicitly in the simulation models, both to make them more realistic, and to examine the effects of habitat placement more thoroughly. In this example, the recommended policy would be incentives on grazing reduction to benefit black grouse.

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia.

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DeBiasse, Melissa B; Hellberg, Michael E

2015-02-01

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.

The importance of education in managing invasive plant species

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Invasive plant species can establish in diverse environments and with the increase in human mobility, they are no longer restricted to isolated pockets in remote parts of the world. Cheat grass (Bromus tectorum L.) in rangelands, purple loosestrife (Lythrum salicaria L.) in wet lands and Canada this...

Identification of Shewanella baltica as the most important H2S-producing species during iced storage of danish marine fish

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Vogel, Birte Fonnesbech; Venkateswaran, K.; Satomi, M.

2005-01-01

are important in fish spoilage. More than 500 H2S-producing strains were isolated from iced stored marine fish (cod, plaice, and flounder) caught in the Baltic Sea during winter or summer time. All strains were identified as Shewanella species by phenotypic tests. Different Shewanella species were present...... unchanged (i.e., trimethylamine-N-oxide reduction and H2S production); however, the main H2S-producing organism was identified as S. baltica....

On the reasons that natural regeneration is important for species coexistence in tropical forests

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Natalia Norden

2014-12-01

Full Text Available Plant regeneration plays a critical role in the maintenance of species diversity in tropical rainforests. This is a multistage process, including seed production, dispersal, germination and subsequent seedling establishment. All these stages represent major bottlenecks in plant demography, as early stages in the plant cycle (seeds and seedlings are the most vulnerable to environmental hazards, and are therefore subject to high mortality risks. The outcome of these ecological filters will determine not only seedling spatial distribution, but also the potential area of tree distribution. Seed dispersal and subsequent seedling establishment therefore play a critical role in the structuring of tree communities. Here, I review the main four ecological processes driving seedling recruitment in tropical forests. First, dispersal limitation is the failure of seeds to reach suitable microsites for seedling establishment. Once this filter is overcome, environmental factors can considerably affect seedling spatial distribution. Temporal fluctuations in these processes result in an important variation in recruitment success over time, and add a stochastic component to seedling regeneration. Finally, negative-density dependence regulates species relative abundance in the seedling layer by limiting conspecific recruitment through the attack of pathogen, fungi and herbivores.

Assessment of traditional ecological knowledge and beliefs in the utilisation of important plant species: The case of Buhanga sacred forest, Rwanda

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Runyambo Irakiza

2016-07-01

Full Text Available Traditional ecological knowledge is an integrated part of the African people and indeed the Rwandese for cultural purpose. Buhanga sacred forest is a relict forest of tremendous ecological importance to Rwandan society located in Musanze District. The aim of this study was to assess the traditional ecological knowledge and belief in the utilisation of some important plant species for the conservation of Buhanga sacred forest. Ecological information about ethnomedicinal and traditional practices were collected following structured questionnaire through interview involving eight traditional healers and three focus group discussions. Data were collected from the natural habitats, home gardens, farmlands and roadsides of Buhanga sacred forest. A total of 45 botanical taxa belonging to 28 families were reported to be used by the local community. Species such as Brillantaisia cicatricosa and Senna septemtrionalis were the popular species cited by traditional healers to treat human and animal diseases and ailments, respectively. The results of the study indicated that because of the cultural norms and values associated with the sacred forest, this has led to non-exploitation. The study presents key sites and plant species in which their use and belief can lead to their conservation. However, not only is it imperative to conserve traditional local knowledge for biocultural conservation motives but there is also need to train traditional healers on how to domesticate indigenous species as conservation measure because some species have become susceptible to extinction. Conservation implications: Highlighting indigenous species investigated in this research will provide a powerful tool for ensuring biodiversity conservation through community participation in a country of high population density in Africa. Some plant species that provided satisfactory Local Health Traditions among communities surrounding Buhanga can contribute as good material for further

Development of a laboratory model of a phototroph-heterotroph mixed-species biofilm at the stone/air interface

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Federica eVilla

2015-11-01

Full Text Available Recent scientific investigations have shed light on the ecological importance and physiological complexity of subaerial biofilms (SABs inhabiting lithic surfaces. In the field of sustainable cultural heritage (CH preservation, mechanistic approaches aimed at investigation of the spatiotemporal patterns of interactions between the biofilm, the stone, and the atmosphere are of outstanding importance. However, these interactions have proven difficult to explore with field experiments due to the inaccessibility of samples, the complexity of the ecosystem under investigation and the temporal resolution of the experiments.To overcome these limitations, we aimed at developing a unifying methodology to reproduce a fast-growing, phototroph-heterotroph mixed species biofilm at the stone/air interface. Our experiments underscore the ability of the dual-species SAB model to capture functional traits characteristic of biofilms inhabiting lithic substrate such as: i microcolonies of aggregated bacteria; ii network like structure following surface topography; iii cooperation between phototrophs and heterotrophs and cross feeding processes; iv ability to change the chemical parameters that characterize the microhabitats; v survival under desiccation and vi biocide tolerance. With its advantages in control, replication, range of different experimental scenarios and matches with the real ecosystem, the developed model system is a powerful tool to advance our mechanistic understanding of the stone-biofilm-atmosphere interplay in different environments.

High Resolution Habitat Suitability Modelling For Restricted-Range Hawaiian Alpine Arthropod Species

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Stephenson, N. M.

2016-12-01

Mapping potentially suitable habitat is critical for effective species conservation and management but can be challenging in areas exhibiting complex heterogeneity. An approach that combines non-intrusive spatial data collection techniques and field data can lead to a better understanding of landscapes and species distributions. Nysius wekiuicola, commonly known as the wēkiu bug, is the most studied arthropod species endemic to the Maunakea summit in Hawai`i, yet details about its geographic distribution and habitat use remain poorly understood. To predict the geographic distribution of N. wekiuicola, MaxEnt habitat suitability models were generated from a diverse set of input variables, including fifteen years of species occurrence data, high resolution digital elevation models, surface mineralogy maps derived from hyperspectral remote sensing, and climate data. Model results indicate that elevation (78.2 percent), and the presence of nanocrystalline hematite surface minerals (13.7 percent) had the highest influence, with lesser contributions from aspect, slope, and other surface mineral classes. Climatic variables were not included in the final analysis due to auto-correlation and coarse spatial resolution. Biotic factors relating to predation and competition also likely dictate wēkiu bug capture patterns and influence our results. The wēkiu bug range and habitat suitability models generated as a result of this study will be directly incorporated into management and restoration goals for the summit region and can also be adapted for other arthropod species present, leading to a more holistic understanding of metacommunity dynamics. Key words: Microhabitat, Structure from Motion, Lidar, MaxEnt, Habitat Suitability

Predicting geographic distributions of Phacellodomus species (Aves: Furnariidae in South America based on ecological niche modeling

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Maria da Salete Gurgel Costa

2014-08-01

Full Text Available Phacellodomus Reichenbach, 1853, comprises nine species of Furnariids that occur in South America in open and generally dry areas. This study estimated the geographic distributions of Phacellodomus species in South America by ecological niche modeling. Applying maximum entropy method, models were produced for eight species based on six climatic variables and 949 occurrence records. Since highest climatic suitability for Phacellodomus species has been estimated in open and dry areas, the Amazon rainforest areas are not very suitable for these species. Annual precipitation and minimum temperature of the coldest month are the variables that most influence the models. Phacellodomus species occurred in 35 ecoregions of South America. Chaco and Uruguayan savannas were the ecoregions with the highest number of species. Despite the overall connection of Phacellodomus species with dry areas, species such as P. ruber, P. rufifrons, P. ferrugineigula and P. erythrophthalmus occurred in wet forests and wetland ecoregions.

Determining Predictor Importance in Hierarchical Linear Models Using Dominance Analysis

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Luo, Wen; Azen, Razia

2013-01-01

Dominance analysis (DA) is a method used to evaluate the relative importance of predictors that was originally proposed for linear regression models. This article proposes an extension of DA that allows researchers to determine the relative importance of predictors in hierarchical linear models (HLM). Commonly used measures of model adequacy in…

Tree Species Abundance Predictions in a Tropical Agricultural Landscape with a Supervised Classification Model and Imbalanced Data

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Sarah J. Graves

2016-02-01

Full Text Available Mapping species through classification of imaging spectroscopy data is facilitating research to understand tree species distributions at increasingly greater spatial scales. Classification requires a dataset of field observations matched to the image, which will often reflect natural species distributions, resulting in an imbalanced dataset with many samples for common species and few samples for less common species. Despite the high prevalence of imbalanced datasets in multiclass species predictions, the effect on species prediction accuracy and landscape species abundance has not yet been quantified. First, we trained and assessed the accuracy of a support vector machine (SVM model with a highly imbalanced dataset of 20 tropical species and one mixed-species class of 24 species identified in a hyperspectral image mosaic (350–2500 nm of Panamanian farmland and secondary forest fragments. The model, with an overall accuracy of 62% ± 2.3% and F-score of 59% ± 2.7%, was applied to the full image mosaic (23,000 ha at a 2-m resolution to produce a species prediction map, which suggested that this tropical agricultural landscape is more diverse than what has been presented in field-based studies. Second, we quantified the effect of class imbalance on model accuracy. Model assessment showed a trend where species with more samples were consistently over predicted while species with fewer samples were under predicted. Standardizing sample size reduced model accuracy, but also reduced the level of species over- and under-prediction. This study advances operational species mapping of diverse tropical landscapes by detailing the effect of imbalanced data on classification accuracy and providing estimates of tree species abundance in an agricultural landscape. Species maps using data and methods presented here can be used in landscape analyses of species distributions to understand human or environmental effects, in addition to focusing conservation

Species Distribution Modelling of Aedes aegypti in two dengue-endemic regions of Pakistan.

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Fatima, Syeda Hira; Atif, Salman; Rasheed, Syed Basit; Zaidi, Farrah; Hussain, Ejaz

2016-03-01

Statistical tools are effectively used to determine the distribution of mosquitoes and to make ecological inferences about the vector-borne disease dynamics. In this study, we utilised species distribution models to understand spatial patterns of Aedes aegypti in two dengue-prevalent regions of Pakistan, Lahore and Swat. Species distribution models can potentially indicate the probability of suitability of Ae. aegypti once introduced to new regions like Swat, where invasion of this species is a recent phenomenon. The distribution of Ae. aegypti was determined by applying the MaxEnt algorithm on a set of potential environmental factors and species sample records. The ecological dependency of species on each environmental variable was analysed using response curves. We quantified the statistical performance of the models based on accuracy assessment and spatial predictions. Our results suggest that Ae. aegypti is widely distributed in Lahore. Human population density and urban infrastructure are primarily responsible for greater probability of mosquito occurrence in this region. In Swat, Ae. aegypti has clumped distribution, where urban patches provide refuge to the species in an otherwise hostile heterogeneous environment and road networks are assumed to have facilitated in passive-mediated dispersal of species. In Pakistan, Ae. aegypti is expanding its range northwards; this could be associated with rapid urbanisation, trade and travel. The main implication of this expansion is that more people are at risk of dengue fever in the northern highlands of Pakistan. © 2016 John Wiley & Sons Ltd.

The predictive skill of species distribution models for plankton in a changing climate

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Brun, Philipp Georg; Kiørboe, Thomas; Licandro, Priscilla

2016-01-01

Statistical species distribution models (SDMs) are increasingly used to project spatial relocations of marine taxa under future climate change scenarios. However, tests of their predictive skill in the real-world are rare. Here, we use data from the Continuous Plankton Recorder program, one...... null models, is essential to assess the robustness of projections of marine planktonic species under climate change...

Reranking candidate gene models with cross-species comparison for improved gene prediction

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Pereira Fernando CN

2008-10-01

Full Text Available Abstract Background Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc. Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.

Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

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Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

2016-01-01

Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

Detecting biodiversity hotspots by species-area relationships: a case study of Mediterranean beetles.

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Fattorini, Simone

2006-08-01

Any method of identifying hotspots should take into account the effect of area on species richness. I examined the importance of the species-area relationship in determining tenebrionid (Coleoptera: Tenebrionidae) hotspots on the Aegean Islands (Greece). Thirty-two islands and 170 taxa (species and subspecies) were included in this study. I tested several species-area relationship models with linear and nonlinear regressions, including power exponential, negative exponential, logistic, Gompertz, Weibull, Lomolino, and He-Legendre functions. Islands with positive residuals were identified as hotspots. I also analyzed the values of the C parameter of the power function and the simple species-area ratios. Species richness was significantly correlated with island area for all models. The power function model was the most convenient one. Most functions, however identified certain islands as hotspots. The importance of endemics in insular biotas should be evaluated carefully because they are of high conservation concern. The simple use of the species-area relationship can be problematic when areas with no endemics are included. Therefore the importance of endemics should be evaluated according to different methods, such as percentages, to take into account different levels of endemism and different kinds of "endemics" (e.g., endemic to single islands vs. endemic to the archipelago). Because the species-area relationship is a key pattern in ecology, my findings can be applied at broader scales.

Metapopulation modelling of riparian tree species persistence in river networks under climate change.

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Van Looy, Kris; Piffady, Jérémy

2017-11-01

Floodplain landscapes are highly fragmented by river regulation resulting in habitat degradation and flood regime perturbation, posing risks to population persistence. Climate change is expected to pose supplementary risks in this context of fragmented landscapes, and especially for river systems adaptation management programs are developed. The association of habitat quality and quantity with the landscape dynamics and resilience to human-induced disturbances is still poorly understood in the context of species survival and colonization processes, but essential to prioritize conservation and restoration actions. We present a modelling approach that elucidates network connectivity and landscape dynamics in spatial and temporal context to identify vital corridors and conservation priorities in the Loire river and its tributaries. Alteration of flooding and flow regimes is believed to be critical to population dynamics in river ecosystems. Still, little is known of critical levels of alteration both spatially and temporally. We applied metapopulation modelling approaches for a dispersal-limited tree species, white elm; and a recruitment-limited tree species, black poplar. In different model steps the connectivity and natural dynamics of the river landscape are confronted with physical alterations (dams/dykes) to species survival and then future scenarios for climatic changes and potential adaptation measures are entered in the model and translated in population persistence over the river basin. For the two tree species we highlighted crucial network zones in relation to habitat quality and connectivity. Where the human impact model already shows currently restricted metapopulation development, climate change is projected to aggravate this persistence perspective substantially. For both species a significant drawback to the basin population is observed, with 1/3 for elm and ¼ for poplar after 25 years already. But proposed adaptation measures prove effective to even

Identification of cultured isolates of clinically important yeast species using fluorescent fragment length analysis of the amplified internally transcribed rRNA spacer 2 region

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Muylaert An

2002-07-01

Full Text Available Abstract Background The number of patients with yeast infection has increased during the last years. Also the variety of species of clinical importance has increased. Correct species identification is often important for efficient therapy, but is currently mostly based on phenotypic features and is sometimes time-consuming and depends largely on the expertise of technicians. Therefore, we evaluated the feasibility of PCR-based amplification of the internally transcribed spacer region 2 (ITS2, followed by fragment size analysis on the ABI Prism 310 for the identification of clinically important yeasts. Results A rapid DNA-extraction method, based on simple boiling-freezing was introduced. Of the 26 species tested, 22 could be identified unambiguously by scoring the length of the ITS2-region. No distinction could be made between the species Trichosporon asteroides and T. inkin or between T. mucoides and T. ovoides. The two varieties of Cryptococcus neoformans (var. neoformans and var. gattii could be differentiated from each other due to a one bp length difference of the ITS2 fragment. The three Cryptococcus laurentii isolates were split into two groups according to their ITS2-fragment lengths, in correspondence with the phylogenetic groups described previously. Since the obtained fragment lengths compare well to those described previously and could be exchanged between two laboratories, an internationally usable library of ITS2 fragment lengths can be constructed. Conclusions The existing ITS2 size based library enables identification of most of the clinically important yeast species within 6 hours starting from a single colony and can be easily updated when new species are described. Data can be exchanged between laboratories.