Science.gov

Sample records for abundant molecular species

  1. Molecular abundances and low-mass star formation. 1: Si- and S-bearing species toward IRAS 16293-2422

    NASA Technical Reports Server (NTRS)

    Blake, Geoffrey A.; Dishoek, Ewine F. Van; Jansen, David J.; Groesbeck, T. D.; Mundy, Lee G.

    1994-01-01

    Results from millimeter and submillimeter spectral line surveys of the protobinary source Infrared Astronomical Satellite (IRAS) 16293-2422 are presented. Here we outline the abundances of silicon- and sulfur-containing species. A combination of rotation diagram and full statistical equilibrium/radiative transfer calculations is used to constrain the physical conditions toward IRAS 16293 and to construct its beam-averaged chemical composition over a 10 to 20 sec (1600 to 3200 AU) scale. The chemical complexity as judged by species such as SiO, OCS, and H2S, is intermediate between that of dark molecular clouds such as L134N and hot molecular cloud cores such as Orion KL. From the richness of the spectra compared to other young stellar objects of similar luminosity, it is clear that molecular abundances do not scale simply with mass; rather, the chemistry is a strong function of evolutionary state, i.e., age.

  2. Molecular determination of abundance of infection with Sarcocystis species in slaughtered sheep of Urmia, Iran

    PubMed Central

    Farhang-Pajuh, Farhad; Yakhchali, Mohammad; Mardani, Karim

    2014-01-01

    Sarcocystis is one of the most prevalent parasites of domestic ruminants worldwide. This study was aimed to determine prevalence of Sarcocystis infection and molecular discrimination of Sarcocystis gigantea and Sarcocystis medusiformis infecting domestic sheep. Tissue samples from 638 sheep slaughtered at Urmia abattoir were randomly collected from February 2011 to January 2012. Genomic DNA extraction and polymerase chain reaction (PCR) was performed to amplify a 964 bp fragment of nuclear 18S rRNA gene. The PCR products were subjected to digestion with endonuclease MboII and/or MvaI for discriminating S. medusiformis and S. gigantea. Results indicated that the overall prevalence of Sarcocystis unspecified species was 36.83% (235/638) in which male (7.63%, 38/498) and female (35.00%, 49/140) sheep over 4 years-old had the highest prevalence. There was no significant difference between prevalence of macrosarcocysts and sex. Two macrosarcocysts forms were found as fat (27.90%, 178/638) and thin (8.93%, 57/638) in striated muscles. There was significant difference between frequency of macrosarcocysts and body distribution. Mixed infection with both fat and thin macrosarcocysts was also found in 11.13% (71/638) of infected sheep. There was no significant difference regarding the prevalence of mixed infection in both age classes. The PCR-RFLP patterns showed that fat sarcocysts were S. gigantea (29.31%, 187/638) and thin sarcocysts were S. medusiformis (7.52%, 48/638). It was concluded that ovine Sarcocystis infection was prevalent in Urmia and a combination of conventional methods and molecular study for sheep sarcocysts could be informative. PMID:25568716

  3. Molecular determination of abundance of infection with Sarcocystis species in slaughtered sheep of Urmia, Iran.

    PubMed

    Farhang-Pajuh, Farhad; Yakhchali, Mohammad; Mardani, Karim

    2014-01-01

    Sarcocystis is one of the most prevalent parasites of domestic ruminants worldwide. This study was aimed to determine prevalence of Sarcocystis infection and molecular discrimination of Sarcocystis gigantea and Sarcocystis medusiformis infecting domestic sheep. Tissue samples from 638 sheep slaughtered at Urmia abattoir were randomly collected from February 2011 to January 2012. Genomic DNA extraction and polymerase chain reaction (PCR) was performed to amplify a 964 bp fragment of nuclear 18S rRNA gene. The PCR products were subjected to digestion with endonuclease MboII and/or MvaI for discriminating S. medusiformis and S. gigantea. Results indicated that the overall prevalence of Sarcocystis unspecified species was 36.83% (235/638) in which male (7.63%, 38/498) and female (35.00%, 49/140) sheep over 4 years-old had the highest prevalence. There was no significant difference between prevalence of macrosarcocysts and sex. Two macrosarcocysts forms were found as fat (27.90%, 178/638) and thin (8.93%, 57/638) in striated muscles. There was significant difference between frequency of macrosarcocysts and body distribution. Mixed infection with both fat and thin macrosarcocysts was also found in 11.13% (71/638) of infected sheep. There was no significant difference regarding the prevalence of mixed infection in both age classes. The PCR-RFLP patterns showed that fat sarcocysts were S. gigantea (29.31%, 187/638) and thin sarcocysts were S. medusiformis (7.52%, 48/638). It was concluded that ovine Sarcocystis infection was prevalent in Urmia and a combination of conventional methods and molecular study for sheep sarcocysts could be informative. PMID:25568716

  4. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications.

    PubMed

    Gu, W; Crawford, E D; O'Donovan, B D; Wilson, M R; Chow, E D; Retallack, H; DeRisi, J L

    2016-03-04

    Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost.

  5. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications.

    PubMed

    Gu, W; Crawford, E D; O'Donovan, B D; Wilson, M R; Chow, E D; Retallack, H; DeRisi, J L

    2016-01-01

    Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost. PMID:26944702

  6. Molecular Abundances in CRL 618

    NASA Astrophysics Data System (ADS)

    Pardo, Juan R.; Cernicharo, José

    2007-01-01

    In previous works we have modeled the different gas regions of the proto-planetary nebula CRL 618 by studying the large number of lines from the cyanopolyynes detected in a millimeter-wave line survey of this object. In this work we retrieve the rotational temperatures (Tr) and abundance ratios R with respect to HC3N (used as reference) for all molecular species detected in the survey by running grids of models in the (R,Tr) space to find the minimum of a weighted χ2 defined for this analysis. This provides the best knowledge to date of the (polar) molecular composition of CRL 618 thanks to the uniform calibration of the whole survey and the large number of lines available from each species, allowing comparisons with predictions made by chemical models of C-rich post-AGB objects. A significantly lower value of the 12C/13C ratio has been revealed in the gas closest to central star with respect to the colder and outer envelope. It can be due to 13C-rich material, produced in a late CNO cycling occurred in the central star, being currently injected into this inner gas envelope.

  7. Molecular identification and relative abundance of cryptic Lophodermium species in natural populations of Scots pine, Pinus sylvestris L.

    PubMed

    Reignoux, Sabrina N A; Green, Sarah; Ennos, Richard A

    2014-01-01

    The multi-locus phylogenetic species recognition approach and population genetic analysis of Amplified Fragment Length Polymorphism (AFLP) markers were used to delineate Lophodermium taxa inhabiting needles of Scots pine (Pinus sylvestris) in native pinewoods within Scotland. These analyses revealed three major lineages corresponding to the morphological species Lophodermium seditiosum and Lophodermium conigenum, fruiting on broken branches, and Lophodermium pinastri, fruiting on naturally fallen needles. Within L. pinastri three well supported sister clades were found representing cryptic taxa designated L. pinastri I, L. pinastri II, and L. pinastri III. Significant differences in mean growth rate in culture were found among the cryptic taxa. Taxon-specific primers based on ITS sequences were designed and used to classify over 500 Lophodermium isolates, derived from fallen needles of P. sylvestris in three Scottish and one French pinewood site, into the three L. pinastri cryptic taxa. Highly significant differences in the relative abundance of the three taxa were found among the Scottish pinewood sites, and between the French and all of the Scottish sites.

  8. Molecular and microscopic analysis of the gut contents of abundant rove beetle species (Coleoptera, Staphylinidae) in the boreal balsam fir forest of Quebec, Canada

    PubMed Central

    Klimaszewski, Jan; Morency, Marie-Josee; Labrie, Philippe; Séguin, Armand; Langor, David; Work, Timothy; Bourdon, Caroline; Thiffault, Evelyne; Paré, David; Newton, Alfred F.; Thayer, Margaret K.

    2013-01-01

    Abstract Experimental research on beetle responses to removal of logging residues following clearcut harvesting in the boreal balsam fir forest of Quebec revealed several abundant rove beetle (Staphylinidae) species potentially important for long-term monitoring. To understand the trophic affiliations of these species in forest ecosystems, it was necessary to analyze their gut contents. We used microscopic and molecular (DNA) methods to identify the gut contents of the following rove beetles: Atheta capsularis Klimaszewski, Atheta klagesi Bernhauer, Oxypoda grandipennis (Casey), Bryophacis smetanai Campbell, Ischnosoma longicorne (Mäklin), Mycetoporus montanus Luze, Tachinus frigidus Erichson, Tachinus fumipennis (Say), Tachinus quebecensis Robert, and Pseudopsis subulata Herman. We found no apparent arthropod fragments within the guts; however, a number of fungi were identified by DNA sequences, including filamentous fungi and budding yeasts [Ascomycota: Candida derodonti Suh & Blackwell (accession number FJ623605), Candida mesenterica (Geiger) Diddens & Lodder (accession number FM178362), Candida railenensis Ramirez and Gonzáles (accession number JX455763), Candida sophie-reginae Ramirez & González (accession number HQ652073), Candida sp. (accession number AY498864), Pichia delftensis Beech (accession number AY923246), Pichia membranifaciens Hansen (accession number JQ26345), Pichia misumaiensis Y. Sasaki and Tak. Yoshida ex Kurtzman 2000 (accession number U73581), Pichia sp. (accession number AM261630), Cladosporium sp. (accession number KF367501), Acremoniumpsammosporum W. Gams (accession number GU566287), Alternaria sp. (accession number GU584946), Aspergillus versicolor Bubak (accession number AJ937750), and Aspergillusamstelodami (L. Mangin) Thom and Church (accession number HQ728257)]. In addition, two species of bacteria [Bradyrhizobium japonicum (Kirchner) Jordan (accession number BA000040) and Serratia marcescens Bizio accession number CP003942] were

  9. Clonal growth and plant species abundance

    PubMed Central

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  10. Species Abundance Patterns in Complex Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Tokita, Kei

    2004-10-01

    An analytic theory of species abundance patterns (SAPs) in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka-Volterra equation, with diverse interspecies interactions. Various SAPs observed in nature are derived from a single parameter. The abundance distribution is formed like a widely observed left-skewed lognormal distribution. As the model has a general form, the result can be applied to similar patterns in other complex biological networks, e.g., gene expression.

  11. How selection structures species abundance distributions

    PubMed Central

    Magurran, Anne E.; Henderson, Peter A.

    2012-01-01

    How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species. PMID:22787020

  12. Attenuation of species abundance distributions by sampling.

    PubMed

    Shimadzu, Hideyasu; Darnell, Ross

    2015-04-01

    Quantifying biodiversity aspects such as species presence/ absence, richness and abundance is an important challenge to answer scientific and resource management questions. In practice, biodiversity can only be assessed from biological material taken by surveys, a difficult task given limited time and resources. A type of random sampling, or often called sub-sampling, is a commonly used technique to reduce the amount of time and effort for investigating large quantities of biological samples. However, it is not immediately clear how (sub-)sampling affects the estimate of biodiversity aspects from a quantitative perspective. This paper specifies the effect of (sub-)sampling as attenuation of the species abundance distribution (SAD), and articulates how the sampling bias is induced to the SAD by random sampling. The framework presented also reveals some confusion in previous theoretical studies. PMID:26064626

  13. Attenuation of species abundance distributions by sampling

    PubMed Central

    Shimadzu, Hideyasu; Darnell, Ross

    2015-01-01

    Quantifying biodiversity aspects such as species presence/ absence, richness and abundance is an important challenge to answer scientific and resource management questions. In practice, biodiversity can only be assessed from biological material taken by surveys, a difficult task given limited time and resources. A type of random sampling, or often called sub-sampling, is a commonly used technique to reduce the amount of time and effort for investigating large quantities of biological samples. However, it is not immediately clear how (sub-)sampling affects the estimate of biodiversity aspects from a quantitative perspective. This paper specifies the effect of (sub-)sampling as attenuation of the species abundance distribution (SAD), and articulates how the sampling bias is induced to the SAD by random sampling. The framework presented also reveals some confusion in previous theoretical studies. PMID:26064626

  14. Abundance of introduced species at home predicts abundance away in herbaceous communities

    USGS Publications Warehouse

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  15. Molecular abundances in the Sagittarius A molecular cloud.

    PubMed

    Minh, Y C; Irvine, W M; Friberg, P

    1992-01-01

    We have obtained column densities for HCO+, HCO, HCS+, C3H2, HC5N, SiO, OCS, HCOOH, CH3CH2OH, and CH3CCH toward Sgr A. The fractional abundance of SiO relative to molecular hydrogen in Sgr A is comparable to that for the Orion plateau, approximately 10(-7)-10(-8), which may be a typical value for hot clouds. The abundances of HCO, CH3CH2OH and CH3CCH all appear to be enhanced relative to other molecular clouds such as Sgr B2.

  16. Modeling species-abundance relationships in multi-species collections

    USGS Publications Warehouse

    Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

    2003-01-01

    Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

  17. Abundance anomaly of the 13C species of CCH

    NASA Astrophysics Data System (ADS)

    Sakai, N.; Saruwatari, O.; Sakai, T.; Takano, S.; Yamamoto, S.

    2010-03-01

    Aims: We have observed the N = 1-0 lines of CCH and its 13C isotopic species toward a cold dark cloud, TMC-1 and a star-forming region, L1527, to investigate the 13C abundances and formation pathways of CCH. Methods: The observations have been carried out with the IRAM 30 m telescope. Results: We have successfully detected the lines of 13CCH and C13CH toward the both sources and found a significant intensity difference between the two 13C isotopic species. The [C13CH] /[13CCH] abundance ratios are 1.6 ± 0.4 (3σ) and 1.6 ± 0.1 (3σ) for TMC-1 and L1527, respectively. The abundance difference between C13CH and 13CCH means that the two carbon atoms of CCH are not equivalent in the formation pathway. On the other hand, the [CCH]/[C13CH] and [CCH]/[13CCH] ratios are evaluated to be larger than 170 and 250 toward TMC-1, and to be larger than 80 and 135 toward L1527, respectively. Therefore, both of the 13C species are significantly diluted in comparison with the interstellar 12C/13C ratio of 60. The dilution is discussed in terms of a behavior of 13C in molecular clouds.

  18. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  19. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE - 2014

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  20. Ecological niche structure and rangewide abundance patterns of species.

    PubMed

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A Townsend; Yáñez-Arenas, Carlos

    2013-02-23

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance-ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

  1. Geographical Range and Local Abundance of Tree Species in China

    PubMed Central

    Ren, Haibao; Condit, Richard; Chen, Bin; Mi, Xiangcheng; Cao, Min; Ye, Wanhui; Hao, Zhanqing; Ma, Keping

    2013-01-01

    Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1) whether locally abundant species tend to be geographically widespread; 2) whether species are more abundant towards their range-centers; and 3) how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20–25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km2, and >90% of 651 species had ranges >105 km2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species’ abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges. PMID:24130772

  2. Model reduction for stochastic chemical systems with abundant species.

    PubMed

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  3. Model reduction for stochastic chemical systems with abundant species

    SciTech Connect

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-07

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  4. Model reduction for stochastic chemical systems with abundant species

    NASA Astrophysics Data System (ADS)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  5. Ecological niche structure and rangewide abundance patterns of species

    PubMed Central

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos

    2013-01-01

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

  6. Why abundant tropical tree species are phylogenetically old

    PubMed Central

    Wang, Shaopeng; Chen, Anping; Fang, Jingyun; Pacala, Stephen W.

    2013-01-01

    Neutral models of species diversity predict patterns of abundance for communities in which all individuals are ecologically equivalent. These models were originally developed for Panamanian trees and successfully reproduce observed distributions of abundance. Neutral models also make macroevolutionary predictions that have rarely been evaluated or tested. Here we show that neutral models predict a humped or flat relationship between species age and population size. In contrast, ages and abundances of tree species in the Panamanian Canal watershed are found to be positively correlated, which falsifies the models. Speciation rates vary among phylogenetic lineages and are partially heritable from mother to daughter species. Variable speciation rates in an otherwise neutral model lead to a demographic advantage for species with low speciation rate. This demographic advantage results in a positive correlation between species age and abundance, as found in the Panamanian tropical forest community. PMID:24043767

  7. Why abundant tropical tree species are phylogenetically old.

    PubMed

    Wang, Shaopeng; Chen, Anping; Fang, Jingyun; Pacala, Stephen W

    2013-10-01

    Neutral models of species diversity predict patterns of abundance for communities in which all individuals are ecologically equivalent. These models were originally developed for Panamanian trees and successfully reproduce observed distributions of abundance. Neutral models also make macroevolutionary predictions that have rarely been evaluated or tested. Here we show that neutral models predict a humped or flat relationship between species age and population size. In contrast, ages and abundances of tree species in the Panamanian Canal watershed are found to be positively correlated, which falsifies the models. Speciation rates vary among phylogenetic lineages and are partially heritable from mother to daughter species. Variable speciation rates in an otherwise neutral model lead to a demographic advantage for species with low speciation rate. This demographic advantage results in a positive correlation between species age and abundance, as found in the Panamanian tropical forest community. PMID:24043767

  8. Multiple peaks of species abundance distributions induced by sparse interactions.

    PubMed

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-08-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction u, we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of u below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all species coexistence and multiple peaks in the species abundance distributions. PMID:27627322

  9. Multiple peaks of species abundance distributions induced by sparse interactions

    NASA Astrophysics Data System (ADS)

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-08-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction u , we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of u below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all species coexistence and multiple peaks in the species abundance distributions.

  10. Percolation Theory for the Distribution and Abundance of Species

    NASA Astrophysics Data System (ADS)

    He, Fangliang; Hubbell, Stephen P.

    2003-11-01

    We develop and test new models that unify the mathematical relationships among the abundance of a species, the spatial dispersion of the species, the number of patches occupied by the species, the edge length of the occupied patches, and the scale on which the distribution of species is mapped. The models predict that species distributions will exhibit percolation critical thresholds, i.e., critical population abundances at which the fragmented patches (as measured by the number of patches and edge length) start to coalesce to form large patches.

  11. Diversity is maintained by seasonal variation in species abundance

    PubMed Central

    2013-01-01

    Background Some of the most marked temporal fluctuations in species abundances are linked to seasons. In theory, multispecies assemblages can persist if species use shared resources at different times, thereby minimizing interspecific competition. However, there is scant empirical evidence supporting these predictions and, to the best of our knowledge, seasonal variation has never been explored in the context of fluctuation-mediated coexistence. Results Using an exceptionally well-documented estuarine fish assemblage, sampled monthly for over 30 years, we show that temporal shifts in species abundances underpin species coexistence. Species fall into distinct seasonal groups, within which spatial resource use is more heterogeneous than would be expected by chance at those times when competition for food is most intense. We also detect seasonal variation in the richness and evenness of the community, again linked to shifts in resource availability. Conclusions These results reveal that spatiotemporal shifts in community composition minimize competitive interactions and help stabilize total abundance. PMID:24007204

  12. Modelling occurrence and abundance of species when detection is imperfect

    USGS Publications Warehouse

    Royle, J. Andrew; Nichols, J.D.; Kery, M.

    2005-01-01

    Relationships between species abundance and occupancy are of considerable interest in metapopulation biology and in macroecology. Such relationships may be described concisely using probability models that characterize variation in abundance of a species. However, estimation of the parameters of these models in most ecological problems is impaired by imperfect detection. When organisms are detected imperfectly, observed counts are biased estimates of true abundance, and this induces bias in stated occupancy or occurrence probability. In this paper we consider a class of models that enable estimation of abundance/occupancy relationships from counts of organisms that result from surveys in which detection is imperfect. Under such models, parameter estimation and inference are based on conventional likelihood methods. We provide an application of these models to geographically extensive breeding bird survey data in which alternative models of abundance are considered that include factors that influence variation in abundance and detectability. Using these models, we produce estimates of abundance and occupancy maps that honor important sources of spatial variation in avian abundance and provide clearly interpretable characterizations of abundance and occupancy adjusted for imperfect detection.

  13. How well can we predict forage species occurrence and abundance?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As part of a larger effort focused on forage species production and management, we have been developing a statistical modeling approach to predict the probability of species occurrence and the abundance for Orchard Grass over the Northeast region of the United States using two selected statistical m...

  14. Estimating abundance in the presence of species uncertainty

    USGS Publications Warehouse

    Chambert, Thierry A; Hossack, Blake R.; Fishback, LeeAnn; Davenport, Jon M.

    2016-01-01

    1.N-mixture models have become a popular method for estimating abundance of free-ranging animals that are not marked or identified individually. These models have been used on count data for single species that can be identified with certainty. However, co-occurring species often look similar during one or more life stages, making it difficult to assign species for all recorded captures. This uncertainty creates problems for estimating species-specific abundance and it can often limit life stages to which we can make inference. 2.We present a new extension of N-mixture models that accounts for species uncertainty. In addition to estimating site-specific abundances and detection probabilities, this model allows estimating probability of correct assignment of species identity. We implement this hierarchical model in a Bayesian framework and provide all code for running the model in BUGS-language programs. 3.We present an application of the model on count data from two sympatric freshwater fishes, the brook stickleback (Culaea inconstans) and the ninespine stickleback (Pungitius pungitius), ad illustrate implementation of covariate effects (habitat characteristics). In addition, we used a simulation study to validate the model and illustrate potential sample size issues. We also compared, for both real and simulated data, estimates provided by our model to those obtained by a simple N-mixture model when captures of unknown species identification were discarded. In the latter case, abundance estimates appeared highly biased and very imprecise, while our new model provided unbiased estimates with higher precision. 4.This extension of the N-mixture model should be useful for a wide variety of studies and taxa, as species uncertainty is a common issue. It should notably help improve investigation of abundance and vital rate characteristics of organisms’ early life stages, which are sometimes more difficult to identify than adults.

  15. Rapid divergence of microsatellite abundance among species of Drosophila.

    PubMed

    Ross, Charles L; Dyer, Kelly A; Erez, Tamar; Miller, Susan J; Jaenike, John; Markow, Therese A

    2003-07-01

    Among major taxonomic groups, microsatellites exhibit considerable variation in composition and allele length, but they also show considerable conservation within many major groups. This variation may be explained by slow microsatellite evolution so that all species within a group have similar patterns of variation, or by taxon-specific mutational or selective constraints. Unfortunately, comparing microsatellites across species and studies can be problematic because of biases that may exist among different isolation and analysis protocols. We present microsatellite data from five Drosophila species in the Drosophila subgenus: D. arizonae, D. mojavensis, and D. pachea (three cactophilic species), and D. neotestacea and D. recens (two mycophagous species), all isolated at the same time using identical protocols. For each species, we compared the relative abundance of motifs, the distribution of repeat size, and the average number of repeats. Dimers were the most abundant microsatellites for each species. However, we found considerable variation in the relative abundance of motif size classes among species, even between sister taxa. Frequency differences among motifs within size classes for the three cactophilic species, but not the two mycophagous species, are consistent with other studied Drosophila. Frequency distributions of repeat number, as well as mean size, show significant differences among motif size classes but not across species. Sizes of microsatellites in these five species are consistent with D. virilis, another species in the subgenus Drosophila, but they have consistently higher means than in D. melanogaster, in the subgenus Sophophora. These results confirm that many aspects of microsatellite variation evolve quickly but also are subject to taxon-specific constraints. In addition, the nature of microsatellite evolution is dependent on temporal and taxonomic scales, and some variation is conserved across broad taxonomic levels despite relatively high

  16. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    USGS Publications Warehouse

    Keeley, J.E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2 due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  17. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    USGS Publications Warehouse

    Keeley, Jon E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  18. Antarctic mixotrophic protist abundances by microscopy and molecular methods.

    PubMed

    Gast, Rebecca J; McKie-Krisberg, Zaid M; Fay, Scott A; Rose, Julie M; Sanders, Robert W

    2014-08-01

    Protists are traditionally described as either phototrophic or heterotrophic, but studies have indicated that mixotrophic species, organisms that combine both strategies, can have significant impacts on prey populations in marine microbial food webs. While estimates of active mixotroph abundances in environmental samples are determined microscopically by fluorescent particle ingestion, species identification is difficult. We developed SYBR-based qPCR strategies for three Antarctic algal species that we identified as mixotrophic. This method and traditional ingestion experiments were applied to determine the total mixotroph abundance in Antarctic water samples, to ascertain the abundance of known mixotrophic species, and to identify environmental variables that impact the distribution and abundance of these species. Despite differences in sampling locations and years, mixotroph distribution was strongly influenced by season. Environmental variables that best explained variation in the individual mixotroph species abundances included temperature, oxygen, date, fluorescence, conductivity, and latitude. Phosphate was identified as an additional explanatory variable when nutrients were included in the analysis. Utilizing culture-based grazing rates and qPCR abundances, the estimated summed impact on bacterial populations by the three mixotrophs was usually < 2% of the overall mixotrophic grazing, but in one sample, Pyramimonas was estimated to contribute up to 80% of mixotrophic grazing.

  19. The effects of acoustic misclassification on cetacean species abundance estimation.

    PubMed

    Caillat, Marjolaine; Thomas, Len; Gillespie, Douglas

    2013-09-01

    To estimate the density or abundance of a cetacean species using acoustic detection data, it is necessary to correctly identify the species that are detected. Developing an automated species classifier with 100% correct classification rate for any species is likely to stay out of reach. It is therefore necessary to consider the effect of misidentified detections on the number of observed data and consequently on abundance or density estimation, and develop methods to cope with these misidentifications. If misclassification rates are known, it is possible to estimate the true numbers of detected calls without bias. However, misclassification and uncertainties in the level of misclassification increase the variance of the estimates. If the true numbers of calls from different species are similar, then a small amount of misclassification between species and a small amount of uncertainty around the classification probabilities does not have an overly detrimental effect on the overall variance. However, if there is a difference in the encounter rate between species calls and/or a large amount of uncertainty in misclassification rates, then the variance of the estimates becomes very large and this dramatically increases the variance of the final abundance estimate.

  20. Abundance of common species, not species richness, drives delivery of a real-world ecosystem service.

    PubMed

    Winfree, Rachael; Fox, Jeremy W; Williams, Neal M; Reilly, James R; Cariveau, Daniel P

    2015-07-01

    Biodiversity-ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real-world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large-scale, associational data. Here, we use a novel analytical approach, the Price equation, to partition the contribution to ecosystem services made by species richness, composition and abundance in four large-scale data sets on crop pollination by native bees. We found that abundance fluctuations of dominant species drove ecosystem service delivery, whereas richness changes were relatively unimportant because they primarily involved rare species that contributed little to function. Thus, the mechanism behind our results was the skewed species-abundance distribution. Our finding that a few common species, not species richness, drive ecosystem service delivery could have broad generality given the ubiquity of skewed species-abundance distributions in nature.

  1. Abundance of common species, not species richness, drives delivery of a real-world ecosystem service.

    PubMed

    Winfree, Rachael; Fox, Jeremy W; Williams, Neal M; Reilly, James R; Cariveau, Daniel P

    2015-07-01

    Biodiversity-ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real-world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large-scale, associational data. Here, we use a novel analytical approach, the Price equation, to partition the contribution to ecosystem services made by species richness, composition and abundance in four large-scale data sets on crop pollination by native bees. We found that abundance fluctuations of dominant species drove ecosystem service delivery, whereas richness changes were relatively unimportant because they primarily involved rare species that contributed little to function. Thus, the mechanism behind our results was the skewed species-abundance distribution. Our finding that a few common species, not species richness, drive ecosystem service delivery could have broad generality given the ubiquity of skewed species-abundance distributions in nature. PMID:25959973

  2. Factors affecting Culicoides species composition and abundance in avian nests.

    PubMed

    Martínez-de la Puente, J; Merino, S; Tomás, G; Moreno, J; Morales, J; Lobato, E; Talavera, S; Sarto I Monteys, V

    2009-08-01

    Mechanisms affecting patterns of vector distribution among host individuals may influence the population and evolutionary dynamics of vectors, hosts and the parasites transmitted. We studied the role of different factors affecting the species composition and abundance of Culicoides found in nests of the blue tit (Cyanistes caeruleus). We identified 1531 females and 2 males of 7 different Culicoides species in nests, with C. simulator being the most abundant species, followed by C. kibunensis, C. festivipennis, C. segnis, C. truncorum, C. pictipennis and C. circumscriptus. We conducted a medicationxfumigation experiment randomly assigning bird's nests to different treatments, thereby generating groups of medicated and control pairs breeding in fumigated and control nests. Medicated pairs were injected with the anti-malarial drug Primaquine diluted in saline solution while control pairs were injected with saline solution. The fumigation treatment was carried out using insecticide solution or water for fumigated and control nests respectively. Brood size was the main factor associated with the abundance of biting midges probably because more nestlings may produce higher quantities of vector attractants. In addition, birds medicated against haemoparasites breeding in non-fumigated nests supported a higher abundance of C. festivipennis than the rest of the groups. Also, we found that the fumigation treatment reduced the abundance of engorged Culicoides in both medicated and control nests, thus indicating a reduction of feeding success produced by the insecticide. These results represent the first evidence for the role of different factors in affecting the Culicoides infracommunity in wild avian nests.

  3. Capitalizing on opportunistic data for monitoring relative abundances of species.

    PubMed

    Giraud, Christophe; Calenge, Clément; Coron, Camille; Julliard, Romain

    2016-06-01

    With the internet, a massive amount of information on species abundance can be collected by citizen science programs. However, these data are often difficult to use directly in statistical inference, as their collection is generally opportunistic, and the distribution of the sampling effort is often not known. In this article, we develop a general statistical framework to combine such "opportunistic data" with data collected using schemes characterized by a known sampling effort. Under some structural assumptions regarding the sampling effort and detectability, our approach makes it possible to estimate the relative abundance of several species in different sites. It can be implemented through a simple generalized linear model. We illustrate the framework with typical bird datasets from the Aquitaine region in south-western France. We show that, under some assumptions, our approach provides estimates that are more precise than the ones obtained from the dataset with a known sampling effort alone. When the opportunistic data are abundant, the gain in precision may be considerable, especially for rare species. We also show that estimates can be obtained even for species recorded only in the opportunistic scheme. Opportunistic data combined with a relatively small amount of data collected with a known effort may thus provide access to accurate and precise estimates of quantitative changes in relative abundance over space and/or time. PMID:26496390

  4. Effectiveness of mosquito traps in measuring species abundance and composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mosquito species abundance and composition estimates provided by trapping devices are commonly used to guide control efforts, but knowledge of trap biases is necessary for accurately interpreting results. We compared the Mosquito Magnet – Pro, the Mosquito Magnet – X and the CDC Miniature Light Trap...

  5. Measuring β-diversity with species abundance data.

    PubMed

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  6. Measuring β-diversity with species abundance data.

    PubMed

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  7. Analytical formulae for computing dominance from species-abundance distributions.

    PubMed

    Fung, Tak; Villain, Laura; Chisholm, Ryan A

    2015-12-01

    The evenness of an ecological community affects ecosystem structure, functioning and stability, and has implications for biodiversity conservation. In uneven communities, most species are rare while a few dominant species drive ecosystem-level properties. In even communities, dominance is lower, with possibly many species playing key ecological roles. The dominance aspect of evenness can be measured as a decreasing function of the proportion of species required to make up a fixed fraction (e.g., half) of individuals in a community. Here we sought general rules about dominance in ecological communities by linking dominance mathematically to the parameters of common theoretical species-abundance distributions (SADs). We found that if a community's SAD was log-series or lognormal, then dominance was almost inevitably high, with fewer than 40% of species required to account for 90% of all individuals. Dominance for communities with an exponential SAD was lower but still typically high, with fewer than 40% of species required to account for 70% of all individuals. In contrast, communities with a gamma SAD only exhibited high dominance when the average species abundance was below a threshold of approximately 100. Furthermore, we showed that exact values of dominance were highly scale-dependent, exhibiting non-linear trends with changing average species abundance. We also applied our formulae to SADs derived from a mechanistic community model to demonstrate how dominance can increase with environmental variance. Overall, our study provides a rigorous basis for theoretical explorations of the dynamics of dominance in ecological communities, and how this affects ecosystem functioning and stability. PMID:26409166

  8. Assessing introduction risk using species' rank-abundance distributions.

    PubMed

    Chan, Farrah T; Bradie, Johanna; Briski, Elizabeta; Bailey, Sarah A; Simard, Nathalie; MacIsaac, Hugh J

    2015-01-22

    Mixed-species assemblages are often unintentionally introduced into new ecosystems. Analysing how assemblage structure varies during transport may provide insights into how introduction risk changes before propagules are released. Characterization of introduction risk is typically based on assessments of colonization pressure (CP, the number of species transported) and total propagule pressure (total PP, the total abundance of propagules released) associated with an invasion vector. Generally, invasion potential following introduction increases with greater CP or total PP. Here, we extend these assessments using rank-abundance distributions to examine how CP : total PP relationships change temporally in ballast water of ocean-going ships. Rank-abundance distributions and CP : total PP patterns varied widely between trans-Atlantic and trans-Pacific voyages, with the latter appearing to pose a much lower risk than the former. Responses also differed by taxonomic group, with invertebrates experiencing losses mainly in total PP, while diatoms and dinoflagellates sustained losses mainly in CP. In certain cases, open-ocean ballast water exchange appeared to increase introduction risk by uptake of new species or supplementation of existing ones. Our study demonstrates that rank-abundance distributions provide new insights into the utility of CP and PP in characterizing introduction risk. PMID:25473007

  9. Species richness, equitability, and abundance of ants in disturbed landscapes

    USGS Publications Warehouse

    Graham, J.H.; Krzysik, A.J.; Kovacic, D.A.; Duda, J.J.; Freeman, D.C.; Emlen, J.M.; Zak, J.C.; Long, W.R.; Wallace, M.P.; Chamberlin-Graham, C.; Nutter, J.P.; Balbach, H.E.

    2009-01-01

    Ants are used as indicators of environmental change in disturbed landscapes, often without adequate understanding of their response to disturbance. Ant communities in the southeastern United States displayed a hump-backed species richness curve against an index of landscape disturbance. Forty sites at Fort Benning, in west-central Georgia, covered a spectrum of habitat disturbance (military training and fire) in upland forest. Sites disturbed by military training had fewer trees, less canopy cover, more bare ground, and warmer, more compact soils with shallower A-horizons. We sampled ground-dwelling ants with pitfall traps, and measured 15 habitat variables related to vegetation and soil. Ant species richness was greatest with a relative disturbance of 43%, but equitability was greatest with no disturbance. Ant abundance was greatest with a relative disturbance of 85%. High species richness at intermediate disturbance was associated with greater within-site spatial heterogeneity. Species richness was also associated with intermediate values of the normalized difference vegetation index (NDVI), a correlate of net primary productivity (NPP). Available NPP (the product of NDVI and the fraction of days that soil temperature exceeded 25 ??C), however, was positively correlated with species richness, though not with ant abundance. Species richness was unrelated to soil texture, total ground cover, and fire frequency. Ant species richness and equitability are potential state indicators of the soil arthropod community. Moreover, equitability can be used to monitor ecosystem change. ?? 2008 Elsevier Ltd.

  10. Molecular characterisation of Brucella species.

    PubMed

    Scholz, H C; Vergnaud, G

    2013-04-01

    The genus Brucella (Mayer and Shaw, 1920) currently consists often species with validly published names. Within most species further differentiation into biovars exists. Genetically, all Brucella species are highly related to each other, exhibiting sequence similarity values of 98% to 100% in aligned regions (core genome). The population structure is clonal. Despite this close genetic relatedness, the various species can be clearly distinguished from each other by application of high-resolution molecular typing tools, in addition to assessment of phenotype and host preference. Accurate species delineation can be achieved by conventional multiplex polymerase chain reaction (PCR), single nucleotide polymorphism (SNP) analysis and multilocus sequence typing (MLST) or multilocus sequence analysis (MLSA). The last is also suitable for phylogenetic reconstructions, owing to the highly clonal evolution of the different species. Highly discriminatory multilocus variable number of tandem repeats (VNTR) analysis (MLVA) allows both species delineation and differentiation of individual isolates and thus represents a perfect first-line toolfor molecular epidemiological studies within outbreak investigations. More recently,whole genome sequencing (WGS)and the resulting global genome-wide SNP analysis have become available. These novel approaches should help in further understanding the evolution, host specificity and pathogenicity of the genus Brucella.

  11. Mean molecular weight and hydrogen abundance of Titan's atmosphere

    NASA Technical Reports Server (NTRS)

    Samuelson, R. E.; Hanel, R. A.; Kunde, V. G.; Maguire, W. C.

    1981-01-01

    The 200-600/cm continuum opacity in the troposphere and lower stratosphere of Titan is inferred from thermal emission spectra from the Voyager 1 IR spectrometer (IRIS). The surface temperature and mean molecular weight are between 94 and 97 K and between 28.3 and 29.2 AMU, respectively. The mole fraction of molecular hydrogen is 0.002 + or - 0.001, which is equivalent to an abundance of approximately 0.2 + or - 0.1 km amagat.

  12. Foraminifera Species Richness, Abundance, and Diversity Research in Bolinas, California

    NASA Astrophysics Data System (ADS)

    Brunwin, N.; Ingram, Z.; Mendez, M.; Sandoval, K.

    2015-12-01

    Foraminifera are abundant, diverse, respond rapidly to environmental change, and are present in all marine and estuarine environments, making them important indicator species. A survey of occurrence and distribution of foraminifera in the Bolinas Lagoon, Marin County, California was carried out by Hedman in 1975, but no study since has focused on foraminiferal composition within this important ecosystem. In July 2015, the Careers in Science (CiS) Intern Program collected samples at 12 sites previously examined in the 1975 study. Thirty-six samples were collected from the upper few centimeters of sediment from a variety of intertidal and subtidal environments within the lagoon. Foraminifera from each sample were isolated, identified and species richness, abundance and diversity quantified. Furthermore, comparisons of faunal composition represented in our recent collection and that of Hedman's 1975 report are made.

  13. Measurement scale in maximum entropy models of species abundance

    PubMed Central

    Frank, Steven A.

    2010-01-01

    The consistency of the species abundance distribution across diverse communities has attracted widespread attention. In this paper, I argue that the consistency of pattern arises because diverse ecological mechanisms share a common symmetry with regard to measurement scale. By symmetry, I mean that different ecological processes preserve the same measure of information and lose all other information in the aggregation of various perturbations. I frame these explanations of symmetry, measurement, and aggregation in terms of a recently developed extension to the theory of maximum entropy. I show that the natural measurement scale for the species abundance distribution is log-linear: the information in observations at small population sizes scales logarithmically and, as population size increases, the scaling of information grades from logarithmic to linear. Such log-linear scaling leads naturally to a gamma distribution for species abundance, which matches well with the observed patterns. Much of the variation between samples can be explained by the magnitude at which the measurement scale grades from logarithmic to linear. This measurement approach can be applied to the similar problem of allelic diversity in population genetics and to a wide variety of other patterns in biology. PMID:21265915

  14. Neutral theory and relative species abundance in ecology

    NASA Astrophysics Data System (ADS)

    Volkov, Igor; Banavar, Jayanth R.; Hubbell, Stephen P.; Maritan, Amos

    2003-08-01

    The theory of island biogeography asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell generalized this neutral theory to explore the expected steady-state distribution of relative species abundance (RSA) in the local community under restricted immigration. Here we present a theoretical framework for the unified neutral theory of biodiversity and an analytical solution for the distribution of the RSA both in the metacommunity (Fisher's log series) and in the local community, where there are fewer rare species. Rare species are more extinction-prone, and once they go locally extinct, they take longer to re-immigrate than do common species. Contrary to recent assertions, we show that the analytical solution provides a better fit, with fewer free parameters, to the RSA distribution of tree species on Barro Colorado Island, Panama, than the lognormal distribution.

  15. GASEOUS CO ABUNDANCE-AN EVOLUTIONARY TRACER FOR MOLECULAR CLOUDS

    SciTech Connect

    Liu Tie; Wu Yuefang; Zhang Huawei E-mail: ywu@pku.edu.cn

    2013-09-20

    Planck cold clumps are among the most promising objects to investigate the initial conditions of the evolution of molecular clouds. In this work, by combing the dust emission data from the survey of the Planck satellite with the molecular data of {sup 12}CO/{sup 13}CO/C{sup 18}O (1-0) lines from observations with the Purple Mountain Observatory 13.7 m telescope, we investigate the CO abundance, CO depletion, and CO-to-H{sub 2} conversion factor of 674 clumps in the early cold cores sample. The median and mean values of the CO abundance are 0.89 Multiplication-Sign 10{sup -4} and 1.28 Multiplication-Sign 10{sup -4}, respectively. The mean and median of CO depletion factor are 1.7 and 0.9, respectively. The median value of X{sub CO-to-H{sub 2}} for the whole sample is 2.8 Multiplication-Sign 10{sup 20} cm{sup -2} K{sup -1} km{sup -1} s. The CO abundance, CO depletion factor, and CO-to-H{sub 2} conversion factor are strongly (anti-)correlated to other physical parameters (e.g., dust temperature, dust emissivity spectral index, column density, volume density, and luminosity-to-mass ratio). To conclude, the gaseous CO abundance can be used as an evolutionary tracer for molecular clouds.

  16. Estimating the number of species in a stochastic abundance model.

    PubMed

    Chao, Anne; Bunge, John

    2002-09-01

    Consider a stochastic abundance model in which the species arrive in the sample according to independent Poisson processes, where the abundance parameters of the processes follow a gamma distribution. We propose a new estimator of the number of species for this model. The estimator takes the form of the number of duplicated species (i.e., species represented by two or more individuals) divided by an estimated duplication fraction. The duplication fraction is estimated from all frequencies including singleton information. The new estimator is closely related to the sample coverage estimator presented by Chao and Lee (1992, Journal of the American Statistical Association 87, 210-217). We illustrate the procedure using the Malayan butterfly data discussed by Fisher, Corbet, and Williams (1943, Journal of Animal Ecology 12, 42-58) and a 1989 Christmas Bird Count dataset collected in Florida, U.S.A. Simulation studies show that this estimator compares well with maximum likelihood estimators (i.e., empirical Bayes estimators from the Bayesian viewpoint) for which an iterative numerical procedure is needed and may be infeasible.

  17. When can species abundance data reveal non-neutrality?

    PubMed

    Al Hammal, Omar; Alonso, David; Etienne, Rampal S; Cornell, Stephen J

    2015-03-01

    Species abundance distributions (SAD) are probably ecology's most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable. PMID:25793889

  18. When Can Species Abundance Data Reveal Non-neutrality?

    PubMed Central

    Al Hammal, Omar; Alonso, David; Etienne, Rampal S.; Cornell, Stephen J.

    2015-01-01

    Species abundance distributions (SAD) are probably ecology’s most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable. PMID:25793889

  19. Which Models Are Appropriate for Six Subtropical Forests: Species-Area and Species-Abundance Models

    PubMed Central

    Wei, Shi Guang; Li, Lin; Chen, Zhen Cheng; Lian, Ju Yu; Lin, Guo Jun; Huang, Zhong Liang; Yin, Zuo Yun

    2014-01-01

    The species-area relationship is one of the most important topic in the study of species diversity, conservation biology and landscape ecology. The species-area relationship curves describe the increase of species number with increasing area, and have been modeled by various equations. In this paper, we used detailed data from six 1-ha subtropical forest communities to fit three species-area relationship models. The coefficient of determination and F ratio of ANOVA showed all the three models fitted well to the species-area relationship data in the subtropical communities, with the logarithm model performing better than the other two models. We also used the three species-abundance distributions, namely the lognormal, logcauchy and logseries model, to fit them to the species-abundance data of six communities. In this case, the logcauchy model had the better fit based on the coefficient of determination. Our research reveals that the rare species always exist in the six communities, corroborating the neutral theory of Hubbell. Furthermore, we explained why all species-abundance figures appeared to be left-side truncated. This was due to subtropical forests have high diversity, and their large species number includes many rare species. PMID:24755956

  20. Species composition and abundance of Brevipalpus spp. on different citrus species in Mexican orchards.

    PubMed

    Salinas-Vargas, D; Santillán-Galicia, M T; Valdez-Carrasco, J; Mora-Aguilera, G; Atanacio-Serrano, Y; Romero-Pescador, P

    2013-08-01

    We studied the abundance of Brevipalpus spp. in citrus orchards in the Mexican states of Yucatan, Quintana Roo and Campeche. Mites were collected from 100 trees containing a mixture of citrus species where sweet orange was always the main species. Eight collections were made at each location from February 2010 to February 2011. Mites from the genus Brevipalpus were separated from other mites surveyed and their abundance and relationships with the different citrus species were quantified throughout the collection period. A subsample of 25% of the total Brevipalpus mites collected were identified to species level and the interaction of mite species and citrus species were described. Brevipalpus spp. were present on all collection dates and their relative abundance was similar on all citrus species studies. The smallest number of mites collected was during the rainy season. Brevipalpus phoenicis (Geijskes) and Brevipalpus californicus (Banks) were the only two species present and they were found in all locations except Campeche, where only B. phoenicis was present. Yucatan and Campeche are at greater risk of leprosis virus transmission than Quintana Roo because the main vector, B. phoenicis, was more abundant than B. californicus. The implications of our results for the design of more accurate sampling and control methods for Brevipalpus spp. are discussed. PMID:23949863

  1. Community structure influences species' abundance along environmental gradients.

    PubMed

    Eloranta, Antti P; Helland, Ingeborg P; Sandlund, Odd T; Hesthagen, Trygve; Ugedal, Ola; Finstad, Anders G

    2016-01-01

    Species' response to abiotic environmental variation can be influenced by local community structure and interspecific interactions, particularly in restricted habitats such as islands and lakes. In temperate lakes, future increase in water temperature and run-off of terrestrial (allochthonous) dissolved organic carbon (DOC) are predicted to alter community composition and the overall ecosystem productivity. However, little is known about how the present community structure and abiotic environmental variation interact to affect the abundance of native fish populations. We used a space-for-time approach to study how local community structure interact with lake morphometric and climatic characteristics (i.e. temperature and catchment productivity) to affect brown trout (Salmo trutta L.) yield in 283 Norwegian lakes located in different biogeographical regions. Brown trout yield (based on data from standardized survey gill net fishing; g 100 m(-2) gill net night(-1)) was generally lower in lakes where other fish species were present than in lakes with brown trout only. The yield showed an overall negative relationship with increasing temperature and a positive relationship with lake shoreline complexity. Brown trout yield was also negatively correlated with DOC load (measured using Normalized Difference Vegetation Index as a proxy) and lake size and depth (measured using terrain slope as a proxy), but only in lakes where other fish species were present. The observed negative response of brown trout yield to increasing DOC load and proportion of the pelagic open-water area is likely due to restricted (littoral) niche availability and competitive dominance of more pelagic fishes such as Arctic charr (Salvelinus alpinus (L.)). Our study highlights that, through competitive interactions, the local community structure can influence the response of a species' abundance to variation in abiotic conditions. Changes in biomass and niche use of top predators (such as the brown

  2. Analyzing fractal property of species abundance distribution and diversity indexes.

    PubMed

    Su, Qiang

    2016-03-01

    Community diversity is usually characterized by numerical indexes; however it indeed depends on the species abundance distribution (SAD). Diversity indexes and SAD are based on the same information but treating as separate themes. Ranking species abundance from largest to smallest, the decreasing pattern can give the information about the SAD. Frontier proposed such SAD might be a fractal structure, and first applied the Zipf-Mandelbrot model to the SAD study. However, this model fails to include the Zipf model, and also fails to ensure an integer rank. In this study, a fractal model of SAD was reconstructed, and tested with 104 community samples from 8 taxonomic groups. The results show that there was a good fit of the presented model. Fractal parameter (p) determines the SAD of a community. The ecological significance of p relates to the "dominance" of a community. The correlation between p and classical diversity indexes show that Shannon index decreases and Simpson index increases as p increases. The main purpose of this paper is not to compare with other SADs models; it simply provides a new interpretation of SAD model construction, and preliminarily integrates diversity indexes and SAD model into a broader perspective of community diversity. PMID:26746388

  3. Metagenomic abundance estimation and diagnostic testing on species level

    PubMed Central

    Lindner, Martin S.; Renard, Bernhard Y.

    2013-01-01

    One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic diagnostics or microbial community comparison. However, the majority of existing approaches quantify at low resolution (e.g. at phylum level), rely on the existence of special genes (e.g. 16S), or have severe problems discerning species with highly similar genome sequences. Yet, problems as metagenomic diagnostics require accurate quantification on species level. We developed Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC’s superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification. PMID:22941661

  4. Analyzing fractal property of species abundance distribution and diversity indexes.

    PubMed

    Su, Qiang

    2016-03-01

    Community diversity is usually characterized by numerical indexes; however it indeed depends on the species abundance distribution (SAD). Diversity indexes and SAD are based on the same information but treating as separate themes. Ranking species abundance from largest to smallest, the decreasing pattern can give the information about the SAD. Frontier proposed such SAD might be a fractal structure, and first applied the Zipf-Mandelbrot model to the SAD study. However, this model fails to include the Zipf model, and also fails to ensure an integer rank. In this study, a fractal model of SAD was reconstructed, and tested with 104 community samples from 8 taxonomic groups. The results show that there was a good fit of the presented model. Fractal parameter (p) determines the SAD of a community. The ecological significance of p relates to the "dominance" of a community. The correlation between p and classical diversity indexes show that Shannon index decreases and Simpson index increases as p increases. The main purpose of this paper is not to compare with other SADs models; it simply provides a new interpretation of SAD model construction, and preliminarily integrates diversity indexes and SAD model into a broader perspective of community diversity.

  5. SPECIES-ABUNDANCE-BIOMASS RESPONSES BY ESTUARINE MACROBENTHOS TO SEDIMENT CHEMICAL CONTAMINATION.

    EPA Science Inventory

    Macrobenthic community responses can be measured through concerted changes in univariate metrics, including species richness, total abundance, and total biomass. The classic model of pollution effects on marine macroinvertebrate communities recognizes that species/abundance/bioma...

  6. HERSCHEL OBSERVATIONS REVEAL ANOMALOUS MOLECULAR ABUNDANCES TOWARD THE GALACTIC CENTER

    SciTech Connect

    Sonnentrucker, P.; Neufeld, D. A.; Indriolo, N.; Gerin, M.; De Luca, M.; Lis, D. C.; Goicoechea, J. R.

    2013-01-20

    We report the Herschel detections of hydrogen fluoride (HF) and para-water (p-H{sub 2}O) in gas intercepting the sight lines to two well-studied molecular clouds in the vicinity of the Sgr A complex: G-0.02-0.07 (the {sup +}50 km s{sup -1} cloud{sup )} and G-0.13-0.08 (the {sup +}20 km s{sup -1} cloud{sup )}. Toward both sight lines, HF and water absorption components are detected over a wide range of velocities covering {approx}250 km s{sup -1}. For all velocity components with V{sub LSR} > -85 km s{sup -1}, we find that the HF and water abundances are consistent with those measured toward other sight lines probing the Galactic disk gas. The velocity components with V{sub LSR} {<=} -85 km s{sup -1}, which are known to trace gas residing within {approx}200 pc of the Galactic center, however, exhibit water vapor abundances with respect to HF at least a factor three higher than those found in the Galactic disk gas. Comparison with CH data indicates that our observations are consistent with a picture where HF and a fraction of the H{sub 2}O absorption arise in diffuse molecular clouds showing Galactic disk-like abundances while the bulk of the water absorption arises in warmer (T {>=} 400 K) diffuse molecular gas for V{sub LSR} {<=} -85 km s{sup -1}. This diffuse Interstellar Medium (ISM) phase has also been recently revealed through observations of CO, HF, H{sup +}{sub 3}, and H{sub 3}O{sup +} absorption toward other sight lines probing the Galactic center inner region.

  7. Fuel breaks affect nonnative species abundance in Californian plant communities

    USGS Publications Warehouse

    Merriam, K.E.; Keeley, J.E.; Beyers, J.L.

    2006-01-01

    We evaluated the abundance of nonnative plants on fuel breaks and in adjacent untreated areas to determine if fuel treatments promote the invasion of nonnative plant species. Understanding the relationship between fuel treatments and nonnative plants is becoming increasingly important as federal and state agencies are currently implementing large fuel treatment programs throughout the United States to reduce the threat of wildland fire. Our study included 24 fuel breaks located across the State of California. We found that nonnative plant abundance was over 200% higher on fuel breaks than in adjacent wildland areas. Relative nonnative cover was greater on fuel breaks constructed by bulldozers (28%) than on fuel breaks constructed by other methods (7%). Canopy cover, litter cover, and duff depth also were significantly lower on fuel breaks constructed by bulldozers, and these fuel breaks had significantly more exposed bare ground than other types of fuel breaks. There was a significant decline in relative nonnative cover with increasing distance from the fuel break, particularly in areas that had experienced more numerous fires during the past 50 years, and in areas that had been grazed. These data suggest that fuel breaks could provide establishment sites for nonnative plants, and that nonnatives may invade surrounding areas, especially after disturbances such as fire or grazing. Fuel break construction and maintenance methods that leave some overstory canopy and minimize exposure of bare ground may be less likely to promote nonnative plants. ?? 2006 by the Ecological Society of America.

  8. Astrochem: Abundances of chemical species in the interstellar medium

    NASA Astrophysics Data System (ADS)

    Maret, Sébastien; Bergin, Edwin A.

    2015-07-01

    Astrochem computes the abundances of chemical species in the interstellar medium, as function of time. It studies the chemistry in a variety of astronomical objects, including diffuse clouds, dense clouds, photodissociation regions, prestellar cores, protostars, and protostellar disks. Astrochem reads a network of chemical reactions from a text file, builds up a system of kinetic rates equations, and solves it using a state-of-the-art stiff ordinary differential equation (ODE) solver. The Jacobian matrix of the system is computed implicitly, so the resolution of the system is extremely fast: large networks containing several thousands of reactions are usually solved in a few seconds. A variety of gas phase process are considered, as well as simple gas-grain interactions, such as the freeze-out and the desorption via several mechanisms (thermal desorption, cosmic-ray desorption and photo-desorption). The computed abundances are written in a HDF5 file, and can be plotted in different ways with the tools provided with Astrochem. Chemical reactions and their rates are written in a format which is meant to be easy to read and to edit. A tool to convert the chemical networks from the OSU and KIDA databases into this format is also provided. Astrochem is written in C, and its source code is distributed under the terms of the GNU General Public License (GPL).

  9. Molecular Abundances in the Disk of AN Active Galactic Nucleus

    NASA Astrophysics Data System (ADS)

    Harada, N.; Thompson, T. A.; Herbst, E.

    2011-06-01

    There are galactic nuclei that emit high luminosities L˜1044-46 erg S-1 including luminosity produced by X-rays from high mass accretion onto the central black holes. These nuclei are called active galactic nuclei (AGNs), and they are accompanied by molecular disks. Observations show high abundances of CN and HCN in the disks; the molecules are proposed to be probes of X-ray dominated regions (XDRs) created by the X-rays from AGNs. We have constructed a spatially-dependent chemical-abundance model of the molecular disk in NGC 1068, a typical AGN-dominated galaxy. Recently, new observations of CN and HCN have been made at much higher spatial resolution, and there are also detections of polyatomic molecules such as HC3N, c-C3H2, and C2H. We discuss how these observations and our simulations can help us to better understand the physical conditions, the disk structure, and conditions for star formation within molecular disks, which are still uncertain. We also include a comparison with other types of galaxies such as (ultra-) luminous infrared galaxies. Usero et al.Astronomy and Astrophysics. 419 (897), 2004. Initial results were presented at the International Symposium on Molecular Spectroscopy 2010, RF05 Garcia-Burillo et al. Astronomy and Astrophysics. 519 (2), 2010. Garcia-Burillo et al. Journal of Physics Conference Series, 131 (12031), 2008. Costagliola et al. ArXiv e-print arXiv:1101.2122, 2011. Nakajima et al. Astrophysical Journal Letters 728 (L38), 2008.

  10. The CH+ abundance in turbulent, diffuse molecular clouds

    NASA Astrophysics Data System (ADS)

    Myers, Andrew T.; McKee, Christopher F.; Li, Pak Shing

    2015-11-01

    The intermittent dissipation of interstellar turbulence is an important energy source in the diffuse interstellar medium. Though on average smaller than the heating rates due to cosmic rays and the photoelectric effect on dust grains, the turbulent cascade can channel large amounts of energy into a relatively small fraction of the gas that consequently undergoes significant heating and chemical enrichment. In particular, this mechanism has been proposed as a solution to the long-standing problem of the high abundance of CH+ along diffuse molecular sight lines, which steady-state, low-temperature models underproduce by over an order of magnitude. While much work has been done on the structure and chemistry of these small-scale dissipation zones, comparatively little attention has been paid to relating these zones to the properties of the large-scale turbulence. In this paper, we attempt to bridge this gap by estimating the temperature and CH+ column density along diffuse molecular sight lines by post-processing three-dimensional magnetohydrodynamic(s) turbulence simulations. Assuming reasonable values for the cloud density (bar{n}H = 30 cm-3), size (L = 20 pc), and velocity dispersion (σv = 2.3 km s-1), we find that our computed abundances compare well with CH+ column density observations, as well as with observations of emission lines from rotationally excited H2 molecules.

  11. Daughter Species Abundances in Comet C/2014 Q2 (Lovejoy)

    NASA Astrophysics Data System (ADS)

    McKay, Adam; Cochran, Anita; Dello Russo, Neil; Kelley, Michael

    2015-11-01

    We present analysis of high spectral resolution optical spectra of C/2014 Q2 (Lovejoy) acquired with the Tull Coude spectrometer on the 2.7-meter Harlan J. Smith Telescope at McDonald Observatory and the ARCES spectrometer mounted on the 3.5-meter Astrophysical Research Consortium Telescope at Apache Point Observatory. Both Tull Coude and ARCES provide high spectral resolution (R=30,000-60,000) and a large spectral range of approximately 3500-10000 Angstroms. We obtained two observation epochs, one in February 2015 at a heliocentric distance of 1.3 AU, and another in May 2015 at a heliocentric distance of 1.9 AU. Another epoch in late August 2015 at a heliocentric distance of 3.0 AU is scheduled. We will present production rates of the daughter species CN, C3, CH, C2, and NH2. We will also present H2O production rates derived from the [OI]6300 emission, as well as measurements of the flux ratio of the [OI]5577 Angstrom line to the sum of the [OI]6300 and [OI]6364 Angstrom lines (sometimes referred to as the oxygen line ratio). This ratio is indicative of the CO2 abundance of the comet. As we have observations at several heliocentric distances, we will examine how production rates and mixing ratios of the various species change with heliocentric distance. We will compare our oxygen line measurements to observations of CO2 made with Spitzer, as well as our other daughter species observations to those of candidate parent molecules made at IR wavelengths.

  12. Abundance changes and habitat availability drive species' responses to climate change

    NASA Astrophysics Data System (ADS)

    Mair, Louise; Hill, Jane K.; Fox, Richard; Botham, Marc; Brereton, Tom; Thomas, Chris D.

    2014-02-01

    There is little consensus as to why there is so much variation in the rates at which different species' geographic ranges expand in response to climate warming. Here we show that the relative importance of species' abundance trends and habitat availability for British butterfly species vary over time. Species with high habitat availability expanded more rapidly from the 1970s to mid-1990s, when abundances were generally stable, whereas habitat availability effects were confined to the subset of species with stable abundances from the mid-1990s to 2009, when abundance trends were generally declining. This suggests that stable (or positive) abundance trends are a prerequisite for range expansion. Given that species' abundance trends vary over time for non-climatic as well as climatic reasons, assessment of abundance trends will help improve predictions of species' responses to climate change, and help us to understand the likely success of different conservation strategies for facilitating their expansions.

  13. Predicting the species abundance distribution using a model food web.

    PubMed

    Powell, Craig R; McKane, Alan J

    2008-12-21

    A large number of models of the species abundance distribution (SAD) have been proposed, many of which are generically similar to the log-normal distribution, from which they are often indistinguishable when describing a given data set. Ecological data sets are necessarily incomplete samples of an ecosystem, subject to statistical noise, and cannot readily be combined to yield a closer approximation to the underlying distribution. In this paper, we adopt the Webworld ecosystem model to study the predicted SAD in detail. The Webworld model is complex, and does not allow analytic examination of such features; rather, we use simulation data and an approach similar to that of ecologists analysing empirical data. By examining large sets of fully described data we are able to resolve features which can distinguish between models but which have not been investigated in detail in field data. We find that the power-law normal distribution is superior to both the log-normal and logit-normal distributions, and that the data can improve on even this at the high-population cut-off.

  14. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies.

  15. Commonly Rare and Rarely Common: Comparing Population Abundance of Invasive and Native Aquatic Species

    PubMed Central

    Hansen, Gretchen J. A.; Vander Zanden, M. Jake; Blum, Michael J.; Clayton, Murray K.; Hain, Ernie F.; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S.; McIntyre, Peter B.; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D.; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  16. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  17. RELATIONSHIPS OF ALIEN PLANT SPECIES ABUNDANCE TO RIPARIAN VEGETATION, ENVIRONMENT, AND DISTURBANCE

    EPA Science Inventory

    Riparian ecosystems are often invaded by alien species. We evaluated vegetation, environment, and disturbance conditions and their interrelationships with alien species abundance along reaches of 29 streams in eastern Oregon, USA. Using flexible-BETA clustering, indicator species...

  18. Plant Trait-Species Abundance Relationships Vary with Environmental Properties in Subtropical Forests in Eastern China

    PubMed Central

    Yan, En-Rong; Yang, Xiao-Dong; Chang, Scott X.; Wang, Xi-Hua

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests. PMID:23560114

  19. Plant trait-species abundance relationships vary with environmental properties in subtropical forests in eastern china.

    PubMed

    Yan, En-Rong; Yang, Xiao-Dong; Chang, Scott X; Wang, Xi-Hua

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests. PMID:23560114

  20. Molecular mass and location of the most abundant peak of the molecular ion isotopomeric cluster.

    PubMed

    Goraczko, Andrzej J

    2005-09-01

    The location of the most abundant peak of the molecular-ion pattern often differs from the molecular mass published in scientific databases. The location is also distinct from the value expected from average atomic masses. The cause of this phenomenon is a large number of atoms of carbon, sulfur, chlorine, bromine, silicon and boron. This due to the natural isotope abundances of some elements forming organic compounds. A parameter called location of the most abundant peak of an isotopometric cluster (LAPIC) denotes the location of the most abundant (the main) peak of an isotopomeric cluster, which is determined, e.g., by mass spectrometry and can be important for medium- and high-molecular mass compounds. The equations for LAPIC calculation are presented for elements usually observed in organic compounds. The LAPIC with elemental formula helps effectively, e.g., in mass spectra interpretation since the prediction of LAPIC allows the correct connection of the main peak of the investigated ion with the expected ion formula and the mass of the ion considered. This solution can be a substitute for the much more complex method of isotopometric analysis applied in mass spectra interpretation. [Figure: see text]. Differences of the most abundant peak location (Delta LAPIC(C)=f(n)) for carbon aggregates C(n).

  1. Molecular abundances in the inner layers of IRC +10216

    NASA Astrophysics Data System (ADS)

    Agúndez, M.; Fonfría, J. P.; Cernicharo, J.; Kahane, C.; Daniel, F.; Guélin, M.

    2012-07-01

    Context. The inner layers of circumstellar envelopes around asymptotic giant branch stars are sites where a variety of processes such as thermochemical equilibrium, shocks induced by the stellar pulsation, and condensation of dust grains determine the chemical composition of the material that is expelled into the outer envelope layers and, ultimately, into interstellar space. Aims: We aim at studying the abundances, throughout the whole circumstellar envelope of the carbon star IRC +10216, of several molecules formed in the inner layers in order to constrain the different processes at work in such regions. Methods: Observations towards IRC +10216 of CS, SiO, SiS, NaCl, KCl, AlCl, AlF, and NaCN have been carried out with the IRAM 30-m telescope in the 80-357.5 GHz frequency range. A large number of rotational transitions covering a wide range of energy levels, including highly excited vibrational states, are detected in emission and serve to trace different regions of the envelope. Radiative transfer calculations based on the LVG formalism have been performed to derive molecular abundances from the innermost out to the outer layers. The excitation calculations include infrared pumping to excited vibrational states and inelastic collisions, for which up-to-date rate coefficients for rotational and, in some cases, ro-vibrational transitions are used. Results: We find that in the inner layers CS, SiO, and SiS have abundances relative to H2 of 4 × 10-6, 1.8 × 10-7, and 3 × 10-6, respectively, and that CS and SiS have significant lower abundances in the outer envelope, which implies that they actively contribute to the formation of dust. Moreover, in the inner layers, the amount of sulfur and silicon in gas phase molecules is only 27% for S and 5.6% for Si, implying that these elements have already condensed onto grains, most likely in the form of MgS and SiC. Metal-bearing molecules lock up a relatively small fraction of metals, although our results indicate that Na

  2. Modelling community dynamics based on species-level abundance models from detection/nondetection data

    USGS Publications Warehouse

    Yamaura, Yuichi; Royle, J. Andrew; Kuboi, Kouji; Tada, Tsuneo; Ikeno, Susumu; Makino, Shun'ichi

    2011-01-01

    1. In large-scale field surveys, a binary recording of each species' detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species-, functional group-, and community-levels from such binary data. 2. We developed a novel hierarchical multi-species abundance model based on species-level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species-level detection/nondetection is linked to species- level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9-year dataset composed of the detection/nondetection of forest birds, at a single post-fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post-fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications. Understanding and prediction of large-scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species-, functional group-, and community-levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance-based diversity and similarity

  3. Fish and Phytoplankton Exhibit Contrasting Temporal Species Abundance Patterns in a Dynamic North Temperate Lake

    PubMed Central

    Hansen, Gretchen J. A.; Carey, Cayelan C.

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of “core” (common occurrence and high abundance) and “occasional” (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  4. Fish and phytoplankton exhibit contrasting temporal species abundance patterns in a dynamic north temperate lake.

    PubMed

    Hansen, Gretchen J A; Carey, Cayelan C

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of "core" (common occurrence and high abundance) and "occasional" (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  5. Molecular Epidemiology of Fonsecaea Species

    PubMed Central

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A.; Klaassen, Corne H.W.; Bonifaz, Alexandro; van den Ende, A.H.G. Gerrits; Menken, Steph B.J.

    2011-01-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, β-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration. PMID:21392438

  6. Molecular epidemiology of Fonsecaea species.

    PubMed

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A; Klaassen, Corne H W; Bonifaz, Alexandro; Gerrits van den Ende, A H G; Menken, Steph B J; de Hoog, G Sybren

    2011-03-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, beta-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration.

  7. Molecular hydrogen abundances of galaxies in the EAGLE simulations

    NASA Astrophysics Data System (ADS)

    Lagos, Claudia del P.; Crain, Robert A.; Schaye, Joop; Furlong, Michelle; Frenk, Carlos S.; Bower, Richard G.; Schaller, Matthieu; Theuns, Tom; Trayford, James W.; Bahé, Yannick M.; Dalla Vecchia, Claudio

    2015-10-01

    We investigate the abundance of galactic molecular hydrogen (H2) in the `Evolution and Assembly of GaLaxies and their Environments' (EAGLE) cosmological hydrodynamic simulations. We assign H2 masses to gas particles in the simulations in post-processing using two different prescriptions that depend on the local dust-to-gas ratio and the interstellar radiation field. Both result in H2 galaxy mass functions that agree well with observations in the local and high-redshift Universe. The simulations reproduce the observed scaling relations between the mass of H2 and the stellar mass, star formation rate and stellar surface density. Towards high redshifts, galaxies in the simulations display larger H2 mass fractions and lower H2 depletion time-scales, also in good agreement with observations. The comoving mass density of H2 in units of the critical density, Ω _H_2, peaks at z ≈ 1.2-1.5, later than the predicted peak of the cosmic star formation rate activity, at z ≈ 2. This difference stems from the decrease in gas metallicity and increase in interstellar radiation field with redshift, both of which hamper H2 formation. We find that the cosmic H2 budget is dominated by galaxies with M_H_2>10^9 M_{⊙}, star formation rates > 10 M_{⊙} yr^{-1} and stellar masses Mstellar > 1010 M⊙, which are readily observable in the optical and near-IR. The match between the H2 properties of galaxies that emerge in the simulations and observations is remarkable, particularly since H2 observations were not used to adjust parameters in EAGLE.

  8. Importance of the H2 abundance in protoplanetary disk ices for the molecular layer chemical composition

    NASA Astrophysics Data System (ADS)

    Wakelam, V.; Ruaud, M.; Hersant, F.; Dutrey, A.; Semenov, D.; Majumdar, L.; Guilloteau, S.

    2016-10-01

    Context. Protoplanetary disks are the target of many chemical studies (both observational and theoretical) as they contain the building material for planets. Their large vertical and radial gradients in density and temperature make them challenging objects for chemical models. In the outer part of these disks, the large densities and low temperatures provide a particular environment where the binding of species onto the dust grains can be very efficient and can affect the gas-phase chemical composition. Aims: We attempt to quantify to what extent the vertical abundance profiles and the integrated column densities of molecules predicted by a detailed gas-grain code are affected by the treatment of the molecular hydrogen physisorption at the surface of the grains. Methods: We performed three different models using the Nautilus gas-grain code. One model uses a H2 binding energy on the surface of water (440 K) and produces strong sticking of H2. Another model uses a small binding energy of 23 K (as if there were already a monolayer of H2), and the sticking of H2 is almost negligible. Finally, the remaining model is an intermediate solution known as the encounter desorption mechanism. Results: We show that the efficiency of molecular hydrogen binding (and thus its abundance at the surface of the grains) can have a quantitative effect on the predicted column densities in the gas phase of major species such as CO, CS, CN, and HCN.

  9. A New Methodology for the Detection of Low-Abundance Species in the Ism: Detection of Interstellar Carbodiimide (HNCNH)

    NASA Astrophysics Data System (ADS)

    McGuire, Brett A.; Loomis, Ryan A.; Charness, Cameron M.; Corby, Joanna F.; Blake, Geoffrey A.; Hollis, Jan M.; Lovas, Frank J.; Jewell, Philip R.; Remijan, Anthony J.

    2013-06-01

    We present the first interstellar detection of carbodiimide (HNCNH) in observations towards Sgr B2(N) using data from the publicly available Green Bank Telescope PRebiotic Interstellar MOlecular Survey project. Recent laboratory work predicts an abundance of HNCNH of ˜10% of the abundance of its tautomer, cyanamide (NH_2CN), or ˜ 2× 10^{13} cm^{-2} in Sgr B2(N). Given this abundance at LTE conditions, the strongest rotational transitions of HNCNH have intensities at or below the noise level of current observations of this source. A thermal population of HNCNH is therefore likely undetectable. Instead, HNCNH is identified via maser emission features at centimeter wavelengths. This detection presents a new methodology for the detection of low-abundance species and further demonstrates the power of cm-wave observations to make definitive identifications based on a small number of observed features.

  10. From the Cover: Ecological community description using the food web, species abundance, and body size

    NASA Astrophysics Data System (ADS)

    Cohen, Joel E.; Jonsson, Tomas; Carpenter, Stephen R.

    2003-02-01

    Measuring the numerical abundance and average body size of individuals of each species in an ecological community's food web reveals new patterns and illuminates old ones. This approach is illustrated using data from the pelagic community of a small lake: Tuesday Lake, Michigan, United States. Body mass varies almost 12 orders of magnitude. Numerical abundance varies almost 10 orders of magnitude. Biomass abundance (average body mass times numerical abundance) varies only 5 orders of magnitude. A new food web graph, which plots species and trophic links in the plane spanned by body mass and numerical abundance, illustrates the nearly inverse relationship between body mass and numerical abundance, as well as the pattern of energy flow in the community. Species with small average body mass occur low in the food web of Tuesday Lake and are numerically abundant. Larger-bodied species occur higher in the food web and are numerically rarer. Average body size explains more of the variation in numerical abundance than does trophic height. The trivariate description of an ecological community by using the food web, average body sizes, and numerical abundance includes many well studied bivariate and univariate relationships based on subsets of these three variables. We are not aware of any single community for which all of these relationships have been analyzed simultaneously. Our approach demonstrates the connectedness of ecological patterns traditionally treated as independent. Moreover, knowing the food web gives new insight into the disputed form of the allometric relationship between body mass and abundance.

  11. New Insights on Jupiter's Deep Water Abundance from Disequilibrium Species

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Gierasch, Peter; Lunine, Jonathan; Mousis, Olivier

    2014-11-01

    The bulk water abundance on Jupiter potentially constrains the planet's formation conditions. We aim to improve the chemical constraints on Jupiter's deep water abundance in this paper. The eddy diffusion coefficient is used to model vertical mixing in planetary atmosphere, and based on laboratory studies dedicated to turbulent rotating convection, we propose a new formulation of eddy diffusion coefficient. The new formulation predicts a smooth transition from slow rotation regime (near the equator) to the rapid rotation regime (near the pole). We estimate an uncertainty for newly derived coefficient of less than 25%, which is much better than the one order of magnitude uncertainty used in the literature. We then reevaluate the water constraintprovided by CO, using the newer eddy diffusion coefficient. We considered two updated CO kinetic models, one model constrains the water enrichment (relative to solar) between 0.1 and 0.75, while the other one constrains the water enrichment between 7 and 23. This difference calls for a better assessment of CO kinetic models.

  12. New insights on Jupiter's deep water abundance from disequilibrium species

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Gierasch, Peter J.; Lunine, Jonathan I.; Mousis, Olivier

    2015-04-01

    The bulk water abundance on Jupiter potentially constrains the planet's formation conditions. We improve the chemical constraints on Jupiter's deep water abundance in this paper. The eddy diffusion coefficient is used to model vertical mixing in planetary atmosphere, and based on laboratory studies dedicated to turbulent rotating convection, we propose a new formulation of the eddy diffusion coefficient for the troposphere of giant planets. The new formulation predicts a smooth transition from the slow rotation regime (near the equator) to the rapid rotation regime (near the pole). We estimate an uncertainty for the newly derived coefficient of less than 25%, which is much better than the one order of magnitude uncertainty used in the literature. We then reevaluate the water constraint provided by CO, using the newer eddy diffusion coefficient. We considered two updated CO kinetic models, one model constrains the water enrichment (relative to solar) between 0.1 and 0.75, while the other constrains the water enrichment between 3 and 11.

  13. Mosquitoes of Zika Forest, Uganda: species composition and relative abundance.

    PubMed

    Kaddumukasa, M A; Mutebi, J-P; Lutwama, J J; Masembe, C; Akol, A M

    2014-01-01

    Mosquito collections were conducted in Zika Forest near Entebbe, Uganda, from July 2009 through June 2010 using CO2-baited light traps, ovitraps, and human-baited catches. In total, 163,790 adult mosquitoes belonging to 12 genera and 58 species were captured. Of these, 22 species (38%) were captured in Zika Forest for the first time. All the new records found in the forest in this study had previously been captured in other regions of Uganda, implying that they are native to the country and do not represent new introductions. More than 20 species previously collected in Zika Forest were not detected in our collections, and this may suggest a change in the mosquito fauna during the past 40 yr or variation in species composition from year to year. Arboviruses of public health importance have previously been isolated from >50% of the 58 mosquito species captured in Zika Forest, which suggests ahigh potential for transmission and maintenance of a wide range of arboviruses in Zika Forest.

  14. Estimating abundances of interacting species using morphological traits, foraging guilds, and habitat

    USGS Publications Warehouse

    Dorazio, Robert M.; Connor, Edward F.

    2014-01-01

    We developed a statistical model to estimate the abundances of potentially interacting species encountered while conducting point-count surveys at a set of ecologically relevant locations - as in a metacommunity of species. In the model we assume that abundances of species with similar traits (e.g., body size) are potentially correlated and that these correlations, when present, may exist among all species or only among functionally related species (such as members of the same foraging guild). We also assume that species-specific abundances vary among locations owing to systematic and stochastic sources of heterogeneity. For example, if abundances differ among locations due to differences in habitat, then measures of habitat may be included in the model as covariates. Naturally, the quantitative effects of these covariates are assumed to differ among species. Our model also accounts for the effects of detectability on the observed counts of each species. This aspect of the model is especially important for rare or uncommon species that may be difficult to detect in community-level surveys. Estimating the detectability of each species requires sampling locations to be surveyed repeatedly using different observers or different visits of a single observer. As an illustration, we fitted models to species-specific counts of birds obtained while sampling an avian community during the breeding season. In the analysis we examined whether species abundances appeared to be correlated due to similarities in morphological measures (body mass, beak length, tarsus length, wing length, tail length) and whether these correlations existed among all species or only among species of the same foraging guild. We also used the model to estimate the effects of forested area on species abundances and the effects of sound power output (as measured by body size) on species detection probabilities.

  15. Species abundance in a forest community in South China: A case of poisson lognormal distribution

    USGS Publications Warehouse

    Yin, Z.-Y.; Ren, H.; Zhang, Q.-M.; Peng, S.-L.; Guo, Q.-F.; Zhou, G.-Y.

    2005-01-01

    Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m??20 m, 5 m??5 m, and 1 m??1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal; (ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (?? and ??) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the ?? and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/?? should be an alternative measure of diversity.

  16. Lactobacillus and Pediococcus species richness and relative abundance in the vagina of rhesus monkeys (Macaca mulatta)

    PubMed Central

    Gravett, Michael G.; Jin, Ling; Pavlova, Sylvia I.; Tao, Lin

    2012-01-01

    Background The rhesus monkey is an important animal model to study human vaginal health to which lactic acid bacteria play a significant role. However, the vaginal lactic acid bacterial species richness and relative abundance in rhesus monkeys is largely unknown. Methods Vaginal swab samples were aseptically obtained from 200 reproductive aged female rhesus monkeys. Following Rogosa agar plating, single bacterial colonies representing different morphotypes were isolated and analyzed for whole-cell protein profile, species-specifc PCR, and 16S rRNA gene sequence. Results A total of 510 Lactobacillus strains of 17 species and one Pediococcus acidilactici were identified. The most abundant species was L. reuteri, which colonized the vaginas of 86% monkeys. L. johnsonii was the second most abundant species, which colonized 36% of monkeys. The majority of monkeys were colonized by multiple Lactobacillus species. Conclusions The vaginas of rhesus monkeys are frequently colonized by multiple Lactobacillus species, dominated by L. reuteri. PMID:22429090

  17. Urbanization Level and Woodland Size Are Major Drivers of Woodpecker Species Richness and Abundance

    PubMed Central

    Myczko, Łukasz; Rosin, Zuzanna M.; Skórka, Piotr; Tryjanowski, Piotr

    2014-01-01

    Urbanization is a process globally responsible for loss of biodiversity and for biological homogenization. Urbanization may have a direct negative impact on species behaviour and indirect effects on species populations through alterations of their habitats, for example patch size and habitat quality. Woodpeckers are species potentially susceptible to urbanization. These birds are mostly forest specialists and the development of urban areas in former forests may be an important factor influencing their richness and abundance, but documented examples are rare. In this study we investigated how woodpeckers responded to changes in forest habitats as a consequence of urbanization, namely size and isolation of habitat patches, and other within-patch characteristics. We selected 42 woodland patches in a gradient from a semi-natural rural landscape to the city centre of Poznań (Western Poland) in spring 2010. Both species richness and abundance of woodpeckers correlated positively to woodland patch area and negatively to increasing urbanization. Abundance of woodpeckers was also positively correlated with shrub cover and percentage of deciduous tree species. Furthermore, species richness and abundance of woodpeckers were highest at moderate values of canopy openness. Ordination analyses confirmed that urbanization level and woodland patch area were variables contributing most to species abundance in the woodpecker community. Similar results were obtained in presence-absence models for particular species. Thus, to sustain woodpecker species within cities it is important to keep woodland patches large, multi-layered and rich in deciduous tree species. PMID:24740155

  18. Urbanization level and woodland size are major drivers of woodpecker species richness and abundance.

    PubMed

    Myczko, Lukasz; Rosin, Zuzanna M; Skórka, Piotr; Tryjanowski, Piotr

    2014-01-01

    Urbanization is a process globally responsible for loss of biodiversity and for biological homogenization. Urbanization may have a direct negative impact on species behaviour and indirect effects on species populations through alterations of their habitats, for example patch size and habitat quality. Woodpeckers are species potentially susceptible to urbanization. These birds are mostly forest specialists and the development of urban areas in former forests may be an important factor influencing their richness and abundance, but documented examples are rare. In this study we investigated how woodpeckers responded to changes in forest habitats as a consequence of urbanization, namely size and isolation of habitat patches, and other within-patch characteristics. We selected 42 woodland patches in a gradient from a semi-natural rural landscape to the city centre of Poznań (Western Poland) in spring 2010. Both species richness and abundance of woodpeckers correlated positively to woodland patch area and negatively to increasing urbanization. Abundance of woodpeckers was also positively correlated with shrub cover and percentage of deciduous tree species. Furthermore, species richness and abundance of woodpeckers were highest at moderate values of canopy openness. Ordination analyses confirmed that urbanization level and woodland patch area were variables contributing most to species abundance in the woodpecker community. Similar results were obtained in presence-absence models for particular species. Thus, to sustain woodpecker species within cities it is important to keep woodland patches large, multi-layered and rich in deciduous tree species.

  19. Associations of forest cover, fragment area, and connectivity with neotropical understory bird species richness and abundance.

    PubMed

    Martensen, Alexandre Camargo; Ribeiro, Milton Cezar; Banks-Leite, Cristina; Prado, Paulo Inácio; Metzger, Jean Paul

    2012-12-01

    Theoretical and empirical studies demonstrate that the total amount of forest and the size and connectivity of fragments have nonlinear effects on species survival. We tested how habitat amount and configuration affect understory bird species richness and abundance. We used mist nets (almost 34,000 net hours) to sample birds in 53 Atlantic Forest fragments in southeastern Brazil. Fragments were distributed among 3 10,800-ha landscapes. The remaining forest in these landscapes was below (10% forest cover), similar to (30%), and above (50%) the theoretical fragmentation threshold (approximately 30%) below which the effects of fragmentation should be intensified. Species-richness estimates were significantly higher (F= 3715, p = 0.00) where 50% of the forest remained, which suggests a species occurrence threshold of 30-50% forest, which is higher than usually occurs (<30%). Relations between forest cover and species richness differed depending on species sensitivity to forest conversion and fragmentation. For less sensitive species, species richness decreased as forest cover increased, whereas for highly sensitive species the opposite occurred. For sensitive species, species richness and the amount of forest cover were positively related, particularly when forest cover was 30-50%. Fragment size and connectivity were related to species richness and abundance in all landscapes, not just below the 30% threshold. Where 10% of the forest remained, fragment size was more related to species richness and abundance than connectivity. However, the relation between connectivity and species richness and abundance was stronger where 30% of the landscape was forested. Where 50% of the landscape was forested, fragment size and connectivity were both related to species richness and abundance. Our results demonstrated a rapid loss of species at relatively high levels of forest cover (30-50%). Highly sensitive species were 3-4 times more common above the 30-50% threshold than below it

  20. Abundance of minor ion species at Mars: ASPERA-3 observations

    NASA Astrophysics Data System (ADS)

    Zhang, Yiteng; Nilsson, Hans; Barabash, Stas; Li, Lei

    2012-07-01

    The main species at Mars are O+, O2+, CO2+, while there are also some minor species. This article successfully separates minor species of O++, He+ and H2+ with about 12eV by integrating from two and a half years ASPERA-3 data on Mars Express and by integrating and taking some corrections and data processing. At the same time some space statistic Statistics of these Mars ions and estimating are taken place. The result indicates O++ ions density reduce quickly in the region without sunlight, and have moreis higher at subsolar than in the high alatitude place,. and reduces quickly in the region without sunlight. He+ and H2+ have similar distribution in space mainly above in the high altitude ionosphere, and relatively reduce sparse in the midnight space. O++ and He+ have a comparable volume density about 0.1% of O+, and H2+ is muchone order of magnitude lowerless for one order. Our results imply that O++ ions in the martian space are mainly the product of phtoionization in the ionosphere, while H2+ and He+ might also be originated in the planet.

  1. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    NASA Astrophysics Data System (ADS)

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-11-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g-1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  2. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

    PubMed

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  3. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

    PubMed

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  4. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    PubMed Central

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  5. Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory.

    PubMed

    Chao, Anne; Hsieh, T C; Chazdon, Robin L; Colwell, Robert K; Gotelli, Nicholas J

    2015-05-01

    Based on a sample of individuals, we focus on inferring the vector of species relative abundance of an entire assemblage and propose a novel estimator of the complete species-rank abundance distribution (RAD). Nearly all previous estimators of the RAD use the conventional "plug-in" estimator Pi (sample relative abundance) of the true relative abundance pi of species i. Because most biodiversity samples are incomplete, the plug-in estimators are applied only to the subset of species that are detected in the sample. Using the concept of sample coverage and its generalization, we propose a new statistical framework to estimate the complete RAD by separately adjusting the sample relative abundances for the set of species detected in the sample and estimating the relative abundances for the set of species undetected in the sample but inferred to be present in the assemblage. We first show that P, is a positively biased estimator of pi for species detected in the sample, and that the degree of bias increases with increasing relative rarity of each species. We next derive a method to adjust the sample relative abundance to reduce the positive bias inherent in j. The adjustment method provides a nonparametric resolution to the longstanding challenge of characterizing the relationship between the true relative abundance in the entire assemblage and the observed relative abundance in a sample. Finally, we propose a method to estimate the true relative abundances of the undetected species based on a lower bound of the number of undetected species. We then combine the adjusted RAD for the detected species and the estimated RAD for the undetected species to obtain the complete RAD estimator. Simulation results show that the proposed RAD curve can unveil the true RAD and is more accurate than the empirical RAD. We also extend our method to incidence data. Our formulas and estimators are illustrated using empirical data sets from surveys of forest spiders (for abundance data) and

  6. Species-abundance--seed-size patterns within a plant community affected by grazing disturbance.

    PubMed

    Wu, Gao-lin; Shang, Zhan-huan; Zhu, Yuan-jun; Ding, Lu-ming; Wang, Dong

    2015-04-01

    Seed size has been advanced as a key factor that influences the dynamics of plant communities, but there are few empirical or theoretical predictions of how community dynamics progress based on seed size patterns. Information on the abundance of adults, seedlings, soil seed banks, seed rains, and the seed mass of 96 species was collected in alpine meadows of the Qinghai-Tibetan Plateau (China), which had different levels of grazing disturbance. The relationships between seed-mass-abundance patterns for adults, seedlings, the soil seed bank, and seed rain in the plant community were evaluated using regression models. Results showed that grazing levels affected the relationship between seed size and abundance properties of adult species, seedlings, and the soil seed bank, suggesting that there is a shift in seed-size--species-abundance relationships as a response to the grazing gradient. Grazing had no effect on the pattern of seed-size-seed-rain-abundance at four grazing levels. Grazing also had little effect on the pattern of seed-size--species-abundance and pattern of seed-size--soil-seed-bank-abundance in meadows with no grazing, light grazing, and moderate grazing), but there was a significant negative effect in meadows with heavy grazing. Grazing had little effect on the pattern of seed-size--seedling-abundance with no grazing, but had significant negative effects with light, moderate, and heavy grazing, and the |r| values increased with grazing levels. This indicated that increasing grazing pressure enhanced the advantage of smaller-seeded species in terms of the abundances of adult species, seedlings, and soil seed banks, whereas only the light grazing level promoted the seed rain abundance of larger-seeded species in the plant communities. This study suggests that grazing disturbances are favorable for increasing the species abundance for smaller-seeded species but not for the larger-seeded species in an alpine meadow community. Hence, there is a clear

  7. Species Composition and Abundance of Stink Bugs (Hemiptera: Heteroptera: Pentatomidae) in Minnesota Field Corn.

    PubMed

    Koch, Robert L; Pahs, Tiffany

    2015-04-01

    In response to concerns of increasing significance of stink bugs (Hemiptera: Heteroptera: Pentatomidae) in northern states, a survey was conducted over 2 yr in Minnesota to characterize the Pentatomidae associated with field corn, Zea mays L. Halyomorpha halys (Stål), an exotic species, was not detected in this survey, despite continued detection of this species as an invader of human-made structures in Minnesota. Five species of Pentatomidae (four herbivorous; one predatory) were collected from corn. Across years, Euschistus variolarius (Palisot de Beauvois) and Euschistus servus euschistoides (Vollenhoven) had the greatest relative abundances and frequencies of detection. In 2012, the abundance of herbivorous species exceeded 25 nymphs and adults per 100 plants (i.e., an economic threshold) in 0.48% of fields. However, the abundance of herbivorous species did not reach economic levels in any fields sampled in 2013. The frequency of detection of herbivorous species and ratio of nymphs to adults was highest during reproductive growth stages of corn. The predator species, Podisus maculiventris (Say), was detected in 0 to 0.32% of fields. These results provide baseline information on the species composition and abundance of Pentatomidae in Minnesota field corn, which will be necessary for documentation of changes to this fauna as a result of the invasion of H. halys and to determine if some native species continue to increase in abundance in field crops.

  8. Species Composition and Abundance of Stink Bugs (Hemiptera: Heteroptera: Pentatomidae) in Minnesota Field Corn.

    PubMed

    Koch, Robert L; Pahs, Tiffany

    2015-04-01

    In response to concerns of increasing significance of stink bugs (Hemiptera: Heteroptera: Pentatomidae) in northern states, a survey was conducted over 2 yr in Minnesota to characterize the Pentatomidae associated with field corn, Zea mays L. Halyomorpha halys (Stål), an exotic species, was not detected in this survey, despite continued detection of this species as an invader of human-made structures in Minnesota. Five species of Pentatomidae (four herbivorous; one predatory) were collected from corn. Across years, Euschistus variolarius (Palisot de Beauvois) and Euschistus servus euschistoides (Vollenhoven) had the greatest relative abundances and frequencies of detection. In 2012, the abundance of herbivorous species exceeded 25 nymphs and adults per 100 plants (i.e., an economic threshold) in 0.48% of fields. However, the abundance of herbivorous species did not reach economic levels in any fields sampled in 2013. The frequency of detection of herbivorous species and ratio of nymphs to adults was highest during reproductive growth stages of corn. The predator species, Podisus maculiventris (Say), was detected in 0 to 0.32% of fields. These results provide baseline information on the species composition and abundance of Pentatomidae in Minnesota field corn, which will be necessary for documentation of changes to this fauna as a result of the invasion of H. halys and to determine if some native species continue to increase in abundance in field crops. PMID:26313176

  9. A Common Scaling Rule for Abundance, Energetics, and Production of Parasitic and Free-Living Species

    PubMed Central

    Hechinger, Ryan F.; Lafferty, Kevin D.; Dobson, Andy P.; Brown, James H.; Kuris, Armand M.

    2011-01-01

    The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This is unfortunate because parasites represent at least half of species diversity. We show that metabolic scaling theory could not account for the abundance of parasitic or free-living species in three estuarine food webs until accounting for trophic dynamics. Analyses then revealed that the abundance of all species uniformly scaled with body mass to the −¾ power. This result indicates “production equivalence,” where biomass production within trophic levels is invariant of body size across all species and functional groups: invertebrate or vertebrate, ectothermic or endothermic, and free-living or parasitic. PMID:21778398

  10. A common scaling rule for abundance, energetics, and production of parasitic and free-living species

    USGS Publications Warehouse

    Hechinger, Ryan F.; Lafferty, Kevin D.; Dobson, Andy P.; Brown, James H.; Kuris, Armand M.

    2011-01-01

    The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This is unfortunate because parasites represent at least half of species diversity. We show that metabolic scaling theory could not account for the abundance of parasitic or free-living species in three estuarine food webs until accounting for trophic dynamics. Analyses then revealed that the abundance of all species uniformly scaled with body mass to the - 3/4 power. This result indicates "production equivalence," where biomass production within trophic levels is invariant of body size across all species and functional groups: invertebrate or vertebrate, ectothermic or endothermic, and free-living or parasitic.

  11. Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances

    PubMed Central

    Boulangeat, Isabelle; Gravel, Dominique; Thuiller, Wilfried

    2014-01-01

    Although abiotic factors, together with dispersal and biotic interactions, are often suggested to explain the distribution of species and their abundances, species distribution models usually focus on abiotic factors only. We propose an integrative framework linking ecological theory, empirical data and statistical models to understand the distribution of species and their abundances together with the underlying community assembly dynamics. We illustrate our approach with 21 plant species in the French Alps. We show that a spatially nested modelling framework significantly improves the model’s performance and that the spatial variations of species presence–absence and abundances are predominantly explained by different factors. We also show that incorporating abiotic, dispersal and biotic factors into the same model bring new insights to our understanding of community assembly. This approach, at the crossroads between community ecology and biogeography, is a promising avenue for a better understanding of species co-existence and biodiversity distribution. PMID:22462813

  12. The effect of soil-borne pathogens depends on the abundance of host tree species.

    PubMed

    Liu, Yu; Fang, Suqin; Chesson, Peter; He, Fangliang

    2015-01-01

    The overarching issue for understanding biodiversity maintenance is how fitness advantages accrue to a species as it becomes rare, as this is the defining feature of stable coexistence mechanisms. Without these fitness advantages, average fitness differences between species will lead to exclusion. However, empirical evidence is lacking, especially for forests, due to the difficulty of manipulating density on a large-enough scale. Here we took advantage of naturally occurring contrasts in abundance between sites of a subtropical tree species, Ormosia glaberrima, to demonstrate how low-density fitness advantages accrue by the Janzen-Connell mechanism. The results showed that soil pathogens suppressed seedling recruitment of O. glaberrima when it is abundant but had little effect on the seedlings when it is at low density due to the lack of pathogens. The difference in seedling survival between abundant and low-density sites demonstrates strong dependence of pathogenic effect on the abundance of host species. PMID:26632594

  13. The effect of soil-borne pathogens depends on the abundance of host tree species

    PubMed Central

    Liu, Yu; Fang, Suqin; Chesson, Peter; He, Fangliang

    2015-01-01

    The overarching issue for understanding biodiversity maintenance is how fitness advantages accrue to a species as it becomes rare, as this is the defining feature of stable coexistence mechanisms. Without these fitness advantages, average fitness differences between species will lead to exclusion. However, empirical evidence is lacking, especially for forests, due to the difficulty of manipulating density on a large-enough scale. Here we took advantage of naturally occurring contrasts in abundance between sites of a subtropical tree species, Ormosia glaberrima, to demonstrate how low-density fitness advantages accrue by the Janzen–Connell mechanism. The results showed that soil pathogens suppressed seedling recruitment of O. glaberrima when it is abundant but had little effect on the seedlings when it is at low density due to the lack of pathogens. The difference in seedling survival between abundant and low-density sites demonstrates strong dependence of pathogenic effect on the abundance of host species. PMID:26632594

  14. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations

    PubMed Central

    Dashko, Sofia; Liu, Ping; Volk, Helena; Butinar, Lorena; Piškur, Jure; Fay, Justin C.

    2016-01-01

    Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance. PMID:26941733

  15. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations.

    PubMed

    Dashko, Sofia; Liu, Ping; Volk, Helena; Butinar, Lorena; Piškur, Jure; Fay, Justin C

    2016-01-01

    Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance. PMID:26941733

  16. Spatial covariation of local abundance among different parasite species: the effect of shared hosts.

    PubMed

    Lagrue, C; Poulin, R

    2015-10-01

    Within any parasite species, abundance varies spatially, reaching higher values in certain localities than in others, presumably reflecting the local availability of host resources or the local suitability of habitat characteristics for free-living stages. In the absence of strong interactions between two species of helminths with complex life cycles, we might predict that the degree to which their abundances covary spatially is determined by their common resource requirements, i.e. how many host species they share throughout their life cycles. We test this prediction using five trematode species, all with a typical three-host cycle, from multiple lake sampling sites in New Zealand's South Island: Stegodexamene anguillae, Telogaster opisthorchis, Coitocaecum parvum, Maritrema poulini, and an Apatemon sp. Pairs of species from this set of five share the same host species at either one, two, or all three life cycle stages. Our results show that when two trematode species share the same host species at all three life stages, they show positive spatial covariation in abundance (of metacercarial and adult stages) across localities. When they share hosts at two life stages, they show positive spatial covariation in abundance in some cases but not others. Finally, if two trematode species share only one host species, at a single life stage, their abundances do not covary spatially. These findings indicate that the extent of resource sharing between parasite species can drive the spatial match-mismatch between their abundances, and thus influence their coevolutionary dynamics and the degree to which host populations suffer from additive or synergistic effects of multiple infections. PMID:26113509

  17. Assessing the sensitivity of avian species abundance to land cover and climate

    USGS Publications Warehouse

    LeBrun, Jaymi J.; Thogmartin, Wayne E.; Thompson, Frank R.; Dijak, William D.; Millspaugh, Joshua J.

    2016-01-01

    Climate projections for the Midwestern United States predict southerly climates to shift northward. These shifts in climate could alter distributions of species across North America through changes in climate (i.e., temperature and precipitation), or through climate-induced changes on land cover. Our objective was to determine the relative impacts of land cover and climate on the abundance of five bird species in the Central United States that have habitat requirements ranging from grassland and shrubland to forest. We substituted space for time to examine potential impacts of a changing climate by assessing climate and land cover relationships over a broad latitudinal gradient. We found positive and negative relationships of climate and land cover factors with avian abundances. Habitat variables drove patterns of abundance in migratory and resident species, although climate was also influential in predicting abundance for some species occupying more open habitat (i.e., prairie warbler, blue-winged warbler, and northern bobwhite). Abundance of northern bobwhite increased with winter temperature and was the species exhibiting the most significant effect of climate. Models for birds primarily occupying early successional habitats performed better with a combination of habitat and climate variables whereas models of species found in contiguous forest performed best with land cover alone. These varied species-specific responses present unique challenges to land managers trying to balance species conservation over a variety of land covers. Management activities focused on increasing forest cover may play a role in mitigating effects of future climate by providing habitat refugia to species vulnerable to projected changes. Conservation efforts would be best served focusing on areas with high species abundances and an array of habitats. Future work managing forests for resilience and resistance to climate change could benefit species already susceptible to climate impacts.

  18. Molecular Genetic Analysis of Chlamydia Species.

    PubMed

    Sixt, Barbara S; Valdivia, Raphael H

    2016-09-01

    Species of Chlamydia are the etiologic agent of endemic blinding trachoma, the leading cause of bacterial sexually transmitted diseases, significant respiratory pathogens, and a zoonotic threat. Their dependence on an intracellular growth niche and their peculiar developmental cycle are major challenges to elucidating their biology and virulence traits. The last decade has seen tremendous advances in our ability to perform a molecular genetic analysis of Chlamydia species. Major achievements include the generation of large collections of mutant strains, now available for forward- and reverse-genetic applications, and the introduction of a system for plasmid-based transformation enabling complementation of mutations; expression of foreign, modified, or reporter genes; and even targeted gene disruptions. This review summarizes the current status of the molecular genetic toolbox for Chlamydia species and highlights new insights into their biology and new challenges in the nascent field of Chlamydia genetics. PMID:27607551

  19. How to Predict Molecular Interactions between Species?

    PubMed Central

    Schulze, Sylvie; Schleicher, Jana; Guthke, Reinhard; Linde, Jörg

    2016-01-01

    Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We

  20. Remembrance of things past: modelling the relationship between species' abundances in living communities and death assemblages

    PubMed Central

    Olszewski, Thomas D.

    2012-01-01

    Accumulations of dead skeletal material are a valuable archive of past ecological conditions. However, such assemblages are not equivalent to living communities because they mix the remains of multiple generations and are altered by post-mortem processes. The abundance of a species in a death assemblage can be quantitatively modelled by successively integrating the product of an influx time series and a post-mortem loss function (a decay function with a constant half-life). In such a model, temporal mixing increases expected absolute dead abundance relative to average influx as a linear function of half-life and increases variation in absolute dead abundance values as a square-root function of half-life. Because typical abundance distributions of ecological communities are logarithmically distributed, species' differences in preservational half-life would have to be very large to substantially alter species' abundance ranks (i.e. make rare species common or vice-versa). In addition, expected dead abundances increase at a faster rate than their range of variation with increased time averaging, predicting greater consistency in the relative abundance structure of death assemblages than their parent living community. PMID:21653564

  1. Gradients in the Number of Species at Reef-Seagrass Ecotones Explained by Gradients in Abundance

    PubMed Central

    Tuya, Fernando; Vanderklift, Mathew A.; Wernberg, Thomas; Thomsen, Mads S.

    2011-01-01

    Gradients in the composition and diversity (e.g. number of species) of faunal assemblages are common at ecotones between juxtaposed habitats. Patterns in the number of species, however, can be confounded by patterns in abundance of individuals, because more species tend to be found wherever there are more individuals. We tested whether proximity to reefs influenced patterns in the composition and diversity (‘species density’ = number of species per area and ‘species richness’ = number of species per number of individuals) of prosobranch gastropods in meadows of two seagrasses with different physiognomy: Posidonia and Amphibolis. A change in the species composition was observed from reef-seagrass edges towards the interiors of Amphibolis, but not in Posidonia meadows. Similarly, the abundance of gastropods and species density was higher at edges relative to interiors of Amphibolis meadows, but not in Posidonia meadows. However, species richness was not affected by proximity to reefs in either type of seagrass meadow. The higher number of species at the reef-Amphibolis edge was therefore a consequence of higher abundance, rather than species richness per se. These results suggest that patterns in the composition and diversity of fauna with proximity to adjacent habitats, and the underlying processes that they reflect, likely depend on the physiognomy of the habitat. PMID:21629654

  2. Long-Term Changes in Species Composition and Relative Abundances of Sharks at a Provisioning Site

    PubMed Central

    Brunnschweiler, Juerg M.; Abrantes, Kátya G.; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today’s recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004–2006 and 2007–2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004–2006 and very rare in the period of 2007–2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion

  3. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    PubMed

    Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

  4. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    PubMed

    Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

  5. Estimating species occurrence, abundance, and detection probability using zero-inflated distributions

    USGS Publications Warehouse

    Wenger, S.J.; Freeman, Mary C.

    2008-01-01

    Researchers have developed methods to account for imperfect detection of species with either occupancy (presence-absence) or count data using replicated sampling. We show how these approaches can be combined to simultaneously estimate occurrence, abundance, and detection probability by specifying a zero-inflated distribution for abundance. This approach may be particularly appropriate when patterns of occurrence and abundance arise from distinct processes operating at differing spatial or temporal scales. We apply the model to two data sets: (1) previously published data for a species of duck, Anas platyrhynchos, and (2) data for a stream fish species, Etheostoma scotti. We show that in these cases, an incomplete-detection zero-inflated modeling approach yields a superior fit to the data than other models. We propose that zero-inflated abundance models accounting for incomplete detection be considered when replicate count data are available.

  6. Regional-scale directional changes in abundance of tree species along a temperature gradient in Japan.

    PubMed

    Suzuki, Satoshi N; Ishihara, Masae I; Hidaka, Amane

    2015-09-01

    Climate changes are assumed to shift the ranges of tree species and forest biomes. Such range shifts result from changes in abundances of tree species or functional types. Owing to global warming, the abundance of a tree species or functional type is expected to increase near the colder edge of its range and decrease near the warmer edge. This study examined directional changes in abundance and demographic parameters of forest trees along a temperature gradient, as well as a successional gradient, in Japan. Changes in the relative abundance of each of four functional types (evergreen broad-leaved, deciduous broad-leaved, evergreen temperate conifer, and evergreen boreal conifer) and the demography of each species (recruitment rate, mortality, and population growth rate) were analyzed in 39 permanent forest plots across the Japanese archipelago. Directional changes in the relative abundance of functional types were detected along the temperature gradient. Relative abundance of evergreen broad-leaved trees increased near their colder range boundaries, especially in secondary forests, coinciding with the decrease in deciduous broad-leaved trees. Similarly, relative abundance of deciduous broad-leaved trees increased near their colder range boundaries, coinciding with the decrease in boreal conifers. These functional-type-level changes were mainly due to higher recruitment rates and partly to the lower mortality of individual species at colder sites. This is the first report to show that tree species abundances in temperate forests are changing directionally along a temperature gradient, which might be due to current or past climate changes as well as recovery from past disturbances.

  7. Regional-scale directional changes in abundance of tree species along a temperature gradient in Japan.

    PubMed

    Suzuki, Satoshi N; Ishihara, Masae I; Hidaka, Amane

    2015-09-01

    Climate changes are assumed to shift the ranges of tree species and forest biomes. Such range shifts result from changes in abundances of tree species or functional types. Owing to global warming, the abundance of a tree species or functional type is expected to increase near the colder edge of its range and decrease near the warmer edge. This study examined directional changes in abundance and demographic parameters of forest trees along a temperature gradient, as well as a successional gradient, in Japan. Changes in the relative abundance of each of four functional types (evergreen broad-leaved, deciduous broad-leaved, evergreen temperate conifer, and evergreen boreal conifer) and the demography of each species (recruitment rate, mortality, and population growth rate) were analyzed in 39 permanent forest plots across the Japanese archipelago. Directional changes in the relative abundance of functional types were detected along the temperature gradient. Relative abundance of evergreen broad-leaved trees increased near their colder range boundaries, especially in secondary forests, coinciding with the decrease in deciduous broad-leaved trees. Similarly, relative abundance of deciduous broad-leaved trees increased near their colder range boundaries, coinciding with the decrease in boreal conifers. These functional-type-level changes were mainly due to higher recruitment rates and partly to the lower mortality of individual species at colder sites. This is the first report to show that tree species abundances in temperate forests are changing directionally along a temperature gradient, which might be due to current or past climate changes as well as recovery from past disturbances. PMID:25712048

  8. Regional species richness of families and the distribution of abundance and rarity in a local community of forest Hymenoptera

    NASA Astrophysics Data System (ADS)

    Ulrich, Werner

    2005-09-01

    Recent investigations about the relationship between the number of species of taxonomic lineages and regional patterns of species abundances gave indecisive results. Here, it is shown that mean densities of species of a species-rich community of forest Hymenoptera (673 species out of 25 families) were positively related to the number of European species per family. The fraction of abundant species per family declined and the fraction of rare species increased with species richness. Species rich families contained relatively more species, which were present in only one study year (occasional species), and relatively fewer species present during the whole study period (frequent species).

  9. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches.

    PubMed

    Wagner, Elena L E S; Roche, Dominique G; Binning, Sandra A; Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region.

  10. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches

    PubMed Central

    Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  11. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches.

    PubMed

    Wagner, Elena L E S; Roche, Dominique G; Binning, Sandra A; Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  12. Negative scaling relationship between molecular diversity and resource abundances

    NASA Astrophysics Data System (ADS)

    Kamimura, Atsushi; Kaneko, Kunihiko

    2016-06-01

    Cell reproduction involves replication of diverse molecule species, in contrast to a simple replication system with fewer components. To address this question of diversity, we study theoretically a cell system with catalytic reaction dynamics that grows by uptake of environmental resources. It is shown that limited resources lead to increased diversity of components within the system, and the number of coexisting species increases with a negative power of the resource uptake. The relationship is explained from the optimum growth speed of the cell, determined by a tradeoff between the utility of diverse resources and the concentration onto fewer components to increase the reaction rate.

  13. Abundance and species composition of Tintinnina (ciliophora) in Bahía Blanca estuary, Argentina

    NASA Astrophysics Data System (ADS)

    Barría de Cao, M. S.

    1992-03-01

    Numerical abundance and seasonal cycle of tintinnines species were studied in the inner part of the Bahía Blanca estuary. Sampling was carried out at two fixed stations at approximately weekly intervals over the period March 1986-February 1987. Nineteen species representing five genera were recorded. Most species belonged to the genus Tintinnopsis. Maximal abundances of tintinnines, 10·1 × 10 3 1 -1 and 11·3 × 10 3 1 -1 at each station respectively, were found in summer. Minimal abundances, 0·5 × 10 3 1 -1 and 0·7 × 10 3 1 -1 at each station respectively, were found in winter. Tintinnidium balechi, Tintinnopsis parva and Tintinnopsis glans were present throughout the year. Tintinnopsis gracilis, Tintinnopsis baltica and Tintinnopsis beroidea exhibited seasonal occurrence, the remaining species did not show a clear pattern of distribution. The presence of Favella taraikaensis demonstrated occasional intrusions of typical fauna of the outer estuary.

  14. Species composition, abundance, and seasonal dynamics of stink bugs (Hemiptera: Pentatomidae) in Minnesota soybean fields.

    PubMed

    Koch, Robert L; Pahs, Tiffany

    2014-08-01

    Stink bugs (Hemiptera: Pentatomidae) have historically not been pests of soybean in Minnesota. In response to the invasion of Halyomorpha halys (Stål) and reports of increasing abundance of species native to North America, a state-wide survey of soybean was conducted over 3 yr in Minnesota to determine species composition, abundance, and seasonal dynamics of Pentatomidae associated with soybean. Fourteen species of Pentatomidae (12 herbivorous and two predatory) were collected from soybean. H. halys was not detected in this survey. Among the herbivorous species found, adults of Euschistus variolarius (Palisot de Beauvois) had the greatest relative abundance (60.51%) and frequency of detection (18.44%), followed by Euschistus servus euschistoides (Say) (19.37 and 3.04%, respectively) and Chinavia hilaris (Say) (5.50 and 1.69%, respectively). Abundance of herbivorous nymphs and adults exceeded an economic threshold (20 nymphs and adults per 100 sweeps) in 0.82% of fields in 2012 but not in 2011 or 2013. The frequency of detection of herbivorous species and ratio of nymphs to adults increased with increasing reproductive growth stage of soybean. In two of three years, herbivorous adults were more abundant in the edge compared with interior of fields. Two predatory Pentatomidae, Podisus maculiventris (Say) and Podisus placidus Uhler, comprised 5.95 and 1.62% of the pentatomid adults. Though the species composition of Pentatomidae in Minnesota soybean differs from that in eastern and southern states, the spatial (i.e., greater abundance near field edge) and seasonal dynamics (i.e., increasing abundance and reproduction with increasing reproductive maturity of soybean) in soybean appear similar.

  15. Early MESSENGER Results for Less Abundant or Weakly Emitting Species in Mercury's Exosphere

    NASA Astrophysics Data System (ADS)

    Vervack, R. J., Jr.; Killen, R. M.; Sprague, A. L.; Burger, M. H.; Merkel, A. W.; Sarantos, M.

    2011-10-01

    Now that the MESSENGER spacecraft is in orbit about Mercury, the extended observing time enables searches for exospheric species that are less abundant or weakly emitting compared with those for which emission has previously been detected. Many of these species cannot be observed from the ground because of terrestrial atmospheric absorption. We report here on the status of MESSENGER orbitalphase searches for additional species in Mercury's exosphere.

  16. Early MESSENGER Results for Less Abundant or Weakly Emitting Species in Mercury's Exosphere

    NASA Technical Reports Server (NTRS)

    Vervack, Ronald J., Jr.; McClintock, William E.; Killen, Rosemary M.; Sprague, Ann L.; Burger, Matthew H.; Merkel, Aimee W.; Sarantos, Menelaos

    2011-01-01

    Now that the Messenger spacecraft is in orbit about Mercury, the extended observing time enables searches for exospheric species that are less abundant or weakly emitting compared with those for which emission has previously been detected. Many of these species cannot be observed from the ground because of terrestrial atmospheric absorption. We report here on the status of MESSENGER orbital-phase searches for additional species in Mercury's exosphere.

  17. Decadal variability in abundances of the dominant euphausiid species in southern sectors of the California Current

    NASA Astrophysics Data System (ADS)

    Brinton, Edward; Townsend, Annie

    2003-08-01

    Euphausiid abundance data from broadly based California Cooperative Oceanic Fisheries Investigation surveys in California and Baja California sectors of the California Current provided a time series distinguishing periodic, rhythmic and irregular species patterns. Comparisons with environmental indexes indicate significant correlations with warm-water species, most notably in coastal Nyctiphanes simplex. Oceanic warm-water species were similarly, but less extremely, allied with an index. Coastal warm-water N. simplex was uncommon off southern California before the atmospheric regime shift of the 1970s. It assumed a post-1978 pattern of rhythmic biannual abundance increases and decreases during 1981-2000. The near-tropical oceanic Euphausia eximia and Pacific Central subtropicals patterned similarly, but was more periodic than rhythmic. Euphausia pacifica, the most dominant and broadly ranging Euphausia species, peaked at irregular but distinct bi-decadal abundances during 6 strong La Niña episodes. The peaks uniformly collapsed by 90%, becoming El Niño-associated minima. The cold-water coastal northern species Thysanoessa spinifera frequently ranged far south off Baja California before 1960 but became limited to Central California in the 1980s. The importance of T. spinifera off the Californias is small compared with northern regions, but it extends to southern upwelling centers contributing to dominance, here, by cold-water euphausiids. Decadal periodicity of species abundances decreased in the 1990s, when trends became more common. Differences among sectors were minimal between the two Californias, but were often distinct between southern California and Central Baja California. Species abundances, comparing pre- and post-climate shift species averages, differed insignificantly for all species when logarithmic values were used. With arithmetic values, most 1977-1998 average values were the greater, but with large standard deviations.

  18. Do abundance distributions and species aggregation correctly predict macroecological biodiversity patterns in tropical forests?

    PubMed Central

    Wiegand, Thorsten; Lehmann, Sebastian; Huth, Andreas; Fortin, Marie‐Josée

    2016-01-01

    Abstract Aim It has been recently suggested that different ‘unified theories of biodiversity and biogeography’ can be characterized by three common ‘minimal sufficient rules’: (1) species abundance distributions follow a hollow curve, (2) species show intraspecific aggregation, and (3) species are independently placed with respect to other species. Here, we translate these qualitative rules into a quantitative framework and assess if these minimal rules are indeed sufficient to predict multiple macroecological biodiversity patterns simultaneously. Location Tropical forest plots in Barro Colorado Island (BCI), Panama, and in Sinharaja, Sri Lanka. Methods We assess the predictive power of the three rules using dynamic and spatial simulation models in combination with census data from the two forest plots. We use two different versions of the model: (1) a neutral model and (2) an extended model that allowed for species differences in dispersal distances. In a first step we derive model parameterizations that correctly represent the three minimal rules (i.e. the model quantitatively matches the observed species abundance distribution and the distribution of intraspecific aggregation). In a second step we applied the parameterized models to predict four additional spatial biodiversity patterns. Results Species‐specific dispersal was needed to quantitatively fulfil the three minimal rules. The model with species‐specific dispersal correctly predicted the species–area relationship, but failed to predict the distance decay, the relationship between species abundances and aggregations, and the distribution of a spatial co‐occurrence index of all abundant species pairs. These results were consistent over the two forest plots. Main conclusions The three ‘minimal sufficient’ rules only provide an incomplete approximation of the stochastic spatial geometry of biodiversity in tropical forests. The assumption of independent interspecific placements is most

  19. Global patterns in sandy beach macrofauna: Species richness, abundance, biomass and body size

    NASA Astrophysics Data System (ADS)

    Defeo, Omar; McLachlan, Anton

    2013-10-01

    Global patterns in species richness in sandy beach ecosystems have been poorly understood until comparatively recently, because of the difficulty of compiling high-resolution databases at continental scales. We analyze information from more than 200 sandy beaches around the world, which harbor hundreds of macrofauna species, and explore latitudinal trends in species richness, abundance and biomass. Species richness increases from temperate to tropical sites. Abundance follows contrasting trends depending on the slope of the beach: in gentle slope beaches, it is higher at temperate sites, whereas in steep-slope beaches it is higher at the tropics. Biomass follows identical negative trends for both climatic regions at the whole range of beach slopes, suggesting decreasing rates in carrying capacity of the environment towards reflective beaches. Various morphodynamic variables determine global trends in beach macrofauna. Species richness, abundance and biomass are higher at dissipative than at reflective beaches, whereas a body size follows the reverse pattern. A generalized linear model showed that large tidal range (which determines the vertical dimension of the intertidal habitat), small size of sand particles and flat beach slope (a product of the interaction among wave energy, tidal range and grain size) are correlated with high species richness, suggesting that these parameters represent the most parsimonious variables for modelling patterns in sandy beach macrofauna. Large-scale patterns indicate a scaling of abundance to a body size, suggesting that dissipative beaches harbor communities with highest abundance and species with the smallest body sizes. Additional information for tropical and northern hemisphere sandy beaches (underrepresented in our compilation) is required to decipher more conclusive trends, particularly in abundance, biomass and body size. Further research should integrate meaningful oceanographic variables, such as temperature and primary

  20. Use of community-composition data to predict the fecundity and abundance of species.

    PubMed

    Elmendorf, Sarah C; Moore, Kara A

    2008-12-01

    Species distribution models are critical tools for the prediction of invasive species spread and conservation of biodiversity. The majority of species distribution models have been built with environmental data. Community ecology theory suggests that species co-occurrence data could also be used to predict current and potential distributions of species. Species assemblages are the products of biotic and environmental constraints on the distribution of individual species and as a result may contain valuable information for niche modeling. We compared the predictive ability of distribution models of annual grassland plants derived from either environmental or community-composition data. Composition-based models were built with the presence or absence of species at a site as predictors of site quality, whereas environment-based models were built with soil chemistry, moisture content, above-ground biomass, and solar radiation as predictors. The reproductive output of experimentally seeded individuals of 4 species and the abundance of 100 species were used to evaluate the resulting models. Community-composition data were the best predictors of both the site-specific reproductive output of sown individuals and the site-specific abundance of existing populations. Successful community-based models were robust to omission of data on the occurrence of rare species, which suggests that even very basic survey data on the occurrence of common species may be adequate for generating such models. Our results highlight the need for increased public availability of ecological survey data to facilitate community-based modeling at scales relevant to conservation. PMID:18847440

  1. The anomalous molecular abundances of Comet P/Wolf-Harrington

    NASA Technical Reports Server (NTRS)

    Schleicher, David G.; Bus, Schelte J.; Osip, David J.

    1993-01-01

    Production rates of OH, CN, C2, C3, NH, and NH2 were derived from different data sets for the Comet P/Wolf-Harrington, and a dust production measure was calculated. This comet is found to be depleted by more than an order of magnitude in its pure carbon species compared with OH and CN. The data obtained suggest that a nonnegligible fraction of comets or their constituent components formed at a different temperature and thus at a different location and/or time than the majority of comets.

  2. Copepod abundance and species composition in the Eastern subtropical/tropical Atlantic

    NASA Astrophysics Data System (ADS)

    Schnack-Schiel, Sigrid B.; Mizdalski, Elke; Cornils, Astrid

    2010-12-01

    Abundance and species composition of copepods were studied during the expedition ANT XXI/1 on a latitudinal transect in the eastern Atlantic from 34°49.5'N to 27°28.1'S between 2-20 November 2002. Stratified zooplankton tows were carried out at 19 stations with a multiple opening-closing net between 300 m water depth and the surface. Cyclopoid and calanoid copepods showed similar patterns of distribution and abundance. Oithona was the most abundant cyclopoid genus, followed by Oncaea. A total of 149 calanoid copepod species were identified. Clausocalanus was by far the most abundant genus, comprising on average about 45% of all calanoids, followed by Calocalanus (13%), Delibus (9%), Paracalanus (6%), and Pleuromamma (5%). All other genera comprised on average less than 5% each, with 40 genera less than 1%. The calanoid copepod communities were distinguished broadly in accordance with sea surface temperature, separating the subtropical from the tropical stations, and were largely determined by variation in species composition and species abundance. Nine Clausocalanus species were identified. The most numerous Clausocalanus species was C. furcatus, which on average comprised half of all adult of this genus. C. pergens, C. paululus, and C. jobei, contributed an average of 19%, 9%, and 9%, respectively. The Clausocalanus species differed markedly in their horizontal and vertical distributions: C. furcatus, C. jobei, and C. mastigophorus had widespread distributions and inhabited the upper water layers. Major differences between the species were found in abundance. C. paululus and C. arcuicornis were biantitropical and were absent or occurred in very low numbers in the equatorial zone. C. parapergens was found at all stations and showed a bimodal distribution pattern with maxima in the subtropics. C. pergens occurred in higher numbers only at the southern stations, where it replaced C. furcatus in dominance. In contrast to the widespread species, the bulk of the C

  3. Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees

    PubMed Central

    Chave, Jérôme

    2016-01-01

    Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.

  4. Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees

    PubMed Central

    Chave, Jérôme

    2016-01-01

    Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin. PMID:27651991

  5. Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees.

    PubMed

    Dexter, Kyle; Chave, Jérôme

    2016-01-01

    Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.

  6. Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees.

    PubMed

    Dexter, Kyle; Chave, Jérôme

    2016-01-01

    Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin. PMID:27651991

  7. Species richness and relative abundance of birds in natural and anthropogenic fragments of Brazilian Atlantic forest.

    PubMed

    dos Anjos, Luiz

    2004-06-01

    Bird communities were studied in two types of fragmented habitat of Atlantic forest in the State of Paraná, southern Brazil; one consisted of forest fragments that were created as a result of human activities (forest remnants), the other consisted of a set of naturally occurring forest fragments (forest patches). Using quantitative data obtained by the point counts method in 3 forest patches and 3 forest remnants during one year, species richness and relative abundance were compared in those habitats, considering species groups according to their general feeding habits. Insectivores, omnivores, and frugivores presented similar general tendencies in both habitats (decrease of species number with decreasing size and increasing isolation of forest fragment). However, these tendencies were different, when considering the relative abundance data: the trunk insectivores presented the highest value in the smallest patch while the lowest relative abundance was in the smallest remnant. In the naturally fragmented landscape, time permitted that the loss of some species of trunk insectivores be compensated for the increase in abundance of other species. In contrast, the remnants essentially represented newly formed islands that are not yet at equilibrium and where future species losses would make them similar to the patches.

  8. Predators reduce abundance and species richness of coral reef fish recruits via non-selective predation

    NASA Astrophysics Data System (ADS)

    Heinlein, J. M.; Stier, A. C.; Steele, M. A.

    2010-06-01

    Predators have important effects on coral reef fish populations, but their effects on community structure have only recently been investigated and are not yet well understood. Here, the effect of predation on the diversity and abundance of young coral reef fishes was experimentally examined in Moorea, French Polynesia. Effects of predators were quantified by monitoring recruitment of fishes onto standardized patch reefs in predator-exclosure cages or uncaged reefs. At the end of the 54-day experiment, recruits were 74% less abundant on reefs exposed to predators than on caged ones, and species richness was 42% lower on reefs exposed to predators. Effects of predators varied somewhat among families, however, rarefaction analysis indicated that predators foraged non-selectively among species. These results indicate that predation can alter diversity of reef fish communities by indiscriminately reducing the abundance of fishes soon after settlement, thereby reducing the number of species present on reefs.

  9. Global correlations in tropical tree species richness and abundance reject neutrality.

    PubMed

    Ricklefs, Robert E; Renner, Susanne S

    2012-01-27

    Patterns of species richness and relative abundance at some scales cannot be distinguished from predictions of null models, including zero-sum neutral models of population change and random speciation-extinction models of evolutionary diversification. Both models predict that species richness or population abundance produced by independent iterations of the same processes in different regions should be uncorrelated. We find instead that the number of species and individuals in families of trees in forest plots are strongly correlated across Southeast Asia, Africa, and tropical America. These correlations imply that deterministic processes influenced by evolutionarily conservative family-level traits constrain the number of confamilial tree species and individuals that can be supported in regional species pools and local assemblages in humid tropical forests.

  10. Soil biota effects on local abundances of three grass species along a land-use gradient.

    PubMed

    Heinze, J; Werner, T; Weber, E; Rillig, M C; Joshi, J

    2015-09-01

    Biotic plant-soil interactions and land-use intensity are known to affect plant individual fitness as well as competitiveness and therefore plant-species abundances in communities. Therefore, a link between soil biota and land-use intensity on local abundance of plant species in grasslands can be expected. In two greenhouse experiments, we investigated the effects of soil biota from grassland sites differing in land-use intensity on three grass species that vary in local abundances along this land-use gradient. We were interested in those soil-biota effects that are associated with land-use intensity, and whether these effects act directly or indirectly. Therefore, we grew the three plant species in two separate experiments as single individuals and in mixtures and compared their performance. As single plants, all three grasses showed a similar performance with and without soil biota. In contrast, in mixtures growth of the species in response to the presence or absence of soil biota differed. This resulted in different soil-biota effects that tend to correspond with patterns of species-specific abundances in the field for two of the three species tested. Our results highlight the importance of indirect interactions between plants and soil microorganisms and suggest that combined effects of soil biota and plant-plant interactions are involved in structuring plant communities. In conclusion, our experiments suggest that soil biota may have the potential to alter effects of plant-plant interactions and therefore influence plant-species abundances and diversity in grasslands.

  11. Using species abundance distribution models and diversity indices for biogeographical analyses

    NASA Astrophysics Data System (ADS)

    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

  12. Habitat partitioning by five congeneric and abundant Choerodon species (Labridae) in a large subtropical marine embayment

    NASA Astrophysics Data System (ADS)

    Fairclough, D. V.; Clarke, K. R.; Valesini, F. J.; Potter, I. C.

    2008-04-01

    The habitats occupied by the juveniles and adults of five morphologically similar, diurnally active and abundant Choerodon species in the large subtropical environment of Shark Bay, a "World Heritage Property" on the west coast of Australia, have been determined. The densities of the two life cycle stages of each Choerodon species in those habitats were used in various analyses to test the hypotheses that: (1) habitats are partitioned among these species and between their juveniles and adults; (2) such habitat partitioning is greatest in the case of the two Western Australian endemic species, i.e. Choerodon rubescens and Choerodon cauteroma; and (3) the extent of habitat partitioning between both of these two species and the only species that is widely distributed in the Indo-West Pacific, i.e. Choerodon schoenleinii, will be less pronounced. Initially, catches of each of the five congeneric species, obtained during other studies in Shark Bay by angling, spearfishing and otter trawling, were collated to elucidate the broad distribution of these species in that embayment. Underwater visual census was then used to determine the densities of the juveniles and adults of each Choerodon species at sites representing the four habitat types in which one or more of these species had been caught, i.e. reefs in marine waters at the western boundary of the bay and seagrass, reefs and rocky shorelines in the two inner gulfs. The compositions of the Choerodon species over marine (entrance channel) reefs and in seagrass were significantly different and each differed significantly from those in both inner gulf reefs and rocky shorelines, which were, however, not significantly different. Choerodon rubescens was restricted to exposed marine reefs, and thus occupied a different habitat and location of the bay than C. cauteroma, the other endemic species, which was almost exclusively confined to habitats found in the inner gulfs. Choerodon cauteroma differed from other Choerodon

  13. Differentiation of Lactobacillus Species by Molecular Typing

    PubMed Central

    Zhong, Wei; Millsap, Kevin; Bialkowska-Hobrzanska, Hanna; Reid, Gregor

    1998-01-01

    A total of 64 type, reference, clinical, health food, and stock isolates of microaerophilic Lactobacillus species were examined by restriction fragment length polymorphisms. Of particular interest were members of six of the eight species most commonly recovered from the vaginas of healthy premenopausal women, namely, Lactobacillus jensenii, L. casei, L. rhamnosus, L. acidophilus, L. plantarum, and L. fermentum. Six main groupings were identified on the basis of ribotyping. This technique was able to classify fresh isolates to the species level. In the case of the ribotype A grouping for L. rhamnosus, differences between strains were evident by chromosome typing (chromotyping). Many isolates did not possess plasmids. Six L. rhamnosus strains isolated from four different health food products appeared to be identical to L. rhamnosus ATCC 21052. The molecular typing system is useful for identifying and differentiating Lactobacillus isolates. Studies of strains of potential importance to the urogenital flora should include molecular characterization as a means of comparing genetic traits with those of strains whose characteristics associated with colonization and antagonism against pathogens have been defined. PMID:9647809

  14. Species composition and seasonal abundance of Chaetognatha in the subtropical coastal waters of Hong Kong

    NASA Astrophysics Data System (ADS)

    Tse, P.; Hui, S. Y.; Wong, C. K.

    2007-06-01

    Species composition, species diversity and seasonal abundance of chaetognaths were studied in Tolo Harbour and the coastal waters of eastern Hong Kong. Tolo Harbour is a semi-enclosed and poorly flushed bay with a long history of eutrophication. It opens into the eastern coast of Hong Kong which is fully exposed to water currents from the South China Sea. Zooplankton samples were collected monthly from July 2003 to July 2005 at six stations. Twenty species of chaetognaths were identified. They included six species of the genus Aidanosagitta ( Aidanosagitta neglecta, Aidanosagitta delicata, Aidanosagitta johorensis, Aidanosagitta regularis, Aidanosagitta bedfordii and Aidanosagitta crassa), four species of the genus Zonosagitta ( Zonosagitta nagae, Zonosagitta bedoti, Zonosagitta bruuni and Zonosagitta pulchra), three species of the genus Ferosagitta ( Ferosagitta ferox, Ferosagitta tokiokai and Ferosagitta robusta) and one species each from the genera Serratosagitta ( Serratosagitta pacifica), Decipisagitta ( Decipisagitta decipiens), Flaccisagitta ( Flaccisagitta enflata), Krohnitta ( Krohnitta pacifica), Mesosagitta ( Mesosagitta minima), Pterosagitta ( Pterosagitta draco) and Sagitta ( Sagitta bipunctata). The most abundant species were Flaccisagitta enflata, A. neglecta and A. delicata. Averaged over the entire study period, the densities of Flaccisagitta enflata, A. neglecta and A. delicata were 9.3, 6.6 and 5.2 ind. m -3, respectively. Overall, these species constituted 39.7%, 28.2% and 22.0% of all chaetognaths collected in the study. Averaged over the entire study, the density of most of the low abundance species was <0.6 ind. m -3. Flaccisagitta enflata occurred throughout the year at all sampling stations. Aidanosagitta neglecta occurred at all sampling stations, but was most common in summer. Aidanosagitta delicata was most common in Tolo Harbour during summer. Tolo Harbour supported larger populations, but fewer species of chaetognaths than the

  15. Tree species composition affects the abundance of rowan (Sorbus aucuparia L.) in urban forests in Finland.

    PubMed

    Hamberg, Leena; Lehvävirta, Susanna; Kotze, D Johan; Heikkinen, Juha

    2015-03-15

    Recent studies have shown a considerable increase in the abundance of rowan (Sorbus aucuparia) saplings in urban forests in Finland, yet the reasons for this increase are not well understood. Here we investigated whether canopy cover or tree species composition, i.e., the basal areas of different tree species in Norway spruce dominated urban forests, affects the abundances of rowan seedlings, saplings and trees. Altogether 24 urban forest patches were investigated. We sampled the number of rowan and other saplings, and calculated the basal areas of trees. We showed that rowan abundance was affected by tree species composition. The basal area of rowan trees (≥ 5 cm in diameter at breast height, dbh) decreased with increasing basal area of Norway spruce, while the cover of rowan seedlings increased with an increase in Norway spruce basal area. However, a decrease in the abundance of birch (Betula pendula) and an increase in the broad-leaved tree group (Acer platanoides, Alnus glutinosa, Alnus incana, Amelanchier spicata, Prunus padus, Quercus robur, Rhamnus frangula and Salix caprea) coincided with a decreasing number of rowans. Furthermore, rowan saplings were scarce in the vicinity of mature rowan trees. Although it seems that tree species composition has an effect on rowan, the relationship between rowan saplings and mature trees is complex, and therefore we conclude that regulating tree species composition is not an easy way to keep rowan thickets under control in urban forests in Finland. PMID:25588119

  16. Tree species composition affects the abundance of rowan (Sorbus aucuparia L.) in urban forests in Finland.

    PubMed

    Hamberg, Leena; Lehvävirta, Susanna; Kotze, D Johan; Heikkinen, Juha

    2015-03-15

    Recent studies have shown a considerable increase in the abundance of rowan (Sorbus aucuparia) saplings in urban forests in Finland, yet the reasons for this increase are not well understood. Here we investigated whether canopy cover or tree species composition, i.e., the basal areas of different tree species in Norway spruce dominated urban forests, affects the abundances of rowan seedlings, saplings and trees. Altogether 24 urban forest patches were investigated. We sampled the number of rowan and other saplings, and calculated the basal areas of trees. We showed that rowan abundance was affected by tree species composition. The basal area of rowan trees (≥ 5 cm in diameter at breast height, dbh) decreased with increasing basal area of Norway spruce, while the cover of rowan seedlings increased with an increase in Norway spruce basal area. However, a decrease in the abundance of birch (Betula pendula) and an increase in the broad-leaved tree group (Acer platanoides, Alnus glutinosa, Alnus incana, Amelanchier spicata, Prunus padus, Quercus robur, Rhamnus frangula and Salix caprea) coincided with a decreasing number of rowans. Furthermore, rowan saplings were scarce in the vicinity of mature rowan trees. Although it seems that tree species composition has an effect on rowan, the relationship between rowan saplings and mature trees is complex, and therefore we conclude that regulating tree species composition is not an easy way to keep rowan thickets under control in urban forests in Finland.

  17. Species abundance distribution and population dynamics in a two-community model of neutral ecology

    NASA Astrophysics Data System (ADS)

    Vallade, M.; Houchmandzadeh, B.

    2006-11-01

    Explicit formulas for the steady-state distribution of species in two interconnected communities of arbitrary sizes are derived in the framework of Hubbell’s neutral model of biodiversity. Migrations of seeds from both communities as well as mutations in both of them are taken into account. These results generalize those previously obtained for the “island-continent” model and they allow an analysis of the influence of the ratio of the sizes of the two communities on the dominance/diversity equilibrium. Exact expressions for species abundance distributions are deduced from a master equation for the joint probability distribution of species in the two communities. Moreover, an approximate self-consistent solution is derived. It corresponds to a generalization of previous results and it proves to be accurate over a broad range of parameters. The dynamical correlations between the abundances of a species in both communities are also discussed.

  18. Does beach nourishment have long-term effects on intertidal macroinvertebrate species abundance?

    NASA Astrophysics Data System (ADS)

    Leewis, Lies; van Bodegom, Peter M.; Rozema, Jelte; Janssen, Gerard M.

    2012-11-01

    Coastal squeeze is the largest threat for sandy coastal areas. To mitigate seaward threats, erosion and sea level rise, sand nourishment is commonly applied. However, its long-term consequences for macroinvertebrate fauna, critical to most ecosystem services of sandy coasts, are still unknown. Seventeen sandy beaches - nourished and controls - were sampled along a chronosequence to investigate the abundance of four dominant macrofauna species and their relations with nourishment year and relevant coastal environmental variables. Dean's parameter and latitude significantly explained the abundance of the spionid polychaete Scolelepis squamata, Beach Index (BI), sand skewness, beach slope and latitude explained the abundance of the amphipod Haustorius arenarius and Relative Tide Range (RTR), recreation and sand sorting explained the abundance of Bathyporeia sarsi. For Eurydice pulchra, no environmental variable explained its abundance. For H. arenarius, E. pulchra and B. sarsi, there was no relation with nourishment year, indicating that recovery took place within a year after nourishment. Scolelepis squamata initially profited from the nourishment with "over-recolonisation". This confirms its role as an opportunistic species, thereby altering the initial community structure on a beach after nourishment. We conclude that the responses of the four dominant invertebrates studied in the years following beach nourishment are species specific. This shows the importance of knowing the autecology of the sandy beach macroinvertebrate fauna in order to be able to mitigate the effects of beach nourishment and other environmental impacts.

  19. The Distribution and Abundance of Bird Species: Towards a Satellite, Data Driven Avian Energetics and Species Richness Model

    NASA Technical Reports Server (NTRS)

    Smith, James A.

    2003-01-01

    This paper addresses the fundamental question of why birds occur where and when they do, i.e., what are the causative factors that determine the spatio-temporal distributions, abundance, or richness of bird species? In this paper we outline the first steps toward building a satellite, data-driven model of avian energetics and species richness based on individual bird physiology, morphology, and interaction with the spatio-temporal habitat. To evaluate our model, we will use the North American Breeding Bird Survey and Christmas Bird Count data for species richness, wintering and breeding range. Long term and current satellite data series include AVHRR, Landsat, and MODIS.

  20. Plankton studies in San Francisco Bay; IV, Phytoplankton abundance and species composition, January 1980 - February 1981

    USGS Publications Warehouse

    Wong, R.L.; Cloern, J.E.

    1982-01-01

    Data are presented on the phytoplankton species composition and abundance in San Francisco Bay from January 1980 through February 1981. Phytoplankton were identified and enumerated in surface samples collected approximately every two weeks at selected stations in the main channel of the Bay, and at shoal stations in the central portion of South San Francisco Bay, San Pablo Bay, and Suisun Bay. Also reported are separate species lists for microphytoplankton (< 60 micrometers) and macrophytoplankton (> 60 micrometers). (Author 's abstract)

  1. Individualistic sensitivities and exposure to climate change explain variation in species' distribution and abundance changes.

    PubMed

    Palmer, Georgina; Hill, Jane K; Brereton, Tom M; Brooks, David R; Chapman, Jason W; Fox, Richard; Oliver, Tom H; Thomas, Chris D

    2015-10-01

    The responses of animals and plants to recent climate change vary greatly from species to species, but attempts to understand this variation have met with limited success. This has led to concerns that predictions of responses are inherently uncertain because of the complexity of interacting drivers and biotic interactions. However, we show for an exemplar group of 155 Lepidoptera species that about 60% of the variation among species in their abundance trends over the past four decades can be explained by species-specific exposure and sensitivity to climate change. Distribution changes were less well predicted, but nonetheless, up to 53% of the variation was explained. We found that species vary in their overall sensitivity to climate and respond to different components of the climate despite ostensibly experiencing the same climate changes. Hence, species have undergone different levels of population "forcing" (exposure), driving variation among species in their national-scale abundance and distribution trends. We conclude that variation in species' responses to recent climate change may be more predictable than previously recognized. PMID:26601276

  2. Individualistic sensitivities and exposure to climate change explain variation in species' distribution and abundance changes.

    PubMed

    Palmer, Georgina; Hill, Jane K; Brereton, Tom M; Brooks, David R; Chapman, Jason W; Fox, Richard; Oliver, Tom H; Thomas, Chris D

    2015-10-01

    The responses of animals and plants to recent climate change vary greatly from species to species, but attempts to understand this variation have met with limited success. This has led to concerns that predictions of responses are inherently uncertain because of the complexity of interacting drivers and biotic interactions. However, we show for an exemplar group of 155 Lepidoptera species that about 60% of the variation among species in their abundance trends over the past four decades can be explained by species-specific exposure and sensitivity to climate change. Distribution changes were less well predicted, but nonetheless, up to 53% of the variation was explained. We found that species vary in their overall sensitivity to climate and respond to different components of the climate despite ostensibly experiencing the same climate changes. Hence, species have undergone different levels of population "forcing" (exposure), driving variation among species in their national-scale abundance and distribution trends. We conclude that variation in species' responses to recent climate change may be more predictable than previously recognized.

  3. Estimating species - area relationships by modeling abundance and frequency subject to incomplete sampling.

    PubMed

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

    2016-07-01

    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 to a

  4. Estimating species - area relationships by modeling abundance and frequency subject to incomplete sampling.

    PubMed

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

    2016-07-01

    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 to a

  5. Estimating Lion Abundance using N-mixture Models for Social Species

    PubMed Central

    Belant, Jerrold L.; Bled, Florent; Wilton, Clay M.; Fyumagwa, Robert; Mwampeta, Stanslaus B.; Beyer, Dean E.

    2016-01-01

    Declining populations of large carnivores worldwide, and the complexities of managing human-carnivore conflicts, require accurate population estimates of large carnivores to promote their long-term persistence through well-informed management We used N-mixture models to estimate lion (Panthera leo) abundance from call-in and track surveys in southeastern Serengeti National Park, Tanzania. Because of potential habituation to broadcasted calls and social behavior, we developed a hierarchical observation process within the N-mixture model conditioning lion detectability on their group response to call-ins and individual detection probabilities. We estimated 270 lions (95% credible interval = 170–551) using call-ins but were unable to estimate lion abundance from track data. We found a weak negative relationship between predicted track density and predicted lion abundance from the call-in surveys. Luminosity was negatively correlated with individual detection probability during call-in surveys. Lion abundance and track density were influenced by landcover, but direction of the corresponding effects were undetermined. N-mixture models allowed us to incorporate multiple parameters (e.g., landcover, luminosity, observer effect) influencing lion abundance and probability of detection directly into abundance estimates. We suggest that N-mixture models employing a hierarchical observation process can be used to estimate abundance of other social, herding, and grouping species. PMID:27786283

  6. Regular Patterns for Proteome-Wide Distribution of Protein Abundance across Species

    PubMed Central

    Jiang, Ying; Ying, Wantao; Wu, Songfeng; Zhu, Yunping; Liu, Siqi; Yang, Pengyuan; Qian, Xiaohong; He, Fuchu

    2012-01-01

    A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category) are more abundant than those that act on information modulation (information category). Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function. PMID:22427835

  7. Habitat traits and species interactions differentially affect abundance and body size in pond-breeding amphibians.

    PubMed

    Ousterhout, Brittany H; Anderson, Thomas L; Drake, Dana L; Peterman, William E; Semlitsch, Raymond D

    2015-07-01

    In recent studies, habitat traits have emerged as stronger predictors of species occupancy, abundance, richness and diversity than competition. However, in many cases, it remains unclear whether habitat also mediates processes more subtle than competitive exclusion, such as growth, or whether intra- and interspecific interactions among individuals of different species may be better predictors of size. To test whether habitat traits are a stronger predictor of abundance and body size than intra- and interspecific interactions, we measured the density and body size of three species of larval salamanders in 192 ponds across a landscape. We found that the density of larvae was best predicted by models that included habitat features, while models incorporating interactions among individuals of different species best explained the body size of larvae. Additionally, we found a positive relationship between focal species density and congener density, while focal species body size was negatively related to congener density. We posit that salamander larvae may not experience competitive exclusion and thus reduced densities, but instead compensate for increased competition behaviourally (e.g. reduced foraging), resulting in decreased growth. The discrepancy between larval density and body size, a strong predictor of fitness in this system, also highlights a potential shortcoming in using density or abundance as a metric of habitat quality or population health. PMID:25643605

  8. Habitat traits and species interactions differentially affect abundance and body size in pond-breeding amphibians.

    PubMed

    Ousterhout, Brittany H; Anderson, Thomas L; Drake, Dana L; Peterman, William E; Semlitsch, Raymond D

    2015-07-01

    In recent studies, habitat traits have emerged as stronger predictors of species occupancy, abundance, richness and diversity than competition. However, in many cases, it remains unclear whether habitat also mediates processes more subtle than competitive exclusion, such as growth, or whether intra- and interspecific interactions among individuals of different species may be better predictors of size. To test whether habitat traits are a stronger predictor of abundance and body size than intra- and interspecific interactions, we measured the density and body size of three species of larval salamanders in 192 ponds across a landscape. We found that the density of larvae was best predicted by models that included habitat features, while models incorporating interactions among individuals of different species best explained the body size of larvae. Additionally, we found a positive relationship between focal species density and congener density, while focal species body size was negatively related to congener density. We posit that salamander larvae may not experience competitive exclusion and thus reduced densities, but instead compensate for increased competition behaviourally (e.g. reduced foraging), resulting in decreased growth. The discrepancy between larval density and body size, a strong predictor of fitness in this system, also highlights a potential shortcoming in using density or abundance as a metric of habitat quality or population health.

  9. Observed and predicted effects of climate change on species abundance in protected areas

    NASA Astrophysics Data System (ADS)

    Johnston, Alison; Ausden, Malcolm; Dodd, Andrew M.; Bradbury, Richard B.; Chamberlain, Dan E.; Jiguet, Frédéric; Thomas, Chris D.; Cook, Aonghais S. C. P.; Newson, Stuart E.; Ockendon, Nancy; Rehfisch, Mark M.; Roos, Staffan; Thaxter, Chris B.; Brown, Andy; Crick, Humphrey Q. P.; Douse, Andrew; McCall, Rob A.; Pontier, Helen; Stroud, David A.; Cadiou, Bernard; Crowe, Olivia; Deceuninck, Bernard; Hornman, Menno; Pearce-Higgins, James W.

    2013-12-01

    The dynamic nature and diversity of species' responses to climate change poses significant difficulties for developing robust, long-term conservation strategies. One key question is whether existing protected area networks will remain effective in a changing climate. To test this, we developed statistical models that link climate to the abundance of internationally important bird populations in northwestern Europe. Spatial climate-abundance models were able to predict 56% of the variation in recent 30-year population trends. Using these models, future climate change resulting in 4.0°C global warming was projected to cause declines of at least 25% for more than half of the internationally important populations considered. Nonetheless, most EU Special Protection Areas in the UK were projected to retain species in sufficient abundances to maintain their legal status, and generally sites that are important now were projected to be important in the future. The biological and legal resilience of this network of protected areas is derived from the capacity for turnover in the important species at each site as species' distributions and abundances alter in response to climate. Current protected areas are therefore predicted to remain important for future conservation in a changing climate.

  10. Consequences of organic farming and landscape heterogeneity for species richness and abundance of farmland birds.

    PubMed

    Smith, Henrik G; Dänhardt, Juliana; Lindström, Ake; Rundlöf, Maj

    2010-04-01

    It has been suggested that organic farming may benefit farmland biodiversity more in landscapes that have lost a significant part of its former landscape heterogeneity. We tested this hypothesis by comparing bird species richness and abundance during the breeding season in organic and conventional farms, matched to eliminate all differences not directly linked to the farming practice, situated in either homogeneous plains with only a little semi-natural habitat or in heterogeneous farmland landscapes with abundant field borders and semi-natural grasslands. The effect of farm management on species richness interacted with landscape structure, such that there was a positive relationship between organic farming and diversity only in homogeneous landscapes. This pattern was mainly dependent on the species richness of passerine birds, in particular those that were invertebrate feeders. Species richness of non-passerines was positively related to organic farming independent of the landscape context. Bird abundance was positively related to landscape heterogeneity but not to farm management. This was mainly because the abundance of passerines, particularly invertebrate feeders, was positively related to landscape heterogeneity. We suggest that invertebrate feeders particularly benefit from organic farming because of improved foraging conditions through increased invertebrate abundances in otherwise depauperate homogeneous landscapes. Although many seed-eaters also benefit from increased insect abundance, they may also utilize crop seed resources in homogeneous landscapes and conventional farms. The occurrence of an interactive effect of organic farming and landscape heterogeneity on bird diversity will have consequences for the optimal allocation of resources to restore the diversity of farmland birds.

  11. Do predators control prey species abundance? An experimental test with brown treesnakes on Guam.

    PubMed

    Campbell, Earl W; Adams, Amy A Yackel; Converse, Sarah J; Fritts, Thomas H; Rodda, Gordon H

    2012-05-01

    The effect of predators on the abundance of prey species is a topic of ongoing debate in ecology; the effect of snake predators on their prey has been less debated, as there exists a general consensus that snakes do not negatively influence the abundance of their prey. However, this viewpoint has not been adequately tested. We quantified the effect of brown treesnake (Boiga irregularis) predation on the abundance and size of lizards on Guam by contrasting lizards in two 1-ha treatment plots of secondary forest from which snakes had been removed and excluded vs. two 1-ha control plots in which snakes were monitored but not removed or excluded. We removed resident snakes from the treatment plots with snake traps and hand capture, and snake immigration into these plots was precluded by electrified snake barriers. Lizards were sampled in all plots quarterly for a year following snake elimination in the treatment plots. Following the completion of this experiment, we used total removal sampling to census lizards on a 100-m2 subsample of each plot. Results of systematic lizard population monitoring before and after snake removal suggest that the abundance of the skink, Carlia ailanpalai, increased substantially and the abundance of two species of gekkonids, Lepidodactylus lugubris and Hemidactylus frenatus, also increased on snake-free plots. No treatment effect was observed for the skink Emoia caeruleocauda. Mean snout-vent length of all lizard species only increased following snake removal in the treatment plots. The general increase in prey density and mean size was unexpected in light of the literature consensus that snakes do not control the abundance of their prey species. Our findings show that, at least where alternate predators are lacking, snakes may indeed affect prey populations.

  12. Do predators control prey species abundance? An experimental test with brown treesnakes on Guam

    USGS Publications Warehouse

    Campbell, Earl W.; Yackel Adams, Amy A.; Converse, Sarah J.; Fritts, Thomas H.; Rodda, Gordon H.

    2012-01-01

    The effect of predators on the abundance of prey species is a topic of ongoing debate in ecology; the effect of snake predators on their prey has been less debated, as there exists a general consensus that snakes do not negatively influence the abundance of their prey. However, this viewpoint has not been adequately tested. We quantified the effect of brown treesnake (Boiga irregularis) predation on the abundance and size of lizards on Guam by contrasting lizards in two 1-ha treatment plots of secondary forest from which snakes had been removed and excluded vs. two 1-ha control plots in which snakes were monitored but not removed or excluded. We removed resident snakes from the treatment plots with snake traps and hand capture, and snake immigration into these plots was precluded by electrified snake barriers. Lizards were sampled in all plots quarterly for a year following snake elimination in the treatment plots. Following the completion of this experiment, we used total removal sampling to census lizards on a 100-m2 subsample of each plot. Results of systematic lizard population monitoring before and after snake removal suggest that the abundance of the skink, Carlia ailanpalai, increased substantially and the abundance of two species of gekkonids, Lepidodactylus lugubris and Hemidactylus frenatus, also increased on snake-free plots. No treatment effect was observed for the skink Emoia caeruleocauda. Mean snout–vent length of all lizard species only increased following snake removal in the treatment plots. The general increase in prey density and mean size was unexpected in light of the literature consensus that snakes do not control the abundance of their prey species. Our findings show that, at least where alternate predators are lacking, snakes may indeed affect prey populations.

  13. Abundances of D, O, and other species towards the Halo Star HD 93521

    NASA Astrophysics Data System (ADS)

    Kruk, J. W.; Oliveira, C.; Sembach, K. R.; Savage, B. D.

    2006-06-01

    FUSE spectra of the halo star HD 93521 have been analyzed to determine column densities of D I, O I, N I, Ar I, Fe II, and H2 in the intermediate velocity cloud (IVC) along the line of sight. Combining these results with those from GHRS and ground-based spectra provides a comprehensive inventory of abundances in the IVC. We find a relatively high value for D/H (17.4 ppm), near solar abundances and low depletions for refractory elements, and a very low molecular fraction.

  14. Effects of land-use intensity on arthropod species abundance distributions in grasslands.

    PubMed

    Simons, Nadja K; Gossner, Martin M; Lewinsohn, Thomas M; Lange, Markus; Türke, Manfred; Weisser, Wolfgang W

    2015-01-01

    As a rule, communities consist of few abundant and many rare species, which is reflected in the characteristic shape of species abundance distributions (SADs). The processes that shape these SADs have been a longstanding problem for ecological research. Although many studies found strong negative effects of increasing land-use intensity on diversity, few reports consider land-use effects on SADs. Arthropods (insects and spiders) were sampled on 142 grassland plots in three regions in Germany, which were managed with different modes (mowing, fertilization and/or grazing) and intensities of land use. We analysed the effect of land use on three parameters characterizing the shape of SADs: abundance decay rate (the steepness of the rank abundance curve, represented by the niche-preemption model parameter), dominance (Berger-Parker dominance) and rarity (Fisher's alpha). Furthermore, we tested the core-satellite hypothesis by comparing the species' rank within the SAD to their distribution over the land-use gradient. When data on Araneae, Cicadina, Coleoptera, Heteroptera and Orthoptera were combined, abundance decay rate increased with combined land-use intensity (including all modes). Among the single land-use modes, increasing fertilization and grazing intensity increased the decay rate of all taxa, while increasing mowing frequency significantly affected the decay rate only in interaction with fertilization. Results of single taxa differed in their details, but all significant interaction effects included fertilization intensity. Dominance generally increased with increasing fertilization and rarity decreased with increasing grazing or mowing intensity, despite small differences among taxa and regions. The majority of species found on <10% of the plots per region were generally rare (<10 individuals), which is in accordance with the core-satellite hypothesis. We found significant differences in the rarity and dominance of species between plots of low and high

  15. Habitat Selection and Temporal Abundance Fluctuations of Demersal Cartilaginous Species in the Aegean Sea (Eastern Mediterranean)

    PubMed Central

    Maravelias, Christos D.; Tserpes, George; Pantazi, Maria; Peristeraki, Panagiota

    2012-01-01

    Predicting the occurrence of keystone top predators in a multispecies marine environment, such as the Mediterranean Sea, can be of considerable value to the long-term sustainable development of the fishing industry and to the protection of biodiversity. We analysed fisheries independent scientific bottom trawl survey data of two of the most abundant cartilaginous fish species (Scyliorhinus canicula, Raja clavata) in the Aegean Sea covering an 11-year sampling period. The current findings revealed a declining trend in R. clavata and S. canicula abundance from the late ′90 s until 2004. Habitats with the higher probability of finding cartilaginous fish present were those located in intermediate waters (depth: 200–400 m). The present results also indicated a preferential species' clustering in specific geographic and bathymetric regions of the Aegean Sea. Depth appeared to be one of the key determining factors for the selection of habitats for all species examined. With cartilaginous fish species being among the more biologically sensitive fish species taken in European marine fisheries, our findings, which are based on a standardized scientific survey, can contribute to the rational exploitation and management of their stocks by providing important information on temporal abundance trends and habitat preferences. PMID:22536389

  16. Spatial predictability of juvenile fish species richness and abundance in a coral reef environment

    NASA Astrophysics Data System (ADS)

    Mellin, C.; Andréfouët, S.; Ponton, D.

    2007-12-01

    Juvenile reef fish communities represent an essential component of coral reef ecosystems in the current focus of fish population dynamics and coral reef resilience. Juvenile fish survival depends on habitat characteristics and is, following settlement, the first determinant of the number of individuals within adult populations. The goal of this study was to provide methods for mapping juvenile fish species richness and abundance into spatial domains suitable for micro and meso-scale analysis and management decisions. Generalized Linear Models predicting juvenile fish species richness and abundance were developed according to spatial and temporal environmental variables measured from 10 m up to 10 km in the southwest lagoon of New Caledonia. The statistical model was further spatially generalized using a 1.5-m resolution, independently created, remotely sensed, habitat map. This procedure revealed that : (1) spatial factors at 10 to 100-m scale explained up to 71% of variability in juvenile species richness, (2) a small improvement (75%) was gained when a combination of environmental variables at different spatial and temporal scales was used and (3) the coupling of remotely sensed data, geographical information system tools and point-based ecological data showed that the highest species richness and abundance were predicted along a narrow margin overlapping the coral reef flat and adjacent seagrass beds. Spatially explicit models of species distribution may be relevant for the management of reef communities when strong relationships exist between faunistic and environmental variables and when models are built at appropriate scales.

  17. Abundance of biting midge species (Diptera: Ceratopogonidae, Culicoides spp.) on cattle farms in Korea

    PubMed Central

    Oem, Jae-Ku; Chung, Joon-Yee; Kwon, Mee-Soon; Kim, Toh-Kyung; Lee, Tae-Uk

    2013-01-01

    Culicoides biting midges were collected on three cattle farms weekly using light traps overnight from May to October between 2010 and 2011 in the southern part of Korea. The seasonal and geographical abundance of Culicodes spp. were measured. A total of 16,538 biting midges were collected from 2010 to 2011, including seven species of Culicoides, four of which represented 98.42% of the collected specimens. These four species were Culicodes (C.) punctatus (n = 14,413), C. arakawae (n = 1,120), C. oxystoma (n = 427), and C. maculatus (n = 318). C. punctatus was the predominant species (87.15%). PMID:23388441

  18. Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways.

    PubMed

    Dai, Yu; Wu, Zhen; Xie, Shuguang; Liu, Yong

    2015-11-01

    Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating the methane emission in soil ecosystems to the atmosphere. However, the impact of plant species and plantation ways on the distribution of MOB remains unclear. The present study investigated MOB abundance and structure in plateau soils with different plant species and plantation ways (natural and managed). Soils were collected from unmanaged wild grassland and naturally forested sites, and managed farmland and afforested sites. A large variation in MOB abundance and structure was found in these studied soils. In addition, both type I MOB (Methylocaldum) and type II MOB (Methylocystis) were detected in these soils, while type II MOB usually outnumbered type I MOB. The distribution of soil MOB community was found to be collectively regulated by plantation way, plant species, the altitude of sampling site, and soil properties. PMID:26142389

  19. Historic Mining and Agriculture as Indicators of Occurrence and Abundance of Widespread Invasive Plant Species

    PubMed Central

    Calinger, Kellen; Calhoon, Elisabeth; Chang, Hsiao-chi; Whitacre, James; Wenzel, John; Comita, Liza; Queenborough, Simon

    2015-01-01

    Anthropogenic disturbances often change ecological communities and provide opportunities for non-native species invasion. Understanding the impacts of disturbances on species invasion is therefore crucial for invasive species management. We used generalized linear mixed effects models to explore the influence of land-use history and distance to roads on the occurrence and abundance of two invasive plant species (Rosa multiflora and Berberis thunbergii) in a 900-ha deciduous forest in the eastern U.S.A., the Powdermill Nature Reserve. Although much of the reserve has been continuously forested since at least 1939, aerial photos revealed a variety of land-uses since then including agriculture, mining, logging, and development. By 2008, both R. multiflora and B. thunbergii were widespread throughout the reserve (occurring in 24% and 13% of 4417 10-m diameter regularly-placed vegetation plots, respectively) with occurrence and abundance of each varying significantly with land-use history. Rosa multiflora was more likely to occur in historically farmed, mined, logged or developed plots than in plots that remained forested, (log odds of 1.8 to 3.0); Berberis thunbergii was more likely to occur in plots with agricultural, mining, or logging history than in plots without disturbance (log odds of 1.4 to 2.1). Mining, logging, and agriculture increased the probability that R. multiflora had >10% cover while only past agriculture was related to cover of B. thunbergii. Proximity to roads was positively correlated with the occurrence of R. multiflora (a 0.26 increase in the log odds for every 1-m closer) but not B. thunbergii, and roads had no impact on the abundance of either species. Our results indicated that a wide variety of disturbances may aid the introduction of invasive species into new habitats, while high-impact disturbances such as agriculture and mining increase the likelihood of high abundance post-introduction. PMID:26046534

  20. Historic Mining and Agriculture as Indicators of Occurrence and Abundance of Widespread Invasive Plant Species.

    PubMed

    Calinger, Kellen; Calhoon, Elisabeth; Chang, Hsiao-Chi; Whitacre, James; Wenzel, John; Comita, Liza; Queenborough, Simon

    2015-01-01

    Anthropogenic disturbances often change ecological communities and provide opportunities for non-native species invasion. Understanding the impacts of disturbances on species invasion is therefore crucial for invasive species management. We used generalized linear mixed effects models to explore the influence of land-use history and distance to roads on the occurrence and abundance of two invasive plant species (Rosa multiflora and Berberis thunbergii) in a 900-ha deciduous forest in the eastern U.S.A., the Powdermill Nature Reserve. Although much of the reserve has been continuously forested since at least 1939, aerial photos revealed a variety of land-uses since then including agriculture, mining, logging, and development. By 2008, both R. multiflora and B. thunbergii were widespread throughout the reserve (occurring in 24% and 13% of 4417 10-m diameter regularly-placed vegetation plots, respectively) with occurrence and abundance of each varying significantly with land-use history. Rosa multiflora was more likely to occur in historically farmed, mined, logged or developed plots than in plots that remained forested, (log odds of 1.8 to 3.0); Berberis thunbergii was more likely to occur in plots with agricultural, mining, or logging history than in plots without disturbance (log odds of 1.4 to 2.1). Mining, logging, and agriculture increased the probability that R. multiflora had >10% cover while only past agriculture was related to cover of B. thunbergii. Proximity to roads was positively correlated with the occurrence of R. multiflora (a 0.26 increase in the log odds for every 1-m closer) but not B. thunbergii, and roads had no impact on the abundance of either species. Our results indicated that a wide variety of disturbances may aid the introduction of invasive species into new habitats, while high-impact disturbances such as agriculture and mining increase the likelihood of high abundance post-introduction. PMID:26046534

  1. Historic Mining and Agriculture as Indicators of Occurrence and Abundance of Widespread Invasive Plant Species.

    PubMed

    Calinger, Kellen; Calhoon, Elisabeth; Chang, Hsiao-Chi; Whitacre, James; Wenzel, John; Comita, Liza; Queenborough, Simon

    2015-01-01

    Anthropogenic disturbances often change ecological communities and provide opportunities for non-native species invasion. Understanding the impacts of disturbances on species invasion is therefore crucial for invasive species management. We used generalized linear mixed effects models to explore the influence of land-use history and distance to roads on the occurrence and abundance of two invasive plant species (Rosa multiflora and Berberis thunbergii) in a 900-ha deciduous forest in the eastern U.S.A., the Powdermill Nature Reserve. Although much of the reserve has been continuously forested since at least 1939, aerial photos revealed a variety of land-uses since then including agriculture, mining, logging, and development. By 2008, both R. multiflora and B. thunbergii were widespread throughout the reserve (occurring in 24% and 13% of 4417 10-m diameter regularly-placed vegetation plots, respectively) with occurrence and abundance of each varying significantly with land-use history. Rosa multiflora was more likely to occur in historically farmed, mined, logged or developed plots than in plots that remained forested, (log odds of 1.8 to 3.0); Berberis thunbergii was more likely to occur in plots with agricultural, mining, or logging history than in plots without disturbance (log odds of 1.4 to 2.1). Mining, logging, and agriculture increased the probability that R. multiflora had >10% cover while only past agriculture was related to cover of B. thunbergii. Proximity to roads was positively correlated with the occurrence of R. multiflora (a 0.26 increase in the log odds for every 1-m closer) but not B. thunbergii, and roads had no impact on the abundance of either species. Our results indicated that a wide variety of disturbances may aid the introduction of invasive species into new habitats, while high-impact disturbances such as agriculture and mining increase the likelihood of high abundance post-introduction.

  2. Annual cycle of zooplankton abundance and species composition in Izmit Bay (the northeastern Marmara Sea)

    NASA Astrophysics Data System (ADS)

    Isinibilir, Melek; Kideys, Ahmet E.; Tarkan, Ahmet N.; Yilmaz, I. Noyan

    2008-07-01

    The monthly abundance, biomass and taxonomic composition of zooplankton of Izmit Bay (the northeastern Marmara Sea) were studied from October 2001 to September 2002. Most species within the zooplankton community displayed a clear pattern of succession throughout the year. Generally copepods and cladocerans were the most abundant groups, while the contribution of meroplankton increased at inner-most stations and dominated the zooplankton. Both species number ( S) and diversity ( H') were positively influenced by the increase in salinity of upper layers ( r = 0.30 and r = 0.31, p < 0.001, respectively), while chlorophyll a was negatively affected ( r = -0.36, p < 0.001). Even though Noctiluca scintillans had a significant seasonality ( F11,120 = 8.45, p < 0.001, ANOVA), abundance was not related to fluctuations in temperature and only chlorophyll a was adversely correlated ( r = -0.35, p < 0.001). In general, there are some minor differences in zooplankton assemblages of upper and lower layers. A comparison of the species composition and abundance of Izmit Bay with other Black Sea bays reveals a high similarity between them.

  3. Species richness and relative species abundance of Nymphalidae (Lepidoptera) in three forests with different perturbations in the North-Central Caribbean of Costa Rica.

    PubMed

    Stephen, Carolyn; Sánchez, Ragde

    2014-09-01

    Measurements of species richness and species abundance can have important implications for regulations and conservation. This study investigated species richness and abundance of butterflies in the family Nymphalidae at undisturbed, and disturbed habitats in Tirimbina Biological Reserve and Nogal Private Reserve, Sarapiquí, Costa Rica. Traps baited with rotten banana were placed in the canopy and the understory of three habitats: within mature forest, at a river/forest border, and at a banana plantation/forest border. In total, 71 species and 487 individuals were caught and identified during May and June 2011 and May 2013. Species richness and species abundance were found to increase significantly at perturbed habitats (p < 0.0001, p < 0.0001, respectively). The edge effect, in which species richness and abundance increase due to greater complementary resources from different habitats, could be one possible explanation for increased species richness and abundance. PMID:25412524

  4. Modelling of NO destruction in a low-pressure reactor by an Ar plasma jet: species abundances in the reactor

    NASA Astrophysics Data System (ADS)

    Kutasi, Kinga

    2011-03-01

    The destruction of NO molecules by an Ar plasma jet in a low-pressure (0.2 Torr) reactor is investigated by means of a 3D hydrodynamic model. The density distribution of species created through molecular kinetics triggered by the collision of Ar+ with NO is calculated, showing that in the case of the most abundant species a quasi-homogeneous density distribution builds up in a large part of the reactor. The conversion of NO into stable O2 and N2 molecules is followed under different plasma jet conditions and NO gas flows, and the effect of N2 addition on NO destruction is studied. It is shown that in the present system the reproduction of NO molecules on the surface through surface-assisted recombination of N and O atoms becomes impossible due to the fast disappearance of N atoms in the jet's inlet vicinity.

  5. Ratios of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ratios of regioisomers of 74 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using HPLC and the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lequerella oil. The ratios of relative abundances of the fragment ions fr...

  6. Ratios of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ratios of regioisomers of 72 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lesquerella oil. The ratios of ion signal intensities (or relative abundances) of ...

  7. Rich and rare—First insights into species diversity and abundance of Antarctic abyssal Gastropoda (Mollusca)

    NASA Astrophysics Data System (ADS)

    Schwabe, Enrico; Michael Bohn, Jens; Engl, Winfried; Linse, Katrin; Schrödl, Michael

    2007-08-01

    , and all these 84 species seem endemic to Antarctica south of the Polar Front. Comparing diversity and abundances based on epibenthic sledge samples, there is no clear relationship between Antarctic deep-sea gastropod abundance and species richness with depth. However, both Antarctic and adjacent deep-sea areas are still far from being adequately sampled to allow more comprehensive conclusions.

  8. Species Abundance Distribution of Ectoparasites on Norway Rats (Rattus norvegicus) from a Localized Area in Southwest China

    PubMed Central

    Guo, Xian Guo; Dong, Wen Ge; Men, Xing Yuan; Qian, Ti Jun; Wu, Dian; Ren, Tian Guang; Qin, Feng; Song, Wen Yu; Yang, Zhi Hua; Fletcher, Quinn E

    2016-01-01

    Background: The species of ectoparasites that live on a specific host in a geographical region form an ectoparasite community. Species abundance distributions describe the number of individuals observed for each different species that is encountered within a community. Based on properties of the species abundance distribution, the expected total number of species present in the community can be estimated. Methods: Preston’s lognormal distribution model was used to fit the expected species abundance distribution curve. Using the expected species abundance distribution curve, we estimated the total number of expected parasite species present and the amount of species that were likely missed by our sampling in the field. Results: In total, 8040 ectoparasites (fleas, sucking lice, gamasid mites and chigger mites) were collected from 431 Norway rats (Rattus norvegicus) from a localized area in southwest China. These ectoparasites were identified to be 47 species from 26 genera in 10 families. The majority of ectoparasite species were chigger mites (family Trombiculidae) while the majority of individuals were sucking lice in the family Polyplacidae. The expected species abundance distribution curve demonstrated the classic pattern that the majority of ectoparasite species were rare and that there were a few common species. The total expected number of ectoparasite species on R. norvegicus was estimated to be 85 species, and 38 species were likely missed by our sampling in the field. Conclusions: Norway rats harbor a large suite of ectoparasites. Future field investigations should sample large numbers of host individuals to assess ectoparasite populations. PMID:27308277

  9. Effect of trophic status in lakes on fungal species diversity and abundance.

    PubMed

    Pietryczuk, A; Cudowski, A; Hauschild, T

    2014-11-01

    The objective of this study was to determine the species diversity and abundance of fungi in relation to the hydrochemical conditions, with special emphasis on the trophic status and degree of pollution of lakes. The study was conducted in 14 lakes of the Augustów Lakeland (central Europe, NE Poland) with different hydrological conditions, type of stratification and trophic status. The analyses were performed in the hydrological year 2013. In the waters of the studied lakes, the mean abundance of fungi was 5600±3600 CFU/mL. The minimum value (800 CFU/mL) was recorded for the mesotrophic Płaskie Lake, and the maximum value (14,000 CFU/mL) was recorded for the eutrophic Pobojno Lake. A total of 38 species of fungi were identified, including 11 belonging to the aquatic hyphomycetes; up to 14 species were potentially pathogenic fungi. The potentially pathogenic fungi, particularly Candida albicans and Scopulariopsis fusca, were found in lakes with increased concentrations of chloride and sulphate(VI) ions and may thus serve as indicators of the degree of water pollution. This paper illustrates that the species diversity and abundance of fungi in limnic waters depend on the concentration of organic matter, chlorophyll a concentration, and the degree of water pollution. The results suggest that aquatic fungi can be a valuable indicator of the degree of pollution and the sanitary quality of the water. PMID:25145569

  10. Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

    PubMed Central

    Chisholm, Ryan A.; Pacala, Stephen W.

    2010-01-01

    A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function. PMID:20733073

  11. Culicoides monitoring in Belgium in 2011: analysis of spatiotemporal abundance, species diversity and Schmallenberg virus detection.

    PubMed

    DE Regge, N; DE Deken, R; Fassotte, C; Losson, B; Deblauwe, I; Madder, M; Vantieghem, P; Tomme, M; Smeets, F; Cay, A B

    2015-09-01

    In 2011, Culicoides (Diptera: Ceratopogonidae) were collected at 16 locations covering four regions of Belgium with Onderstepoort Veterinary Institute (OVI) traps and at two locations with Rothamsted suction traps (RSTs). Quantification of the collections and morphological identification showed important variations in abundance and species diversity between individual collection sites, even for sites located in the same region. However, consistently higher numbers of Culicoides midges were collected at some sites compared with others. When species abundance and diversity were analysed at regional level, between-site variation disappeared. Overall, species belonging to the subgenus Avaritia together with Culicoides pulicaris (subgenus Culicoides) were the most abundant, accounting for 80% and 96% of all midges collected with RSTs and OVI traps, respectively. Culicoides were present during most of the year, with Culicoides obsoletus complex midges found from 9 February until 27 December. Real-time reverse-transcription polymerase chain reaction screening for Schmallenberg virus in the heads of collected midges resulted in the first detection of the virus in August 2011 and identified C. obsoletus complex, Culicoides chiopterus and Culicoides dewulfi midges as putative vector species. At Libramont in the south of Belgium, no positive pools were identified. PMID:25761054

  12. SEASONAL ABUNDANCE OF ORGANIC MOLECULAR MARKERS IN URBAN PARTICULATE MATTER FROM PHILADELPHIA, PA

    EPA Science Inventory

    Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundances of key tracer compounds together with their dominant sources. Daily PM10...

  13. Differential effects of cocaine exposure on the abundance of phospholipid species in rat brain and blood*

    PubMed Central

    Cummings, Brian S.; Pati, Sumitra; Sahin, Serap; Scholpa, Natalie E.; Monian, Prashant; Trinquero, Paul O.; Clark, Jason K.; Wagner, John J.

    2015-01-01

    Background Lipid profiles in the blood are altered in human cocaine users, suggesting that cocaine-exposure can induce lipid remodeling. Methods Cocaine-induced locomotor sensitization in rats was followed by shotgun lipidomics using electrospray ionization-mass spectrometry (ESI-MS) and determined changes in brain tissues. To determine if any lipidomic changes were also reflected in the blood, we performed principal component analysis (PCA) of lipidomic spectra isolated from cocaine-treated animals. Alterations in the abundance of phospholipid species were correlated with behavioral changes in the magnitude of either the initial response to drug or locomotor sensitization. Results Behavioral sensitization altered the relative abundance of several phospholipid species in the hippocampus and cerebellum, measured one week following the final exposure to cocaine. In contrast, relatively few effects on phospholipids in either the dorsal or the ventral striatum were observed. PCA analysis demonstrated that cocaine altered the relative abundance of several glycerophospholipid species as compared to saline-injected controls. Subsequent MS/MS analysis identified some of these lipids as phosphatidylethanolamines, phosphatidylserines and phosphatidylcholines. The relative abundance of some of these phospholipid species were well correlated (R2 of 0.7 or higher) with either the initial response to cocaine or locomotor sensitization. Conclusion Taken together, these data demonstrate that a cocaine-conditioning experience results in the remodeling of specific phospholipids in rat brain tissue in a region-specific manner and also alters the intensities and types of phospholipid species in rat blood. These results further suggest that such changes may serve as biomarkers to assess the neuroadaptations occurring following repeated exposure to cocaine. PMID:25960140

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

    USGS Publications Warehouse

    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

  15. Abundance, species composition of microzooplankton from the coastal waters of Port Blair, South Andaman Island

    PubMed Central

    2012-01-01

    Background Microzooplankton consisting of protists and metazoa <200 μm. It displays unique feeding mechanisms and behaviours that allow them to graze cells up to five times their own volume. They can grow at rates which equal or exceed prey growth and can serve as a viable food source for metazoans. Moreover, they are individually inconspicuous, their recognition as significant consumers of oceanic primary production. The microzooplankton can be the dominant consumers of phytoplankton production in both oligo- and eutrophic regions of the ocean and are capable of consuming >100% of primary production. Results The microzooplankton of the South Andaman Sea were investigated during September 2011 to January 2012. A total of 44 species belong to 19 genera were recorded in this study. Tintinnids made larger contribution to the total abundance (34%) followed in order by dinoflagellates (24%), ciliates (20%) and copepod nauplii (18%). Foraminifera were numerically less (4%). Tintinnids were represented by 20 species belong to 13 genera, Heterotrophic dinoflagellates were represented by 17 species belong to 3 genera and Ciliates comprised 5 species belong to 3 genera. Eutintinus tineus, Tintinnopsis cylindrical, T. incertum, Protoperidinium divergens, Lomaniella oviformes, Strombidium minimum were the most prevalent microzooplankton. Standing stock of tintinnids ranged from 30–80 cells.L-1 and showed a reverse distribution with the distribution of chlorophyll a relatively higher species diversity and equitability was found in polluted harbour areas. Conclusions The change of environmental variability affects the species composition and abundance of microzooplankton varied spatially and temporarily. The observations clearly demonstrated that the harbor area differed considerably from other area in terms of species present and phytoplankton biomass. Further, the phytoplankton abundance is showed to be strongly influenced by tintinnid with respect to the relationship of

  16. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change.

  17. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change. PMID:25413866

  18. The control of rank-abundance distributions by a competitive despotic species.

    PubMed

    Mac Nally, Ralph; McAlpine, Clive A; Possingham, Hugh P; Maron, Martine

    2014-11-01

    Accounting for differences in abundances among species remains a high priority for community ecology. While there has been more than 80 years of work on trying to explain the characteristic S shape of rank-abundance distributions (RADs), there has been recent conjecture that the form may not depend on ecological processes per se but may be a general phenomenon arising in many unrelated disciplines. We show that the RAD shape can be influenced by an ecological process, namely, interference competition. The noisy miner (Manorina melanocephala) is a hyperaggressive, 'despotic' bird that occurs over much of eastern Australia (>10(6) km(2)). We compiled data for bird communities from 350 locations within its range, which were collected using standard avian survey methods. We used hierarchical Bayesian models to show that the RAD shape was much altered when the abundance of the strong interactor exceeded a threshold density; RADs consistently were steeper when the density of the noisy miner ≥2.5 birds ha(-1). The structure of bird communities at sites where the noisy miner exceeded this density was very different from that at sites where the densities fell below the threshold: species richness and Shannon diversity were much reduced, but mean abundances and mean avian biomass per site did not differ substantially. PMID:25185775

  19. Estimating forest species abundance through linear unmixing of CHRIS/PROBA imagery

    NASA Astrophysics Data System (ADS)

    Stagakis, Stavros; Vanikiotis, Theofilos; Sykioti, Olga

    2016-09-01

    The advancing technology of hyperspectral remote sensing offers the opportunity of accurate land cover characterization of complex natural environments. In this study, a linear spectral unmixing algorithm that incorporates a novel hierarchical Bayesian approach (BI-ICE) was applied on two spatially and temporally adjacent CHRIS/PROBA images over a forest in North Pindos National Park (Epirus, Greece). The scope is to investigate the potential of this algorithm to discriminate two different forest species (i.e. beech - Fagus sylvatica, pine - Pinus nigra) and produce accurate species-specific abundance maps. The unmixing results were evaluated in uniformly distributed plots across the test site using measured fractions of each species derived by very high resolution aerial orthophotos. Landsat-8 images were also used to produce a conventional discrete-type classification map of the test site. This map was used to define the exact borders of the test site and compare the thematic information of the two mapping approaches (discrete vs abundance mapping). The required ground truth information, regarding training and validation of the applied mapping methodologies, was collected during a field campaign across the study site. Abundance estimates reached very good overall accuracy (R2 = 0.98, RMSE = 0.06). The most significant source of error in our results was due to the shadowing effects that were very intense in some areas of the test site due to the low solar elevation during CHRIS acquisitions. It is also demonstrated that the two mapping approaches are in accordance across pure and dense forest areas, but the conventional classification map fails to describe the natural spatial gradients of each species and the actual species mixture across the test site. Overall, the BI-ICE algorithm presented increased potential to unmix challenging objects with high spectral similarity, such as different vegetation species, under real and not optimum acquisition conditions. Its

  20. The fish fauna of Anambra river basin, Nigeria: species abundance and morphometry.

    PubMed

    Odo, Gregory Ejikeme; Didigwu, Nwani Christopher; Eyo, Joseph Effiong

    2009-01-01

    The fish yields of most Nigeria inland waters are generally on the decline for causes that may range from inadequate management of the fisheries to degradation of the water bodies. Sustainable exploitation requires knowledge of the ichthyofaunal composition in the water bodies. We did a survey of fish species in Anambra river basin for 22 months. Fish samples were collected using four different gears -hook and line of size 13, caste nets, gill nets, and cages of mesh sizes of 50 mm, 75 mm, and 100 mm each. We recorded 52 fish species belonging to 17 families: 171, 236, and 169 individuals at Ogurugu, Otuocha, and Nsugbe stations respectively. Two families, Characidae, 19.5%, and Mochokidae, 11.8%, constituted the dominant fish families in the river. The dominant fish species were Citherinus citherius, 9.02%, and Alestes nurse, 7.1%. Other fish species with significant abundance were Synodontis clarias 6.9%, Macrolepidotus curvier 5.7%, Labeo coubie 5.4%, Distichodus rostrtus 4.9%, and Schilbe mystus 4.5%. The meristic features of the two most abundant fish species caught are as follows: Citharinus citharius dorsal fins 20, anal fins 30, caudal fins 21, pectoral fins, 9 and 8 ventral fins, and Alestes nurse 10 dorsal fins, 14 anal fins, 31 caudal fins, 7 pectoral fins and 6 ventral fins. The morphometric features of the two most abundant fish species are Citharinus citharius total length 300 mm, standard length 231 mm, head length 69 mm, body length 101 mm, body girth 176 mm, body weight 900 mg. Alestes nurse total length 200, standard length 140 mm, head length 60 mm, body length 80 mm, body girth 120 mm, body weight 400 mg. The most abundant animal utilizing the basin was Ardea cinerea (D3) with 22.2% occurrence (D4) and this was followed by Caprini with 13.51%, and Varanus niloticus, 10.04%. The least abundant animals utilizing basin were Chephalophus rufilatus, and Erythrocebus patas, with 0.58% each of occurrence. PMID:19637699

  1. Plankton studies in San Francisco Bay; II, Phytoplankton abundance and species composition, July 1977-December 1979

    USGS Publications Warehouse

    Wong, Raymond L. J.; Cloern, James E.

    1981-01-01

    Data are presented on the phytoplankton species composition and abundance in San Francisco Bay from July 1977 through December 1979. Phytoplankton identification and enumerations were made at selected stations. Sample collections were made at selected stations in the main channel of the Bay from Rio Vista on the Sacramento River to Calaveras Point in South San Francisco Bay, and at shoal stations in the central portion of South San Francisco Bay, San Pablo Bay, and Suisun Bay. Also reported, from October 1978 through December 1979, are the calculated phytoplankton carbon and percent nondiatom carbon, and the species list. This study is one component of an ongoing interdisciplinary study of San Francisco Bay. (USGS)

  2. Are the Most Plastic Species the Most Abundant Ones? An Assessment Using a Fish Assemblage

    PubMed Central

    Vidal, Nicolás; Zaldúa, Natalia; D'Anatro, Alejandro; Naya, Daniel E.

    2014-01-01

    Few studies have evaluated phenotypic plasticity at the community level, considering, for example, plastic responses in an entire species assemblage. In addition, none of these studies have addressed the relationship between phenotypic plasticity and community structure. Within this context, here we assessed the magnitude of seasonal changes in digestive traits (seasonal flexibility), and of changes during short-term fasting (flexibility during fasting), occurring in an entire fish assemblage, comprising ten species, four trophic levels, and a 37-fold range in body mass. In addition, we analyzed the relationship between estimates of digestive flexibility and three basic assemblage structure attributes, i.e., species trophic position, body size, and relative abundance. We found that: (1) Seasonal digestive flexibility was not related with species trophic position or with body size; (2) Digestive flexibility during fasting tended to be inversely correlated with body size, as expected from scaling relationships; (3) Digestive flexibility, both seasonal and during fasting, was positively correlated with species relative abundance. In conclusion, the present study identified two trends in digestive flexibility in relation to assemblage structure, which represents an encouraging departure point in the search of general patterns in phenotypic plasticity at the local community scale. PMID:24651865

  3. Sampling designs matching species biology produce accurate and affordable abundance indices

    PubMed Central

    Farley, Sean; Russell, Gareth J.; Butler, Matthew J.; Selinger, Jeff

    2013-01-01

    Wildlife biologists often use grid-based designs to sample animals and generate abundance estimates. Although sampling in grids is theoretically sound, in application, the method can be logistically difficult and expensive when sampling elusive species inhabiting extensive areas. These factors make it challenging to sample animals and meet the statistical assumption of all individuals having an equal probability of capture. Violating this assumption biases results. Does an alternative exist? Perhaps by sampling only where resources attract animals (i.e., targeted sampling), it would provide accurate abundance estimates more efficiently and affordably. However, biases from this approach would also arise if individuals have an unequal probability of capture, especially if some failed to visit the sampling area. Since most biological programs are resource limited, and acquiring abundance data drives many conservation and management applications, it becomes imperative to identify economical and informative sampling designs. Therefore, we evaluated abundance estimates generated from grid and targeted sampling designs using simulations based on geographic positioning system (GPS) data from 42 Alaskan brown bears (Ursus arctos). Migratory salmon drew brown bears from the wider landscape, concentrating them at anadromous streams. This provided a scenario for testing the targeted approach. Grid and targeted sampling varied by trap amount, location (traps placed randomly, systematically or by expert opinion), and traps stationary or moved between capture sessions. We began by identifying when to sample, and if bears had equal probability of capture. We compared abundance estimates against seven criteria: bias, precision, accuracy, effort, plus encounter rates, and probabilities of capture and recapture. One grid (49 km2 cells) and one targeted configuration provided the most accurate results. Both placed traps by expert opinion and moved traps between capture sessions, which

  4. Sampling designs matching species biology produce accurate and affordable abundance indices.

    PubMed

    Harris, Grant; Farley, Sean; Russell, Gareth J; Butler, Matthew J; Selinger, Jeff

    2013-01-01

    Wildlife biologists often use grid-based designs to sample animals and generate abundance estimates. Although sampling in grids is theoretically sound, in application, the method can be logistically difficult and expensive when sampling elusive species inhabiting extensive areas. These factors make it challenging to sample animals and meet the statistical assumption of all individuals having an equal probability of capture. Violating this assumption biases results. Does an alternative exist? Perhaps by sampling only where resources attract animals (i.e., targeted sampling), it would provide accurate abundance estimates more efficiently and affordably. However, biases from this approach would also arise if individuals have an unequal probability of capture, especially if some failed to visit the sampling area. Since most biological programs are resource limited, and acquiring abundance data drives many conservation and management applications, it becomes imperative to identify economical and informative sampling designs. Therefore, we evaluated abundance estimates generated from grid and targeted sampling designs using simulations based on geographic positioning system (GPS) data from 42 Alaskan brown bears (Ursus arctos). Migratory salmon drew brown bears from the wider landscape, concentrating them at anadromous streams. This provided a scenario for testing the targeted approach. Grid and targeted sampling varied by trap amount, location (traps placed randomly, systematically or by expert opinion), and traps stationary or moved between capture sessions. We began by identifying when to sample, and if bears had equal probability of capture. We compared abundance estimates against seven criteria: bias, precision, accuracy, effort, plus encounter rates, and probabilities of capture and recapture. One grid (49 km(2) cells) and one targeted configuration provided the most accurate results. Both placed traps by expert opinion and moved traps between capture sessions

  5. Predicting probability of occurrence and factors affecting distribution and abundance of three Ozark endemic crayfish species at multiple spatial scales

    USGS Publications Warehouse

    Nolen, Matthew S.; Magoulick, Daniel D.; DiStefano, Robert J.; Imhoff, Emily M.; Wagner, Brian K.

    2014-01-01

    We found that a range of environmental variables were important in predicting crayfish distribution and abundance at multiple spatial scales and their importance was species-, response variable- and scale dependent. We would encourage others to examine the influence of spatial scale on species distribution and abundance patterns.

  6. Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression

    PubMed Central

    Henne, Karsten; Fuchs, Felix; Kruth, Sebastian; Horz, Hans-Peter; Conrads, Georg

    2014-01-01

    Background Oral Campylobacter species have been found to be associated with periodontitis progression. While the etiological significance of Campylobacter rectus is quite established, the association of C. gracilis, C. concisus, and C. curvus with health or disease remains contradictory. Objectives This study hypothesizes that the proportion of species within the Campylobacter genus rather than the absolute abundance of a single species is a suitable indicator for periodontitis progression. Design Subgingival plaque from 90 periodontitis patients and gingival sulcus fluid of 32 healthy individuals were subjected to a newly developed nested PCR approach, in which all Campylobacter spp. were amplified simultaneously. The resulting mixture of 16S-rRNA-gene-amplicons were separated by single-stranded conformation polymorphism (SSCP) gel electrophoresis, followed by sequencing and identification of excised bands and relative quantification of band intensities. In all samples, the abundance of selected periodontitis marker species was determined based on DNA hybridization on a microarray. Results The highly prevalent Campylobacter community was composed of varying proportions of C. rectus, C. gracilis, C. concisus, and C. curvus. Cluster analysis based on SSCP-banding pattern resulted in distinct groups which in turn coincided with significant differences in abundance of established periodontitis marker species (Tannerella forsythia, Porphyromonas gingivalis, and Fusobacterium nucleatum) and progression. Conclusions The shift in the Campylobacter community composition seems to display the general microbial community shift during clinical progression in a simplified manner. The focus on members of the Campylobacter in this study suggests that this genus can be an indicator of ecological changes in the subgingival oral microflora. PMID:25412608

  7. Species abundance and diversity of Burkholderia cepacia complex in the environment.

    PubMed

    Ramette, Alban; LiPuma, John J; Tiedje, James M

    2005-03-01

    Despite considerable interest in studying Burkholderia cepacia complex in the environment, we still do not have efficient methods to detect, isolate, and screen large numbers of B. cepacia isolates. To better describe the ecology and diversity of B. cepacia complex, a colony hybridization assay was developed to detect specifically all species of the complex based on polymorphism of the variable V3 region of the 16S rRNA sequence. The sensitivity of the assay was dramatically enhanced by using a probe consisting of three repeats of a B. cepacia complex-specific probe, each separated by a phosphoramidite spacer. In addition, a duplex PCR targeting B. cepacia complex-specific recA and 16S rRNA sequences was developed to enable a fast and reliable diagnostic assay for members of the complex. When applied to maize rhizosphere samples, colony hybridization results were in good agreement with those of most-probable-number duplex PCR, both indicating a >100-fold fluctuation of abundance between individual plants. Using restriction analysis of recA for a total of 285 confirmed isolates of the B. cepacia complex, up to seven B. cepacia complex species were identified; however, their diversity and abundance were not evenly distributed among individual plants, and several allelic variants were commonly found from the same rhizosphere sample. These results indicate that not only complex communities of B. cepacia complex species and closely related strains of the same species may coexist at high population levels but also species composition and abundance may dramatically vary between individual plants. PMID:15746318

  8. Method for coupling a hydrocarbon containing molecular species

    SciTech Connect

    Lingwood, C.A.

    1986-07-01

    A method is described of covalently coupling two molecular species comprising: (a) combining (i) a first molecular species having a functionality reactive with hydrocarbon when photo-activated; and (ii) a solution of at least one, hydrocarbon containing, molecular species in the absence of photo-radiation to which the functionality is sensitive; (b) removing the solvent; (c) irradiating the mixture with photo-radiation to which the functionality is photosensitive.

  9. Diatom species abundance and morphologically-based dissolution proxies in coastal Southern Ocean assemblages

    NASA Astrophysics Data System (ADS)

    Warnock, Jonathan P.; Scherer, Reed P.

    2015-07-01

    Taphonomic processes alter diatom assemblages in sediments, thus potentially negatively impacting paleoclimate records at various rates across space, time, and taxa. However, quantitative taphonomic data is rarely included in diatom-based paleoenvironmental reconstructions and no objective standard exists for comparing diatom dissolution in sediments recovered from marine depositional settings, including the Southern Ocean's opal belt. Furthermore, identifying changes to diatom dissolution through time can provide insight into the efficiency of both upper water column nutrient recycling and the biological pump. This is significant in that reactive metal proxies (e.g. Al, Ti) in the sediments only account for post-depositional dissolution, not the water column where the majority of dissolution occurs. In order to assess the range of variability of responses to dissolution in a typical Southern Ocean diatom community and provide a quantitative guideline for assessing taphonomic variability in diatoms recovered from core material, a sediment trap sample was subjected to controlled, serial dissolution. By evaluating dissolution-induced changes to diatom species' relative abundance, three preservational categories of diatoms have been identified: gracile, intermediate, and robust. The relative abundances of these categories can be used to establish a preservation grade for diatom assemblages. However, changes to the relative abundances of diatom species in sediment samples may reflect taphonomic or ecological factors. In order to address this complication, relative abundance changes have been tied to dissolution-induced morphological change to the areolae of Fragilariopsis curta, a significant sea-ice indicator in Southern Ocean sediments. This correlation allows differentiation between gracile species loss to dissolution versus ecological factors or sediment winnowing. These results mirror a similar morphological dissolution index from a parallel study utilizing

  10. [Variations of fish species diversity, faunal assemblage, and abundances in Daya Bay in 1980-2007].

    PubMed

    Wang, Xue-hui; Du, Fi-yan; Qiu, Yong-song; Li, Chun-hou; Sun, Dian-rong; Jia, Xiao-ping

    2010-09-01

    Based on the 2004-2005 otter trawl survey data and the 1980-2007 relevant historical records, this paper analyzed the variations of fish species composition, faunal assemblage, diversity indices, dominant species, and abundance in Daya Bay. In the 2004-2005 trawl survey, a total of 107 fish species were recorded, belonging to 50 families and 13 orders, among which, meso-demersal fish were predominant, with 48 species recorded, and followed by pelagic and demersal fishes, with 37 and 21 species, respectively. The fishes in the Bay belonged to tropical and subtropical fauna, with the dominance of warm water fishes (97 species) and warm-temperate water fishes (10 species). The diversity index was the highest in summer (3.82), followed by in winter (3.37) and autumn (3.00), and the lowest in spring (2.40). The seasonal variation of Pielou evenness index mimicked that of diversity index. In 1980-2007, the characteristics of fish community in the Bay changed obviously. The species number reduced from 157 species in the 1980s to 110 species in the 1990s and to 107 species in 2004-2005, and the dominant species shifted from the high-value fishes such as hairtail and pomfret in the 1980s to low-value fishes such as sardine fish, anchovy, and juvenile porgy. A non-linear regression model composed of inter-annual trend and seasonal cycle was used to simulate the changes of fish stock density in 1980-1999 and 1990-2007, and the results indicated that in the two periods, the fish stock density in the Bay all showed a decreasing trend, but the decrement was larger in 1990-2007 than in 1980-1999. The seasonal variation of the stock density in 1980-1999 was relatively small, with an amplitude being 0.099, while that in 1990-2007 was relatively larger, with the amplitude being 0.420, illustrating that the fish abundance in the Bay had a larger seasonal fluctuation in 1990-2007.

  11. Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama.

    PubMed

    Crawford, Andrew J; Lips, Karen R; Bermingham, Eldredge

    2010-08-01

    Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.

  12. Understanding Long-Term Changes in Species Abundance Using a Niche-Based Approach

    PubMed Central

    Helaouët, Pierre; Beaugrand, Grégory; Edwards, Martin

    2013-01-01

    One of the major challenges to understanding population changes in ecology for assessment purposes is the difficulty in evaluating the suitability of an area for a given species. Here we used a new simple approach able to faithfully predict through time the abundance of two key zooplanktonic species by focusing on the relationship between the species’ environmental preferences and their observed abundances. The approach is applied to the marine copepods Calanus finmarchicus and C. helgolandicus as a case study characterising the multidecadal dynamics of the North Sea ecosystem. We removed all North Sea data from the Continuous Plankton Recorder (CPR) dataset and described for both species a simplified ecological niche using Sea Surface Temperature (SST) and CPR Phytoplankton Colour Index (PCI). We then modelled the dynamics of each species by associating the North Sea’s environmental parameters to the species’ ecological niches, thus creating a method to assess the suitability of this area. By using both C. finmarchicus and C. helgolandicus as indicators, the procedure reproduces the documented switches from cold to warm temperate states observed in the North Sea. PMID:24265757

  13. Relative abundance and species richness of cerambycid beetles in partial cut and uncut bottomland hardwood forests

    USGS Publications Warehouse

    Newell, P.; King, S.

    2009-01-01

    Partial cutting techniques are increasingly advocated and used to create habitat for priority wildlife. However, partial cutting may or may not benefit species dependent on deadwood; harvesting can supplement coarse woody debris in the form of logging slash, but standing dead trees may be targeted for removal. We sampled cerambycid beetles during the spring and summer of 2006 and 2007 with canopy malaise traps in 1- and 2-year-old partial cut and uncut bottomland hardwood forests of Louisiana. We captured a total of 4195 cerambycid beetles representing 65 species. Relative abundance was higher in recent partial cuts than in uncut controls and with more dead trees in a plot. Total species richness and species composition were not different between treatments. The results suggest partial cuts with logging slash left on site increase the abundance of cerambycid beetles in the first few years after partial cutting and that both partial cuts and uncut forest should be included in the bottomland hardwood forest landscape.

  14. Abundances of ethylene oxide and acetaldehyde in hot molecular cloud cores

    NASA Technical Reports Server (NTRS)

    Nummelin, A.; Dickens, J. E.; Bergman, P.; Hjalmarson, A.; Irvine, W. M.; Ikeda, M.; Ohishi, M.

    1998-01-01

    We have searched for millimetre-wave line emission from ethylene oxide (c-C2H4O) and its structural isomer acetaldehyde (CH3CHO) in 11 molecular clouds using SEST. Ethylene oxide and acetaldehyde were detected through multiple lines in the hot cores NGC 6334F, G327.3-0.6, G31.41+0.31, and G34.3+0.2. Acetaldehyde was also detected towards G10.47+0.03, G322.2+0.6, and Orion 3'N, and one ethylene oxide line was tentatively detected in G10.47+0.03. Column densities and rotational excitation temperatures were derived using a procedure which fits the observed line intensifies by finding the minimum chi 2-value. The resulting rotational excitation temperatures of ethylene oxide and acetaldehyde are in the range 16-38 K, indicating that these species are excited in the outer, cooler parts of the hot cores or that the excitation is significantly subthermal. For an assumed source size of 20", the deduced column densities are (0.6-1)x10(14) cm-2 for ethylene oxide and (2-5)x10(14) cm-2 for acetaldehyde. The fractional abundances with respect to H2 are X[c-C2H4O]=(2-6)xl0(-10), and X[CH3CHO]=(0.8-3)x10(-9). The ratio X[CH3CHO]/X[c-C2H4O] varies between 2.6 (NGC 6334F) and 8.5 (G327.3-0.6). We also detected and analysed multiple transitions of CH3OH, CH3OCH3, C2H5OH, and HCOOH. The chemical, and possibly evolutionary, states of NGC 6334F, G327.3-0.6, G31.41+0.31, and G34.3+0.2 seem to be very similar.

  15. Abundances of ethylene oxide and acetaldehyde in hot molecular cloud cores.

    PubMed

    Nummelin, A; Dickens, J E; Bergman, P; Hjalmarson, A; Irvine, W M; Ikeda, M; Ohishi, M

    1998-09-01

    We have searched for millimetre-wave line emission from ethylene oxide (c-C2H4O) and its structural isomer acetaldehyde (CH3CHO) in 11 molecular clouds using SEST. Ethylene oxide and acetaldehyde were detected through multiple lines in the hot cores NGC 6334F, G327.3-0.6, G31.41+0.31, and G34.3+0.2. Acetaldehyde was also detected towards G10.47+0.03, G322.2+0.6, and Orion 3'N, and one ethylene oxide line was tentatively detected in G10.47+0.03. Column densities and rotational excitation temperatures were derived using a procedure which fits the observed line intensifies by finding the minimum chi 2-value. The resulting rotational excitation temperatures of ethylene oxide and acetaldehyde are in the range 16-38 K, indicating that these species are excited in the outer, cooler parts of the hot cores or that the excitation is significantly subthermal. For an assumed source size of 20", the deduced column densities are (0.6-1)x10(14) cm-2 for ethylene oxide and (2-5)x10(14) cm-2 for acetaldehyde. The fractional abundances with respect to H2 are X[c-C2H4O]=(2-6)xl0(-10), and X[CH3CHO]=(0.8-3)x10(-9). The ratio X[CH3CHO]/X[c-C2H4O] varies between 2.6 (NGC 6334F) and 8.5 (G327.3-0.6). We also detected and analysed multiple transitions of CH3OH, CH3OCH3, C2H5OH, and HCOOH. The chemical, and possibly evolutionary, states of NGC 6334F, G327.3-0.6, G31.41+0.31, and G34.3+0.2 seem to be very similar.

  16. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance.

    PubMed

    Robertson, Gail S; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  17. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance

    PubMed Central

    Robertson, Gail S.; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  18. Bacterial colonization and extinction on marine aggregates: stochastic model of species presence and abundance

    PubMed Central

    Kramer, Andrew M; Lyons, M Maille; Dobbs, Fred C; Drake, John M

    2013-01-01

    Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while colonization increases linearly with background density and aggregate size, extinction rates are expected to be nonlinear on small aggregates in a low background density of the pathogen. Under these conditions, we predict lower probabilities of pathogen presence and reduced abundance on aggregates compared with predictions based solely on colonization. These results suggest that the importance of aggregates to the dynamics of aquatic bacterial pathogens may be dependent on the interaction between aggregate size and background pathogen density, and that these interactions are strongly influenced by ecological interactions and pathogen traits. The model provides testable predictions and can be a useful tool for exploring how species-specific differences in pathogen traits may alter the effect of aggregates on disease transmission. PMID:24340173

  19. Abundance and Spatial Dispersion of Rice Stem Borer Species in Kahama, Tanzania

    PubMed Central

    Leonard, Alfonce; Rwegasira, Gration M.

    2015-01-01

    Species diversity, abundance, and dispersion of rice stem borers in framer’s fields were studied in four major rice growing areas of Kahama District. Stem borer larvae were extracted from the damaged tillers in 16 quadrants established in each field. Adult Moths were trapped by light traps and collected in vials for identification. Results indicated the presence of Chilo partellus, Maliarpha separatella, and Sesamia calamistis in all study areas. The most abundant species was C. partellus (48.6%) followed by M. separatella (35.4%) and S. calamistis was least abundant (16.1%). Stem borers dispersion was aggregated along the edges of rice fields in three locations (wards) namely: Bulige, Chela, and Ngaya. The dispersion in the fourth ward, Kashishi was uniform as established from two of the three dispersion indices tested. Further studies would be required to establish the available alternative hosts, the extent of economic losses and the distribution of rice stem borers in the rest of the Lake zone of Tanzania. PMID:26411785

  20. Abundance and Spatial Dispersion of Rice Stem Borer Species in Kahama, Tanzania.

    PubMed

    Leonard, Alfonce; Rwegasira, Gration M

    2015-01-01

    Species diversity, abundance, and dispersion of rice stem borers in framer's fields were studied in four major rice growing areas of Kahama District. Stem borer larvae were extracted from the damaged tillers in 16 quadrants established in each field. Adult Moths were trapped by light traps and collected in vials for identification. Results indicated the presence of Chilo partellus, Maliarpha separatella, and Sesamia calamistis in all study areas. The most abundant species was C. partellus (48.6%) followed by M. separatella (35.4%) and S. calamistis was least abundant (16.1%). Stem borers dispersion was aggregated along the edges of rice fields in three locations (wards) namely: Bulige, Chela, and Ngaya. The dispersion in the fourth ward, Kashishi was uniform as established from two of the three dispersion indices tested. Further studies would be required to establish the available alternative hosts, the extent of economic losses and the distribution of rice stem borers in the rest of the Lake zone of Tanzania. PMID:26411785

  1. Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity: a first proposal using Shannon's entropy.

    PubMed

    Ricotta, Carlo

    2003-01-01

    Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total information content as special cases of this more general function.

  2. The Human Release Hypothesis for biological invasions: human activity as a determinant of the abundance of invasive plant species.

    PubMed

    Zimmermann, Heike; Brandt, Patric; Fischer, Joern; Welk, Erik; von Wehrden, Henrik

    2014-01-01

    Research on biological invasions has increased rapidly over the past 30 years, generating numerous explanations of how species become invasive. While the mechanisms of invasive species establishment are well studied, the mechanisms driving abundance patterns (i.e. patterns of population density and population size) remain poorly understood. It is assumed that invasive species typically have higher abundances in their new environments than in their native ranges, and patterns of invasive species abundance differ between invaded regions. To explain differences in invasive species abundance, we propose the Human Release Hypothesis. In parallel to the established Enemy Release Hypothesis, this hypothesis states that the differences in abundance of invasive species are found between regions because population expansion is reduced in some regions through continuous land management and associated cutting of the invasive species. The Human Release Hypothesis does not negate other important drivers of species invasions, but rather should be considered as a potentially important complementary mechanism. We illustrate the hypothesis via a case study on an invasive rose species, and hypothesize which locations globally may be most likely to support high abundances of invasive species. We propose that more extensive empirical work on the Human Release Hypothesis could be useful to test its general applicability.

  3. The Human Release Hypothesis for biological invasions: human activity as a determinant of the abundance of invasive plant species.

    PubMed

    Zimmermann, Heike; Brandt, Patric; Fischer, Joern; Welk, Erik; von Wehrden, Henrik

    2014-01-01

    Research on biological invasions has increased rapidly over the past 30 years, generating numerous explanations of how species become invasive. While the mechanisms of invasive species establishment are well studied, the mechanisms driving abundance patterns (i.e. patterns of population density and population size) remain poorly understood. It is assumed that invasive species typically have higher abundances in their new environments than in their native ranges, and patterns of invasive species abundance differ between invaded regions. To explain differences in invasive species abundance, we propose the Human Release Hypothesis. In parallel to the established Enemy Release Hypothesis, this hypothesis states that the differences in abundance of invasive species are found between regions because population expansion is reduced in some regions through continuous land management and associated cutting of the invasive species. The Human Release Hypothesis does not negate other important drivers of species invasions, but rather should be considered as a potentially important complementary mechanism. We illustrate the hypothesis via a case study on an invasive rose species, and hypothesize which locations globally may be most likely to support high abundances of invasive species. We propose that more extensive empirical work on the Human Release Hypothesis could be useful to test its general applicability. PMID:25352979

  4. The Human Release Hypothesis for biological invasions: human activity as a determinant of the abundance of invasive plant species

    PubMed Central

    Zimmermann, Heike; Brandt, Patric; Fischer, Joern; Welk, Erik; von Wehrden, Henrik

    2014-01-01

    Research on biological invasions has increased rapidly over the past 30 years, generating numerous explanations of how species become invasive. While the mechanisms of invasive species establishment are well studied, the mechanisms driving abundance patterns (i.e. patterns of population density and population size) remain poorly understood. It is assumed that invasive species typically have higher abundances in their new environments than in their native ranges, and patterns of invasive species abundance differ between invaded regions. To explain differences in invasive species abundance, we propose the Human Release Hypothesis. In parallel to the established Enemy Release Hypothesis, this hypothesis states that the differences in abundance of invasive species are found between regions because population expansion is reduced in some regions through continuous land management and associated cutting of the invasive species. The Human Release Hypothesis does not negate other important drivers of species invasions, but rather should be considered as a potentially important complementary mechanism. We illustrate the hypothesis via a case study on an invasive rose species, and hypothesize which locations globally may be most likely to support high abundances of invasive species. We propose that more extensive empirical work on the Human Release Hypothesis could be useful to test its general applicability. PMID:25352979

  5. Integration of non-indigenous species within the interspecific abundance-occupancy relationship

    NASA Astrophysics Data System (ADS)

    Rigal, François; Whittaker, Robert J.; Triantis, Kostas A.; Borges, Paulo A. V.

    2013-04-01

    There is a broad consensus that habitat disturbance and introduction of non-indigenous species may dramatically modify community structure, particularly in insular ecosystems. However, it is less clear whether emergent macroecological patterns are similarly affected. The positive interspecific abundance-occupancy relationship (IAOR) is one of the most pervasive macroecological patterns, yet has rarely been analyzed for oceanic island assemblages. We use an extensive dataset for arthropods from six islands within the Azorean archipelago to test: (1) whether indigenous and non-indigenous species are distributed differently within the IAOR; and (2) to the extent that they are, can differences can be attributed to two indices of disturbance. We implemented modeling averaged methods using five of the most common IAOR models to derive an averaged IAOR fit for each island. After testing if species colonization status (indigenous versus non-indigenous) may explain the residuals of the IAOR, we identified true negative and positive outliers and tested the effect of colonization status on the likelihood of a species being a positive or negative outlier. We found that the indigenous and non-indigenous species are randomly distributed on both sides of the overall IAOR. Only for Flores Island, were non-indigenous species more aggregated than indigenous species. We were unable to detect a meaningful relationship between deviation from the IAOR and disturbance, despite the undoubted impact of both severe habitat loss and non-indigenous species on these oceanic islands. Our results show that the non-indigenous species have been integrated alongside indigenous species in the contemporary Azorean arthropod communities such that they are mostly undetectable by the study of the IAOR.

  6. Beyond the Patch: Disturbance Affects Species Abundances in the surrounding Community

    PubMed Central

    Dudgeon, Steve R.

    2009-01-01

    The role of disturbance in community ecology has been studied extensively and is thought to free resources and reset successional sequences at the local scale and create heterogeneity at the regional scale. Most studies have investigated effects on either the disturbed patch or on the entire community, but have generally ignored any effect of or on the community surrounding disturbed patches. We used marine fouling communities to examine the effect of a surrounding community on species abundance within a disturbed patch and the effect of a disturbance on species abudance in the surrounding community. We varied both the magnitude and pattern of disturbance on experimental settlement plates. Settlement plates were dominated by a non-native bryozoan, which may have established because of the large amount of initial space available on plates. Percent cover of each species within the patch were affected by the surrounding community, confirming previous studies’ predictions about edge effects from the surrounding community on dynamics within a patch. Disturbance resulted in lower percent cover in the surrounding community, but there were no differences between magnitudes or spatial patterns of disturbance. Disturbance lowered population growth rates in the surrounding community, potentially by altering the abiotic environment or species interactions. Following disturbance, the recovery of species within a patch may be affected by species in the surrounding community, but the effects of a disturbance can extend beyond the patch and alter abundances in the surrounding community. The dependence of patch dynamics on the surrounding community and the extended effects of disturbance on the surrounding community, suggest an important feedback of disturbance on patch dynamics indirectly via the surrounding community. PMID:20161249

  7. Convergence and divergence in a long-term old-field succession: the importance of spatial scale and species abundance.

    PubMed

    Li, Shao-Peng; Cadotte, Marc W; Meiners, Scott J; Pu, Zhichao; Fukami, Tadashi; Jiang, Lin

    2016-09-01

    Whether plant communities in a given region converge towards a particular stable state during succession has long been debated, but rarely tested at a sufficiently long time scale. By analysing a 50-year continuous study of post-agricultural secondary succession in New Jersey, USA, we show that the extent of community convergence varies with the spatial scale and species abundance classes. At the larger field scale, abundance-based dissimilarities among communities decreased over time, indicating convergence of dominant species, whereas incidence-based dissimilarities showed little temporal tend, indicating no sign of convergence. In contrast, plots within each field diverged in both species composition and abundance. Abundance-based successional rates decreased over time, whereas rare species and herbaceous plants showed little change in temporal turnover rates. Initial abandonment conditions only influenced community structure early in succession. Overall, our findings provide strong evidence for scale and abundance dependence of stochastic and deterministic processes over old-field succession. PMID:27373449

  8. Spatial scale, abundance and the species-energy relationship in British birds.

    PubMed

    Evans, Karl L; Newson, Stuart E; Storch, David; Greenwood, Jeremy J D; Gaston, Kevin J

    2008-03-01

    richness in a single year, is lower in high-energy regions. These negative relationships between turnover and energy appear to be causal as both total and mean occupancy per species increases with energy. 5. While total density in 1 km x 1 km plots correlates positively with energy availability, such relationships are very weak for mean density per species. This suggests that the observed association between total abundance and species richness may not be mediated by population extinction rates, as predicted by the more individuals hypothesis. 6. The sampling mechanism suggests that species-energy relationships arise as high-energy areas support a greater number of individuals, and that random allocation of these individuals to local areas from a regional assemblage will generate species-energy relationships. While randomized local species-energy relationships are linear and positive, predicted richness is consistently greater than that observed. The mismatch between the observed and randomized species-energy relationships probably arises as a consequence of the aggregated nature of species distributions. The sampling mechanism, together with species spatial aggregation driven by limited habitat availability, may thus explain the species-energy relationship observed at this spatial scale.

  9. STUDIES ON THE SPECIES COMPOSITION AND RELATIVE ABUNDANCE OF MOSQUITOES OF MPIGI DISTRICT, CENTRAL UGANDA

    PubMed Central

    Mayanja, Martin; Mutebi, John-Paul; Crabtree, Mary B.; Ssenfuka, Fred; Muwawu, Teddy; Lutwama, Julius J.

    2015-01-01

    Prediction of arboviral disease outbreaks and planning for appropriate control interventions require knowledge of the mosquito vectors involved. Although mosquito surveys have been conducted in different regions of Uganda since the mid 30’s such studies have not been carried out in Mpigi District. In October 2011, we conducted mosquito collections in Mpigi district to determine species composition and relative abundance of the different species. The survey was conducted in four villages, Njeru, Ddela, Kiwumu and Nsumbain Kammengo sub-county, Mpigi district, Uganda. CDC light traps baited with dry ice (carbon dioxide) were used to capture adult mosquitoes. A total of 54,878 mosquitoes comprising 46 species from eight genera were collected. The dominant species at all sites was Coquilletidia (Coquilletidia) fuscopennata Theobald (n=38,059, 69%), followed by Coquillettidia (Coquillettidia) metallica Theobald (n=4,265, 7.8%). The number of species collected varied from 17 in the genus Culex to 1 in the genus Lutzia. Of the 46 species identified, arboviruses had previously been isolated from 28 (60.9%) suggesting a high potential for arboviral transmission and/or maintenance in Mpigi District. PMID:26346305

  10. Direct evidence that density-dependent regulation underpins the temporal stability of abundant species in a diverse animal community

    PubMed Central

    Henderson, Peter A.; Magurran, Anne E.

    2014-01-01

    To understand how ecosystems are structured and stabilized, and to identify when communities are at risk of damage or collapse, we need to know how the abundances of the taxa in the entire assemblage vary over ecologically meaningful timescales. Here, we present an analysis of species temporal variability within a single large vertebrate community. Using an exceptionally complete 33-year monthly time series following the dynamics of 81 species of fishes, we show that the most abundant species are least variable in terms of temporal biomass, because they are under density-dependent (negative feedback) regulation. At the other extreme, a relatively large number of low abundance transient species exhibit the greatest population variability. The high stability of the consistently common high abundance species—a result of density-dependence—is reflected in the observation that they consistently represent over 98% of total fish biomass. This leads to steady ecosystem nutrient and energy flux irrespective of the changes in species number and abundance among the large number of low abundance transient species. While the density-dependence of the core species ensures stability under the existing environmental regime, the pool of transient species may support long-term stability by replacing core species should environmental conditions change. PMID:25100702

  11. Stream salamander species richness and abundance in relation to environmental factors in Shenandoah National Park, Virginia

    USGS Publications Warehouse

    Grant, E.H.C.; Jung, R.E.; Rice, K.C.

    2005-01-01

    Stream salamanders are sensitive to acid mine drainage and may be sensitive to acidification and low acid neutralizing capacity (ANC) of a watershed. Streams in Shenandoah National Park, Virginia, are subject to episodic acidification from precipitation events. We surveyed 25 m by 2 m transects located on the stream bank adjacent to the water channel in Shenandoah National Park for salamanders using a stratified random sampling design based on elevation, aspect and bedrock geology. We investigated the relationships of four species (Eurycea bislineata, Desmognathus fuscus, D. monticola and Gyrinophilus porphyriticus) to habitat and water quality variables. We did not find overwhelming evidence that stream salamanders are affected by the acid-base status of streams in Shenandoah National Park. Desmognathus fuscus and D. monticola abundance was greater both in streams that had a higher potential to neutralize acidification, and in higher elevation (>700 m) streams. Neither abundance of E. bislineata nor species richness were related to any of the habitat variables. Our sampling method preferentially detected the adult age class of the study species and did not allow us to estimate population sizes. We suggest that continued monitoring of stream salamander populations in SNP will determine the effects of stream acidification on these taxa.

  12. Microbial Distribution and Abundance in the Digestive System of Five Shipworm Species (Bivalvia: Teredinidae)

    PubMed Central

    Betcher, Meghan A.; Fung, Jennifer M.; Han, Andrew W.; O’Connor, Roberta; Seronay, Romell; Concepcion, Gisela P.; Distel, Daniel L.; Haygood, Margo G.

    2012-01-01

    Marine bivalves of the family Teredinidae (shipworms) are voracious consumers of wood in marine environments. In several shipworm species, dense communities of intracellular bacterial endosymbionts have been observed within specialized cells (bacteriocytes) of the gills (ctenidia). These bacteria are proposed to contribute to digestion of wood by the host. While the microbes of shipworm gills have been studied extensively in several species, the abundance and distribution of microbes in the digestive system have not been adequately addressed. Here we use Fluorescence In-Situ Hybridization (FISH) and laser scanning confocal microscopy with 16S rRNA directed oligonucleotide probes targeting all domains, domains Bacteria and Archaea, and other taxonomic groups to examine the digestive microbiota of 17 specimens from 5 shipworm species (Bankia setacea, Lyrodus pedicellatus, Lyrodus massa, Lyrodus sp. and Teredo aff. triangularis). These data reveal that the caecum, a large sac-like appendage of the stomach that typically contains large quantities of wood particles and is considered the primary site of wood digestion, harbors only very sparse microbial populations. However, a significant number of bacterial cells were observed in fecal pellets within the intestines. These results suggest that due to low abundance, bacteria in the caecum may contribute little to lignocellulose degradation. In contrast, the comparatively high population density of bacteria in the intestine suggests a possible role for intestinal bacteria in the degradation of lignocellulose. PMID:23028923

  13. Distribution, species composition and relative abundances of sandflies in North Waziristan Agency, Pakistan.

    PubMed

    Ali, N; Ullah, A; Wahid, S; Khisroon, M; Rasheed, S B

    2016-03-01

    This study was conducted to investigate the diversity of sandflies (Psychodidae: Phlebotominae) and the incidence of leishmaniasis in three villages of North Waziristan Agency, Pakistan. Sandflies were sampled monthly during 2012, at dusk and dawn, in selected indoor habitats including both bedrooms and animal sheds using a knock-down spray catch method. A total of 3687 sandflies were collected, including 1444 individuals in Drezanda, 1193 in Damdil and 1050 in Dattakhel. This study revealed 14 species of two genera, Phlebotomus (Phlebotomus sergenti, Phlebotomus papatasi, Phlebotomus caucasicus, Phlebotomus kazeruni, Phlebotomus alexandri and Phlebotomus salehi) and Sergentomyia (Sergentomyia dentate, Sergentomyia baghdadis, Sergentomyia babu, Sergentomyia theodori, Sergentomyia sumbarica, Sergentomyia dreyfussitur kestanica, Sergentomyia hogsoni pawlowskyi and Sergentomyia fallax afghanica) (both: Diptera: Psychodidae). Phlebotomus sergenti was the most abundant species (42.1%), followed by S. dentata (17.7%) and S. baghdadis (17.4%). The number of males collected represented about twice that of female flies, and the maximum number was collected in July, followed by August. The determination of the species composition of sandfly populations, seasonal variations, relative abundances and estimations of infection in the vector population may provide information about the dynamics of leishmaniasis transmission that is useful in planning vector control activities.

  14. Monitoring species richness and abundance of shorebirds in the western Great Basin

    USGS Publications Warehouse

    Warnock, N.; Haig, S.M.; Oring, L.W.

    1998-01-01

    Broad-scale avian surveys have been attempted within North America with mixed results. Arid regions, such as the Great Basin, are often poorly sampled because of the vastness of the region, inacessibilty of sites, and few ornithologist. In addition, extreme variability in wetland habitat conditions present special problems for conducting censuses of species inhabiting these areas. We examined these issues in assessing multi-scale shorebird (order: Charadriiformes) censuses conducted the western Great Basin from 1992-1997. On ground surveys, we recorded 31 species of shorebirds, but were unable to accurately estimate population size. Conversely, on aerial surveys we were able to estimate regional abundance of some shorebirds, but were unable to determined species diversity. Acrial surveys of three large alkali lakcs in Oregon (Goose, Summer, and abert Lakes) revealed > 300,000 shorebirds in one year of this study, of which 67% were American Avocets (Recurvirostra americana) and 30% phalaropes (Phalaropus spp.). These lakes clearly meet Western Hemisphere Shorebird Reserve Network guidelines for designation as important shorebirds sites. Based upon simulations of our monitoring effort and the magnitude and variation of numbers of American Avocets, detection of 5-10% negative declines in population of these birds would take a minimum of 7-23 years comparable effort. We conclude that a combination of ground and aerial surveys must be conducted at multiple sites and years and over a large region to obtain an accurate picture of the diversity, abundance, and trends of shorebirds in the western Great Basin.

  15. Monitoring species richness and abundance of shorebirds in the western Great Basin

    USGS Publications Warehouse

    Warnock, N.; Haig, Susan M.; Oring, L.W.

    1998-01-01

    Broad-scale avian surveys have been attempted within North America with mixed results. Arid regions, such as the Great Basin, are often poorly sampled because of the vastness of the region, inaccessibility of sites, and few ornithologists. In addition, extreme variability in wetland habitat conditions present special problems for conducting censuses of species inhabiting these areas. We examined these issues in assessing multi-scale shorebird (order: Charadriiformes) censuses conducted in the western Great Basin from 1992-1997. On ground surveys, we recorded 31 species of shorebirds, but were unable to accurately estimate population size. Conversely, on aerial surveys we were able to estimate regional abundance of some shorebirds, but were unable to determine species diversity. Aerial surveys of three large alkali lakes in Oregon (Goose, Summer, and Abert Lakes) revealed > 300,000 shorebirds in one year of this study, of which 67% were American Avocets (Recurvirostra americana) and 30% phalaropes (Phalaropus spp.). These lakes clearly meet Western Hemisphere Shorebird Reserve Network guidelines for designation as important shorebird sites. Based upon simulations of our monitoring effort and the magnitude and variation of numbers of American Avocets, detection of S-10% negative declines in populations of these birds would take a minimum of 7-23 years of comparable effort. We conclude that a combination of ground and aerial surveys must be conducted at multiple sites and years and over a large region to obtain an accurate picture of the diversity, abundance, and trends of shorebirds in the western Great Basin.

  16. Analytical Formulae of Molecular Ion Abundances and the N2H+ Ring in Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Aikawa, Yuri; Furuya, Kenji; Nomura, Hideko; Qi, Chunhua

    2015-07-01

    We investigate the chemistry of ion molecules in protoplanetary disks, motivated by the detection of the N2H+ ring around TW Hya. While the ring inner radius coincides with the CO snow line, it is not apparent why N2H+ is abundant outside the CO snow line in spite of the similar sublimation temperatures of CO and N2. Using the full gas-grain network model, we reproduced the N2H+ ring in a disk model with millimeter grains. The chemical conversion of CO and N2 to less volatile species (sink effect hereinafter) is found to affect the N2H+ distribution. Since the efficiency of the sink depends on various parameters such as activation barriers of grain-surface reactions, which are not well constrained, we also constructed the no-sink model; the total (gas and ice) CO and N2 abundances are set constant, and their gaseous abundances are given by the balance between adsorption and desorption. Abundances of molecular ions in the no-sink model are calculated by analytical formulae, which are derived by analyzing the full-network model. The N2H+ ring is reproduced by the no-sink model, as well. The 2D (R-Z) distribution of N2H+, however, is different among the full-network model and no-sink model. The column density of N2H+ in the no-sink model depends sensitively on the desorption rate of CO and N2 and the cosmic-ray flux. We also found that N2H+ abundance can peak at the temperature slightly below the CO sublimation, even if the desorption energies of CO and N2 are the same.

  17. Abundance of Woody Riparian Species in the Western USA in Relation to Phenology, Climate, and Flow Regime

    NASA Astrophysics Data System (ADS)

    Auble, G. T.; Friedman, J. M.; Scott, M. L.; Shafroth, P. B.; Merigliano, M. M.; Freehling, M. D.; Evans, R. E.; Griffin, E. R.

    2004-12-01

    We randomly selected 475 long-term U.S. Geological Survey stream gaging stations in 17 western states to relate the presence and abundance of woody species to environmental factors. Along a 1.3-km reach near each station we measured the cover of all species on a list of the 44 most abundant large woody riparian species in the region. We used logistic regression to fit the response of four abundant species to growing degree days and mean precipitation. Then we related relative abundance of these 4 species to timing of the flood peak in sites where the likelihood of occurrence was greater than 0.5. The exotics Tamarix ramosissima (saltcedar) and Elaeagnus angustifolia (Russian-olive) are now the third and fourth most frequently occurring large woody riparian species in the western U.S. and the second and fifth most abundant. In climatically suitable areas, species differences in reproductive phenology produce different relations of abundance to flow regime. Because of its limited period of seed release and viability in early summer, cottonwood (Populus deltoides) is disadvantaged where floods occur in the spring or fall. Abundances of saltcedar, because of its long period of seed release; Russian-olive, because of seed dormancy; and Salix exigua, because of the importance of vegetative spread, are much less sensitive to flood timing.

  18. Assessing landscape constraints on species abundance: does the neighborhood limit species response to local habitat conservation programs?

    PubMed

    Jorgensen, Christopher F; Powell, Larkin A; Lusk, Jeffery J; Bishop, Andrew A; Fontaine, Joseph J

    2014-01-01

    Landscapes in agricultural systems continue to undergo significant change, and the loss of biodiversity is an ever-increasing threat. Although habitat restoration is beneficial, management actions do not always result in the desired outcome. Managers must understand why management actions fail; yet, past studies have focused on assessing habitat attributes at a single spatial scale, and often fail to consider the importance of ecological mechanisms that act across spatial scales. We located survey sites across southern Nebraska, USA and conducted point counts to estimate Ring-necked Pheasant abundance, an economically important species to the region, while simultaneously quantifying landscape effects using a geographic information system. To identify suitable areas for allocating limited management resources, we assessed land cover relationships to our counts using a Bayesian binomial-Poisson hierarchical model to construct predictive Species Distribution Models of relative abundance. Our results indicated that landscape scale land cover variables severely constrained or, alternatively, facilitated the positive effects of local land management for Ring-necked Pheasants.

  19. Assessing Landscape Constraints on Species Abundance: Does the Neighborhood Limit Species Response to Local Habitat Conservation Programs?

    PubMed Central

    Jorgensen, Christopher F.; Powell, Larkin A.; Lusk, Jeffery J.; Bishop, Andrew A.; Fontaine, Joseph J.

    2014-01-01

    Landscapes in agricultural systems continue to undergo significant change, and the loss of biodiversity is an ever-increasing threat. Although habitat restoration is beneficial, management actions do not always result in the desired outcome. Managers must understand why management actions fail; yet, past studies have focused on assessing habitat attributes at a single spatial scale, and often fail to consider the importance of ecological mechanisms that act across spatial scales. We located survey sites across southern Nebraska, USA and conducted point counts to estimate Ring-necked Pheasant abundance, an economically important species to the region, while simultaneously quantifying landscape effects using a geographic information system. To identify suitable areas for allocating limited management resources, we assessed land cover relationships to our counts using a Bayesian binomial-Poisson hierarchical model to construct predictive Species Distribution Models of relative abundance. Our results indicated that landscape scale land cover variables severely constrained or, alternatively, facilitated the positive effects of local land management for Ring-necked Pheasants. PMID:24918779

  20. Distribution and abundance of decapod crustacean larvae in the southeastern Bering Sea with emphasis on commercial species. Final report

    SciTech Connect

    Armstrong, D.A.; Incze, L.S.; Wencker, D.L.; Armstrong, J.L.

    1981-01-01

    Contents include: Distribution and abundance of king crab larvae, Paralithodes camtschatica and P. platypus in the southeast Bering Sea; Distribution and abundance of the larvae of tanner crabs in the southeastern Bering Sea; Distribution and abundance of other brachyuran larvae in the southeastern Bering Sea with emphasis on Erimacrus isenbeckii; Distribution and abundance of shrimp larvae in the southeastern Bering Sea with emphasis on pandalid species; Distribution and abundance of hermit crabs (Paguridae) in the southeasternBering Sea; Possible oil impacts on decapod larbae in the southeastern Bering Sea with emphesis on the St. George Basin.

  1. Water Mites (Acari: Hydrachnida) of Ozark Streams - Abundance, Species Richness, and Potential as Environmental Indicators

    NASA Astrophysics Data System (ADS)

    Radwell, A. J.; Brown, A. V.

    2005-05-01

    Because water mites are tightly linked to other stream metazoans through parasitism and predation, they are potentially effective indicators of environmental quality. Meiofauna (80 μm to 1 mm) were sampled from headwater riffles of 11 Ozark streams to determine relative abundance and densities of major meiofauna taxa. Water mites comprised 15.3% of the organisms collected exceeded only by chironomids (50.2%) and oligochaetes (17.8%), and mean water mite density among the 11 streams was 265 organisms per liter. The two streams that differed the most in environmental quality were sampled using techniques suitable for identification of species. An estimated 32 species from 20 genera and 13 families were found in the least disturbed stream; an estimated 19 species from 13 genera and 8 families were found in the most disturbed stream. This preliminary finding supports the notion that water mite species richness declines in response to environmental disturbance. Many species could only be identified as morphospecies of particular genera, but the ongoing taxonomic revision of Hydrachnida is expected to provide needed information. A collaborative effort between those interested in taxonomy/systematics of water mites and ecologists interested in the significance of water mites in aquatic communities could prove mutually beneficial.

  2. Molecular instability induced by aluminum stress in Plantago species.

    PubMed

    Correia, Sofia; Matos, Manuela; Ferreira, Vanessa; Martins, Neusa; Gonçalves, Sandra; Romano, Anabela; Pinto-Carnide, Olinda

    2014-08-01

    Aluminum (Al) is one of the most abundant metals on earth's crust and Al toxicity represents one of the major factors that limit plant growth and productivity in acid soils (with a pH≤5.0). In this study the mutagenic/genotoxic effects of Al were evaluated in roots and leaves of two Plantago, species, Plantago almogravensis and Plantago lagopus, using ISSRs markers. Both species were exposed to 400 μM Al during 7 and 21 days. Ten ISSR primers produced polymorphic bands. In P. almogravensis, a total of 257 and 258 bands in roots and 255 and 265 bands in leaves were produced in the presence and absence of Al, respectively. In P. lagopus were produced 279 and 278 a total bands in roots and 275 and 274 bands in leaves, under the same conditions. The changes in ISSR profiles after Al treatment were considered as gain and/or loss of bands compared with the controls. The results suggest that changes in genomic template stability (GTS) could be detected with ISSR profiles. This molecular marker proved to be a good tool to detect the effects of Al on DNA profiles. It seems that Al did not interfere significantly with DNA integrity in both species but generated less ISSR stability in P. almogravensis than in P. lagopus. The results confirm the tolerance of P. almogravensis and suggest the same behavior of P. lagopus. Although further studies are required for confirmation the Al tolerance behavior of P. lagopus, a potential application for phytoremediation can be also considered due its wide distribution.

  3. Molecular instability induced by aluminum stress in Plantago species.

    PubMed

    Correia, Sofia; Matos, Manuela; Ferreira, Vanessa; Martins, Neusa; Gonçalves, Sandra; Romano, Anabela; Pinto-Carnide, Olinda

    2014-08-01

    Aluminum (Al) is one of the most abundant metals on earth's crust and Al toxicity represents one of the major factors that limit plant growth and productivity in acid soils (with a pH≤5.0). In this study the mutagenic/genotoxic effects of Al were evaluated in roots and leaves of two Plantago, species, Plantago almogravensis and Plantago lagopus, using ISSRs markers. Both species were exposed to 400 μM Al during 7 and 21 days. Ten ISSR primers produced polymorphic bands. In P. almogravensis, a total of 257 and 258 bands in roots and 255 and 265 bands in leaves were produced in the presence and absence of Al, respectively. In P. lagopus were produced 279 and 278 a total bands in roots and 275 and 274 bands in leaves, under the same conditions. The changes in ISSR profiles after Al treatment were considered as gain and/or loss of bands compared with the controls. The results suggest that changes in genomic template stability (GTS) could be detected with ISSR profiles. This molecular marker proved to be a good tool to detect the effects of Al on DNA profiles. It seems that Al did not interfere significantly with DNA integrity in both species but generated less ISSR stability in P. almogravensis than in P. lagopus. The results confirm the tolerance of P. almogravensis and suggest the same behavior of P. lagopus. Although further studies are required for confirmation the Al tolerance behavior of P. lagopus, a potential application for phytoremediation can be also considered due its wide distribution. PMID:25344171

  4. Differences in ecological structure, function, and native species abundance between native and invaded Hawaiian streams.

    PubMed

    Holitzki, Tara M; MacKenzie, Richard A; Wiegner, Tracy N; McDermid, Karla J

    2013-09-01

    Poeciliids, one of the most invasive species worldwide, are found on almost every continent and have been identified as an "invasive species of concern" in the United States, New Zealand, and Australia. Despite their global prevalence, few studies have quantified their impacts on tropical stream ecosystem structure, function, and biodiversity. Utilizing Hawaiian streams as model ecosystems, we documented how ecological structure, function, and native species abundance differed between poeciliid-free and poeciliid-invaded tropical streams. Stream nutrient yields, benthic biofilm biomass, densities of macroinvertebrates and fish, and community structures of benthic algae, macroinvertebrates, and fish were compared between streams with and without established poeciliid populations on the island of Hawai'i, Hawaii, USA. Sum nitrate (sigmaNO3(-) = NO3(-) + NO2(-)), total nitrogen, and total organic carbon yields were eight times, six times, and five times higher, respectively, in poeciliid streams than in poeciliid-free streams. Benthic biofilm ash-free dry mass was 1.5x higher in poeciliid streams than in poeciliid-free streams. Percentage contributions of chironomids and hydroptilid caddisflies to macroinvertebrate densities were lower in poeciliid streams compared to poeciliid-free streams, while percentage contributions of Cheumatopsyche analis caddisflies, Dugesia sp. flatworms, and oligochaetes were higher. Additionally, mean densities of native gobies were two times lower in poeciliid streams than in poeciliid-free ones, with poeciliid densities being approximately eight times higher than native fish densities. Our results, coupled with the wide distribution of invasive poeciliids across Hawaii and elsewhere in the tropics, suggest that poeciliids may negatively impact the ecosystem structure, function, and native species abundance of tropical streams they invade. This underscores the need for increased public awareness to prevent future introductions and for

  5. Shrub encroachment affects mammalian carnivore abundance and species richness in semiarid rangelands

    NASA Astrophysics Data System (ADS)

    Blaum, Niels; Rossmanith, Eva; Popp, Alexander; Jeltsch, Florian

    2007-01-01

    Shrub encroachment due to overgrazing has led to dramatic changes of savanna landscapes and is considered to be one of the most threatening forms of rangeland degradation e.g. via habitat fragmentation. Mammalian carnivores are particularly vulnerable to local extinction in fragmented landscapes. However, our understanding of how shrub encroachment affects mammalian carnivores is poor. Here we investigated the relative sensitivities of ten native carnivores to different levels of shrub cover ranging from low (<5%) to high shrub cover (>25%) in 20 southern Kalahari rangeland sites. Relative abundance of carnivores was monitored along 40 sand transects (5 m × 250 m) for each site. Our results show that increasing shrub cover affects carnivore species differently. African wild cats, striped polecats, cape foxes and suricates were negatively affected, whereas we found hump-shaped responses for yellow mongooses, bat-eared foxes and small-spotted genets with maximum abundance at shrub covers between 10 and 18%. In contrast, black-backed jackals, slender mongooses and small spotted cats were not significantly affected by increasing shrub cover. However, a negative impact of high shrub cover above 18% was congruent for all species. We conclude that intermediate shrub cover (10-18%) in savanna landscapes sustain viable populations of small carnivores.

  6. How climate warming impacts the distribution and abundance of two small flatfish species in the North Sea

    NASA Astrophysics Data System (ADS)

    van Hal, Ralf; Smits, Kalle; Rijnsdorp, Adriaan D.

    2010-07-01

    Climate change, specifically temperature, affects the distribution and densities of species in marine and terrestrial ecosystems. Here, we looked at the effect of temperature during winter and spawning period on latitudinal range shifts and changes in abundance of two non-commercial North Sea fish species, solenette ( Buglossidium luteum) and scaldfish ( Arnoglossus laterna). Both species have increased in abundance and moved to the north since the late 1980s, coinciding with a series of mild winters. In 1996, following a very cold winter, the abundance of both species temporarily decreased as they retracted to the south. The shift in temperature affected adult habitat conditions, allowing them to immigrate into new areas where they subsequently reproduced successfully. We can conclude this because recruitment improved following the increase in abundance. The recruitment relates significantly to the higher adult stock and higher temperatures. The predictions of higher average temperatures and milder winters in the North Sea make it likely that these species will increase further in abundance and move northward. The observed increase in abundance of these small flatfish species will affect the North Sea food web and therefore commercial species, e.g. plaice, by predation on juveniles and competition for benthic food resources.

  7. Variation in predator species abundance can cause variable selection pressure on warning signaling prey

    PubMed Central

    Valkonen, Janne K; Nokelainen, Ossi; Niskanen, Martti; Kilpimaa, Janne; Björklund, Mats; Mappes, Johanna

    2012-01-01

    Predation pressure is expected to drive visual warning signals to evolve toward conspicuousness. However, coloration of defended species varies tremendously and can at certain instances be considered as more camouflaged rather than conspicuous. Recent theoretical studies suggest that the variation in signal conspicuousness can be caused by variation (within or between species) in predators' willingness to attack defended prey or by the broadness of the predators' signal generalization. If some of the predator species are capable of coping with the secondary defenses of their prey, selection can favor reduced prey signal conspicuousness via reduced detectability or recognition. In this study, we combine data collected during three large-scale field experiments to assess whether variation in avian predator species (red kite, black kite, common buzzard, short-toed eagle, and booted eagle) affects the predation pressure on warningly and non-warningly colored artificial snakes. Predation pressure varied among locations and interestingly, if common buzzards were abundant, there were disadvantages to snakes possessing warning signaling. Our results indicate that predator community can have important consequences on the evolution of warning signals. Predators that ignore the warning signal and defense can be the key for the maintenance of variation in warning signal architecture and maintenance of inconspicuous signaling. PMID:22957197

  8. Connectivity and conditional models of access and abundance of species in stream networks.

    PubMed

    Chelgren, Nathan D; Dunham, Jason B

    2015-07-01

    Barriers to passage of aquatic organisms at stream road crossings are a major cause of habitat fragmentation in stream networks. Accordingly, large investments have been made to restore passage at these crossings, but often without estimation of population-level benefits. Here, we describe a broad-scale approach to quantifying the effectiveness of passage restoration in terms interpretable at population levels, namely numbers of fish and length of stream gained through restoration, by sampling abundance in a study design that accounts for variable biogeographic species pools, variable stream and barrier configurations, and variable probabilities of capture and detectability for multiple species. We modified an existing zero-inflated negative-binomial model to estimate the probability of site access, abundance conditional on access, and capture probability of individual fish. Therein, we modeled probability of access as a function of gradient, stream road-crossing type, and downstream access by fish simultaneously with a predictive model for abundance at sites accessible to fish. Results indicated that replacement of barriers with new crossing designs intended to allow for greater movement was associated with dramatically higher probability of access for all fishes, including migratory Pacific salmon, trout, sculpin, and lamprey. Conversely, existing non-replaced crossings negatively impacted fish distributions. Assuming no downstream constraints on access, we estimated the potential length of stream restored by the program ranged between 7.33 (lamprey) and 15.28 km (small coastal cutthroat and rainbow trout). These contributions represented a fraction of the total length available upstream (187 km) of replaced crossings. When limited ranges of species were considered, the estimated contributions of culvert replacement were reduced (1.65-km range, for longnose dace to 12.31 km for small coastal cutthroat and rainbow trout). Numbers of fish contributed ranged from

  9. Connectivity and conditional models of access and abundance of species in stream networks.

    PubMed

    Chelgren, Nathan D; Dunham, Jason B

    2015-07-01

    Barriers to passage of aquatic organisms at stream road crossings are a major cause of habitat fragmentation in stream networks. Accordingly, large investments have been made to restore passage at these crossings, but often without estimation of population-level benefits. Here, we describe a broad-scale approach to quantifying the effectiveness of passage restoration in terms interpretable at population levels, namely numbers of fish and length of stream gained through restoration, by sampling abundance in a study design that accounts for variable biogeographic species pools, variable stream and barrier configurations, and variable probabilities of capture and detectability for multiple species. We modified an existing zero-inflated negative-binomial model to estimate the probability of site access, abundance conditional on access, and capture probability of individual fish. Therein, we modeled probability of access as a function of gradient, stream road-crossing type, and downstream access by fish simultaneously with a predictive model for abundance at sites accessible to fish. Results indicated that replacement of barriers with new crossing designs intended to allow for greater movement was associated with dramatically higher probability of access for all fishes, including migratory Pacific salmon, trout, sculpin, and lamprey. Conversely, existing non-replaced crossings negatively impacted fish distributions. Assuming no downstream constraints on access, we estimated the potential length of stream restored by the program ranged between 7.33 (lamprey) and 15.28 km (small coastal cutthroat and rainbow trout). These contributions represented a fraction of the total length available upstream (187 km) of replaced crossings. When limited ranges of species were considered, the estimated contributions of culvert replacement were reduced (1.65-km range, for longnose dace to 12.31 km for small coastal cutthroat and rainbow trout). Numbers of fish contributed ranged from

  10. Occurrence and abundance of anisakid nematode larvae in five species of fish from southern Australian waters.

    PubMed

    Shamsi, Shokoofeh; Eisenbarth, Albert; Saptarshi, Shruti; Beveridge, Ian; Gasser, Robin B; Lopata, Andreas L

    2011-04-01

    The aim of the present study was to conduct, in southern Australian waters, a preliminary epidemiological survey of five commercially significant species of fish (yellow-eye mullet, tiger flathead, sand flathead, pilchard and king fish) for infections with anisakid nematodes larvae using a combined morphological-molecular approach. With the exception of king fish, which was farmed and fed commercial pellets, all other species were infected with at least one species of anisakid nematode, with each individual tiger flathead examined being infected. Five morphotypes, including Anisakis, Contracaecum type I and II and Hysterothylacium type IV and VIII, were defined genetically using mutation scanning and targeted sequencing of the second internal transcribed spacer of nuclear ribosomal DNA. The findings of the present study provide a basis for future investigations of the genetic composition of anisakid populations in a wide range of fish hosts in Australia and for assessing their public health significance. PMID:21057811

  11. Variations in the HCN/HNC abundance ratio in the Orion molecular cloud.

    PubMed

    Goldsmith, P F; Irvine, W M; Hjalmarson, A; Elldér, J

    1986-11-01

    We have used observations of the rare isotopes of HCN and HNC to determine the relative abundance of these two chemical isomers along the central ridge of the Orion molecular cloud. The abundance ratio [HCN]/[HNC] decreases by more than an order of magnitude from the relatively warm plateau and hot core sources toward the KL nebula to the colder, more quiescent clouds to the north and south. Even in the cooler regions, however, the ratio is an order of magnitude larger than that found in previous investigations of cold dark clouds. We determine the kinetic temperature in the regions we have studied from new observations of methylacetylene (CH3CCH), together with other recent estimates of the gas temperature near KL. The results suggest that the warmer portions of the cloud are dominated by different chemical pathways than those in the general interstellar cloud material.

  12. MESSENGER Searches for Less Abundant or Weakly Emitting Species in Mercury's Exosphere

    NASA Astrophysics Data System (ADS)

    Vervack, R. J.; McClintock, W. E.; Killen, R. M.; Sprague, A. L.; Burger, M. H.; Merkel, A. W.; Sarantos, M.

    2011-12-01

    Mercury's exosphere is composed of material that originates at the planet's surface, whether that material is native or delivered by the solar wind and micrometeoroids. Many exospheric species have been detected by remote sensing, including H and He by Mariner 10, Na, K, and Ca by ground-based observations, and H, Na, Ca, Mg, and Ca+ by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft. Other exospheric species, including Fe, Al, Si, O, S, Mn, Cl, Ti, OH, and their ions, are expected to be present on the basis of MESSENGER surface measurements and models of Mercury's surface chemistry. Here we report on searches for these species made with the Ultraviolet and Visible Spectrometer (UVVS) channel of the Mercury Atmospheric and Surface Composition Spectrometer (MASCS). No obvious signatures of the listed species have yet been observed in Mercury's exosphere by the UVVS as of this writing. It is possible that detections are elusive because the optimum regions of the exosphere have not been sampled. The Sun-avoidance constraints on MESSENGER place tight limits on instrument boresight directions, and some regions are probed infrequently. If there are strong spatial gradients in the distribution of weakly emitting species, a high-resolution sampling of specific regions may be required to detect them. Summing spectra over time will also aid in the ability to detect weaker emission. Observations to date nonetheless permit strong upper limits to be placed on the abundances of many undetected species, in some cases as functions of time and space. As those limits are lowered with time, the absence of detections can provide insight into surface composition and the potential source mechanisms of exospheric material.

  13. MESSENGER Searches for Less Abundant or Weakly Emitting Species in Mercury's Exosphere

    NASA Technical Reports Server (NTRS)

    Vervack, Ronald J., Jr.; McClintock, William E.; Killen, Rosemary M.; Sprague, Ann L.; Burger, Matthew H.; Merkel, Aimee W.; Sarantos, Menelaos

    2011-01-01

    Mercury's exosphere is composed of material that originates at the planet's surface, whether that material is native or delivered by the solar wind and micrometeoroids. Many exospheric species have been detected by remote sensing, including H and He by Mariner 10, Na, K, and Ca by ground-based observations, and H, Na, Ca, Mg, and Ca+ by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft. Other exospheric species, including Fe, AI, Si, 0, S, Mn, CI, Ti, OH, and their ions, are expected to be present on the basis of MESSENGER surface measurements and models of Mercury's surface chemistry. Here we report on searches for these species made with the Ultraviolet and Visible Spectrometer (UVVS) channel of the Mercury Atmospheric and Surface Composition Spectrometer (MASCS). No obvious signatures of the listed species have yet been observed in Mercury's exosphere by the UVVS as of this writing. It is possible that detections are elusive because the optimum regions of the exosphere have not been sampled. The Sun-avoidance constraints on MESSENGER place tight limits on instrument boresight directions, and some regions are probed infrequently. If there are strong spatial gradients in the distribution of weakly emitting species, a high-resolution sampling of specific regions may be required to detect them. Summing spectra over time will also aid in the ability to detect weaker emission. Observations to date nonetheless permit strong upper limits to be placed on the abundances of many undetected species, in some cases as functions of time and space. As those limits are lowered with time, the absence of detections can provide insight into surface composition and the potential source mechanisms of exospheric material.

  14. [Species-area and species-abundance relationships of arthropod community in various vegetation restoration areas in Zhifanggou watershed, Shaanxi province of Northwest China].

    PubMed

    Zhang, Feng; Hong, Bo; Li, Ying-Mei; Chen, Zhi-Jie; Zhang, Shu-Lian; Zhao, Hui-Yan

    2013-02-01

    Taking the Zhifanggou watershed in Ansai, Shaanxi Province of Northwest China as a study unit, an investigation on the arthropods in 8 forest stands was conducted from 2006 to 2008, with the species-area and species-abundance relationships of the arthropods in these stands analyzed by various mathematical models. In these forest stands, the species-area relationship of the arthropods accorded with the formula S= CAm With the increase of investigation area, the species number approached to a constant, and the corresponding smallest investigation area was in the order of natural bush > natural forest > Populus davidiana+Robinia pseudoacacia forest > Hippaphae rhamnoides +Caragana mocrophylla forest> Periploca sepium forest > Hippaphae rhamnoides forest > Robinia pseudoacacia forest > Caragana mocrophylla forest, indicating that the more complex the stands, the larger the minimum area needed to be investigated. Based on sampling investigation, the species-abundance models of the arthropods in various stands were established. Lognormal distribution model (LN) was most suitable to fit the arthropod community in natural recovery stands, suggesting that in the arthropod community, there were more species with medial individual amount and fewer abundant species and rare species, and no obvious dominant species. LogCauchy distribution model (LC) was most suitable to fit the arthropod community in mixed and pure stands. As compared with natural recovery stand, mixed and pure stands had more abundant and rare species, and more dominant species.

  15. Accurate measurement of the relative abundance of different DNA species in complex DNA mixtures.

    PubMed

    Jeong, Sangkyun; Yu, Hyunjoo; Pfeifer, Karl

    2012-06-01

    A molecular tool that can compare the abundances of different DNA sequences is necessary for comparing intergenic or interspecific gene expression. We devised and verified such a tool using a quantitative competitive polymerase chain reaction approach. For this approach, we adapted a competitor array, an artificially made plasmid DNA in which all the competitor templates for the target DNAs are arranged with a defined ratio, and melting analysis for allele quantitation for accurate quantitation of the fractional ratios of competitively amplified DNAs. Assays on two sets of DNA mixtures with explicitly known compositional structures of the test sequences were performed. The resultant average relative errors of 0.059 and 0.021 emphasize the highly accurate nature of this method. Furthermore, the method's capability of obtaining biological data is demonstrated by the fact that it can illustrate the tissue-specific quantitative expression signatures of the three housekeeping genes G6pdx, Ubc, and Rps27 by using the forms of the relative abundances of their transcripts, and the differential preferences of Igf2 enhancers for each of the multiple Igf2 promoters for the transcription.

  16. Accurate Measurement of the Relative Abundance of Different DNA Species in Complex DNA Mixtures

    PubMed Central

    Jeong, Sangkyun; Yu, Hyunjoo; Pfeifer, Karl

    2012-01-01

    A molecular tool that can compare the abundances of different DNA sequences is necessary for comparing intergenic or interspecific gene expression. We devised and verified such a tool using a quantitative competitive polymerase chain reaction approach. For this approach, we adapted a competitor array, an artificially made plasmid DNA in which all the competitor templates for the target DNAs are arranged with a defined ratio, and melting analysis for allele quantitation for accurate quantitation of the fractional ratios of competitively amplified DNAs. Assays on two sets of DNA mixtures with explicitly known compositional structures of the test sequences were performed. The resultant average relative errors of 0.059 and 0.021 emphasize the highly accurate nature of this method. Furthermore, the method's capability of obtaining biological data is demonstrated by the fact that it can illustrate the tissue-specific quantitative expression signatures of the three housekeeping genes G6pdx, Ubc, and Rps27 by using the forms of the relative abundances of their transcripts, and the differential preferences of Igf2 enhancers for each of the multiple Igf2 promoters for the transcription. PMID:22334570

  17. Molecular characterization of Eimeria species in macropods.

    PubMed

    Yang, Rongchang; Fenwick, Stan; Potter, Abbey; Elliot, Aileen; Power, Michelle; Beveridge, Ian; Ryan, Una

    2012-10-01

    A total of 597 faecal samples were collected from western grey kangaroos (Macropus fuliginosus), Euros (M. robustus), red kangaroos (M. rufus) in Western Australia and Eastern Grey Kangaroos (M. giganteus) from Victoria and screened for the presence of Eimeria by PCR at the 18S ribosomal RNA (rRNA) locus. The overall prevalence was 24.3% (145/597). At the 18S rRNA locus, sequences were obtained for 25 of the 145 positives. Phylogenetic analysis indicated that all the macropod-derived Eimeria species grouped in a separate marsupial clade that included Eimeria trichosuri from brushtail possums. At least 6 different clades were identified within the marsupial isolates and many of the genotypes identified are likely to be valid species, however morphological and biological data need to be collected to match sequences to previously characterized Eimeria species or identify if they are new species.

  18. Relating large-scale climate variability to local species abundance: ENSO forcing and shrimp in Breton Sound, Louisiana, USA

    USGS Publications Warehouse

    Piazza, Bryan P.; LaPeyre, Megan K.; Keim, B.D.

    2010-01-01

    Climate creates environmental constraints (filters) that affect the abundance and distribution of species. In estuaries, these constraints often result from variability in water flow properties and environmental conditions (i.e. water flow, salinity, water temperature) and can have significant effects on the abundance and distribution of commercially important nekton species. We investigated links between large-scale climate variability and juvenile brown shrimp Farfantepenaeus aztecus abundance in Breton Sound estuary, Louisiana (USA). Our goals were to (1) determine if a teleconnection exists between local juvenile brown shrimp abundance and the El Niño Southern Oscillation (ENSO) and (2) relate that linkage to environmental constraints that may affect juvenile brown shrimp recruitment to, and survival in, the estuary. Our results identified a teleconnection between winter ENSO conditions and juvenile brown shrimp abundance in Breton Sound estuary the following spring. The physical connection results from the impact of ENSO on winter weather conditions in Breton Sound (air pressure, temperature, and precipitation). Juvenile brown shrimp abundance effects lagged ENSO by 3 mo: lower than average abundances of juvenile brown shrimp were caught in springs following winter El Niño events, and higher than average abundances of brown shrimp were caught in springs following La Niña winters. Salinity was the dominant ENSO-forced environmental filter for juvenile brown shrimp. Spring salinity was cumulatively forced by winter river discharge, winter wind forcing, and spring precipitation. Thus, predicting brown shrimp abundance requires incorporating climate variability into models.

  19. Raising groundwater differentially affects mineralization and plant species abundance in dune slacks.

    PubMed

    van Bodegom, Peter M; Oosthoek, Annelies; Broekman, Rob; Bakker, Chris; Aerts, Rien

    2006-10-01

    The experience with restoring high water levels (i.e., rewetting) within restoration ecology is limited, and information on changes in soil nutrient supply is scarce. A reduction in nutrient supply is needed to restore the desired oligotrophic vegetation. We determined the effects of restoration of high water levels on decomposition and net carbon (C), nitrogen (N), and phosphorus (P) mineralization rates in wet dune slacks and its consequences for the relative abundance of eutrophic vs. oligotrophic species in the vegetation. This was done by analyzing these variables for valleys that experienced a large groundwater rise vs. valleys that had a small groundwater rise but the same current water level. In addition, the influences of underlying factors (waterlogging, vegetation dieback, and soil dynamics prior to groundwater rise) were separated in a transplantation experiment. Short-term effects of large groundwater rise were a massive dieback of vegetation, increased thickness of the fermentation layer, increased microbial decomposition activity, increased C mineralization, and decreased net N mineralization. Net P mineralization was not affected. The relative abundance of oligotrophic vs. eutrophic species was greater at large groundwater rise. Changes in decomposition and mineralization by large groundwater rise were, however, not caused by the vegetation dieback, but due to previous soil conditions. Soils experiencing waterlogged conditions for 3-4 years or more prior to large groundwater rise had lower C and higher net N mineralization rates at waterlogged conditions than soils that had experienced aerobic conditions, presumably due to differences in labile soil C contents. Contrary to expectations induced by previously determined nutrient pulses and measured vegetation dieback, large groundwater rise resulted in lower soil nutrient supply rates and more oligotrophic vegetation. If these trends continue on the longer term, restoration of high water levels may be

  20. The use of molecular beacons to directly measure bacterial mRNA abundances and transcript degradation.

    PubMed

    Kuechenmeister, Lisa J; Anderson, Kelsi L; Morrison, John M; Dunman, Paul M

    2009-02-01

    The regulation of mRNA turnover is a dynamic means by which bacteria regulate gene expression. Although current methodologies allow characterization of the stability of individual transcripts, procedures designed to measure alterations in transcript abundance/turnover on a high throughput scale are lacking. In the current report, we describe the development of a rapid and simplified molecular beacon-based procedure to directly measure the mRNA abundances and mRNA degradation properties of well-characterized Staphylococcus aureus pathogenicity factors. This method does not require any PCR-based amplification, can monitor the abundances of multiple transcripts within a single RNA sample, and was successfully implemented into a high throughput screen of transposon mutant library members to detect isolates with altered mRNA turnover properties. It is expected that the described methodology will provide great utility in characterizing components of bacterial RNA degradation processes and can be used to directly measure the mRNA levels of virtually any bacterial transcript.

  1. LogCauchy, log-sech and lognormal distributions of species abundances in forest communities

    USGS Publications Warehouse

    Yin, Z.-Y.; Peng, S.-L.; Ren, H.; Guo, Q.; Chen, Z.-H.

    2005-01-01

    Species-abundance (SA) pattern is one of the most fundamental aspects of biological community structure, providing important information regarding species richness, species-area relation and succession. To better describe the SA distribution (SAD) in a community, based on the widely used lognormal (LN) distribution model with exp(-x2) roll-off on Preston's octave scale, this study proposed two additional models, logCauchy (LC) and log-sech (LS), respectively with roll-offs of simple x-2 and e-x. The estimation of the theoretical total number of species in the whole community, S*, including very rare species not yet collected in sample, was derived from the left-truncation of each distribution. We fitted these three models by Levenberg-Marquardt nonlinear regression and measured the model fit to the data using coefficient of determination of regression, parameters' t-test and distribution's Kolmogorov-Smirnov (KS) test. Examining the SA data from six forest communities (five in lower subtropics and one in tropics), we found that: (1) on a log scale, all three models that are bell-shaped and left-truncated statistically adequately fitted the observed SADs, and the LC and LS did better than the LN; (2) from each model and for each community the S* values estimated by the integral and summation methods were almost equal, allowing us to estimate S* using a simple integral formula and to estimate its asymptotic confidence internals by regression of a transformed model containing it; (3) following the order of LC, LS, and LN, the fitted distributions became lower in the peak, less concave in the side, and shorter in the tail, and overall the LC tended to overestimate, the LN tended to underestimate, while the LS was intermediate but slightly tended to underestimate, the observed SADs (particularly the number of common species in the right tail); (4) the six communities had some similar structural properties such as following similar distribution models, having a common

  2. Species richness and relative abundance of breeding birds in forests of the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Nelms, C.O.; Twedt, D.J.; Smith, Winston Paul

    1993-01-01

    In 1992, the Vicksburg Field Research Station of the National Wetlands Research Center initiated research on the ecology of migratory birds within forests of the Mississippi Alluvial Valley (MAV). The MAV was historically a nearly contiguous bottomland hardwood forest, however, only remnants remain. These remnants are fragmented and often influenced by drainage projects, silviculture, agriculture, and urban development. Our objectives are to assess species richness and relative abundance, and to relate these to the size, quality, and composition of forest stands. Species richness and relative abundance were estimated for 53 randomly selected forest sites using 1 to 8 point counts per site, depending on the size of the forest fragment. However, statistical comparisons among sites will be restricted to an equal number ofpoint counts within the sites being compared. Point counts, lasting five minutes, were conducted from 11 May to 29 June 1992, foltowing Ralph, Sauer, and Droege (Point Count Standards; memo dated 9 March 1992). Vegetation was measured at the first three points on each site using a modification of the methods employed by Martin and Roper (Condor 90: 5 1-57; 1988). During 252 counts, 7 1 species were encountered, but only 62 species were encountered within a 50-m radius of point center. The mean number of species encountered within 50 m of a point, was 7.3 (s.d. = 2.7) and the mean number of individuals was 11.2 (s.d. = 4.2). The mean number of species detected at any distance was 9.6 (s.d, = 2.8) and the mean number of individuals was 15.6 (s.d. = 7.9). The most frequently encountered warblers in the MAV were Prothonotary Warbler and Northern Parula. Rarely encountered warblers were American Redstart and Worm-eating Warbler. The genera, Quercus, Ulmus, Carya, and Celtis were each encountered at 80 or more of the 152 points at which vegetation was sampled. Species most frequentlyencountered were: sugarberry (Celtis laevagata), water hickory (Caqa

  3. Strength of evidence for density dependence in abundance time series of 1198 species.

    PubMed

    Brook, Barry W; Bradshaw, Corey J A

    2006-06-01

    Population limitation is a fundamental tenet of ecology, but the relative roles of exogenous and endogenous mechanisms remain unquantified for most species. Here we used multi-model inference (MMI), a form of model averaging, based on information theory (Akaike's Information Criterion) to evaluate the relative strength of evidence for density-dependent and density-independent population dynamical models in long-term abundance time series of 1198 species. We also compared the MMI results to more classic methods for detecting density dependence: Neyman-Pearson hypothesis-testing and best-model selection using the Bayesian Information Criterion or cross-validation. Using MMI on our large database, we show that density dependence is a pervasive feature of population dynamics (median MMI support for density dependence = 74.7-92.2%), and that this holds across widely different taxa. The weight of evidence for density dependence varied among species but increased consistently, with the number of generations monitored. Best-model selection methods yielded similar results to MMI (a density-dependent model was favored in 66.2-93.9% of species time series), while the hypothesis-testing methods detected density dependence less frequently (32.6-49.8%). There were no obvious differences in the prevalence of density dependence across major taxonomic groups under any of the statistical methods used. These results underscore the value of using multiple modes of analysis to quantify the relative empirical support for a set of working hypotheses that encompass a range of realistic population dynamical behaviors.

  4. Variation in local abundance and species richness of stream fishes in relation to dispersal barriers: Implications for management and conservation

    USGS Publications Warehouse

    Nislow, K.H.; Hudy, M.; Letcher, B.H.; Smith, E.P.

    2011-01-01

    1.Barriers to immigration, all else being equal, should in principle depress local abundance and reduce local species richness. These issues are particularly relevant to stream-dwelling species when improperly designed road crossings act as barriers to migration with potential impacts on the viability of upstream populations. However, because abundance and richness are highly spatially and temporally heterogeneous and the relative importance of immigration on demography is uncertain, population- and community-level effects can be difficult to detect. 2.In this study, we tested the effects of potential barriers to upstream movements on the local abundance and species richness of a diverse assemblage of resident stream fishes in the Monongahela National Forest, West Virginia, U.S.A. Fishes were sampled using simple standard techniques above- and below road crossings that were either likely or unlikely to be barriers to upstream fish movements (based on physical dimensions of the crossing). We predicted that abundance of resident fishes would be lower in the upstream sections of streams with predicted impassable barriers, that the strength of the effect would vary among species and that variable effects on abundance would translate into lower species richness. 3.Supporting these predictions, the statistical model that best accounted for variation in abundance and species richness included a significant interaction between location (upstream or downstream of crossing) and type (passable or impassable crossing). Stream sections located above predicated impassable culverts had fewer than half the number of species and less than half the total fish abundance, while stream sections above and below passable culverts had essentially equivalent richness and abundance. 4.Our results are consistent with the importance of immigration and population connectivity to local abundance and species richness of stream fishes. In turn, these results suggest that when measured at

  5. Molecular species composition of plant cardiolipin determined by liquid chromatography mass spectrometry.

    PubMed

    Zhou, Yonghong; Peisker, Helga; Dörmann, Peter

    2016-07-01

    Cardiolipin (CL), an anionic phospholipid of the inner mitochondrial membrane, provides essential functions for stabilizing respiratory complexes and is involved in mitochondrial morphogenesis and programmed cell death in animals. The role of CL and its metabolism in plants are less well understood. The measurement of CL in plants, including its molecular species composition, is hampered by the fact that CL is of extremely low abundance, and that plants contain large amounts of interfering compounds including galactolipids, neutral lipids, and pigments. We used solid phase extraction by anion exchange chromatography to purify CL from crude plant lipid extracts. LC/MS was used to determine the content and molecular species composition of CL. Thus, up to 23 different molecular species of CL were detected in different plant species, including Arabidopsis, mung bean, spinach, barley, and tobacco. Similar to animals, plant CL is dominated by highly unsaturated species, mostly containing linoleic and linolenic acid. During phosphate deprivation or exposure to an extended dark period, the amount of CL decreased in Arabidopsis, accompanied with an increased degree in unsaturation. The mechanism of CL remodeling during stress, and the function of highly unsaturated CL molecular species, remains to be defined. PMID:27179363

  6. Declines in abundance and species richness of birds following a major flood on the upper Mississippi River

    USGS Publications Warehouse

    Knutson, M.G.; Klaas, E.E.

    1997-01-01

    We examined the abundance and species richness of birds breeding in floodplain forests of the Upper Mississippi River in 1992 through 1994, and used a two-way ANOVA with repeated measures to identify effects of a 1993 flood on the bird community. Sixty-five study plots were divided into treatment and control plots based on whether they were flooded in 1993. Among 84 species observed on all plots, 41 species decreased in abundance from 1992 to 1994, 13 increased, 5 were unchanged. Sample sizes were inadequate to evaluate trends for 25 species. Species richness declined over the three-year period. Of 36 species tested with the ANOVA, 20 had a significant main effect of Year. Cool, wet conditions may have contributed to poor reproductive success in 1993, and resulted in widespread decline in floodplain bird abundance during the year following the flood. Bird abundance increased on most unflooded plots in 1993, probably because birds were displaced from flooded plots. This pattern was most striking for neotropical migrants, species preferring habitat edges, lower canopy nesters, and species that forage in the air. We suggest that periodic major flooding may maintain suitable floodplain habitat for Prothonotary Warblers (Protonotaria citrea) in the face of competition from House Wrens (Troglodytes aedon) for nest sites.

  7. Predicting recovery criteria for threatened and endangered plant species on the basis of past abundances and biological traits.

    PubMed

    Neel, Maile C; Che-Castaldo, Judy P

    2013-04-01

    Recovery plans for species listed under the U.S. Endangered Species Act are required to specify measurable criteria that can be used to determine when the species can be delisted. For the 642 listed endangered and threatened plant species that have recovery plans, we applied recursive partitioning methods to test whether the number of individuals or populations required for delisting can be predicted on the basis of distributional and biological traits, previous abundance at multiple time steps, or a combination of traits and previous abundances. We also tested listing status (threatened or endangered) and the year the recovery plan was written as predictors of recovery criteria. We analyzed separately recovery criteria that were stated as number of populations and as number of individuals (population-based and individual-based criteria, respectively). Previous abundances alone were relatively good predictors of population-based recovery criteria. Fewer populations, but a greater proportion of historically known populations, were required to delist species that had few populations at listing compared with species that had more populations at listing. Previous abundances were also good predictors of individual-based delisting criteria when models included both abundances and traits. The physiographic division in which the species occur was also a good predictor of individual-based criteria. Our results suggest managers are relying on previous abundances and patterns of decline as guidelines for setting recovery criteria. This may be justifiable in that previous abundances inform managers of the effects of both intrinsic traits and extrinsic threats that interact and determine extinction risk.

  8. Molecular Diagnosis of Pathogenic Sporothrix Species

    PubMed Central

    Rodrigues, Anderson Messias; de Hoog, G. Sybren; de Camargo, Zoilo Pires

    2015-01-01

    Background Sporotrichosis is a chronic (sub)cutaneous infection caused by thermodimorphic fungi in the order, Ophiostomatales. These fungi are characterized by major differences in routes of transmission, host predilections, species virulence, and susceptibilities to antifungals. Sporothrix species emerge in the form of outbreaks. Large zoonoses and sapronoses are ongoing in Brazil and China, respectively. Current diagnostic methods based on morphology and physiology are inaccurate due to closely related phenotypes with overlapping components between pathogenic and non-pathogenic Sporothrix. There is a critical need for new diagnostic tools that are specific, sensitive, and cost-effective. Methodology We developed a panel of novel markers, based on calmodulin (CAL) gene sequences, for the large-scale diagnosis and epidemiology of clinically relevant members of the Sporothrix genus, and its relative, Ophiostoma. We identified specific PCR-based markers for S. brasiliensis, S. schenckii, S. globosa, S. mexicana, S. pallida, and O. stenoceras. We employed a murine model of disseminated sporotrichosis to optimize a PCR assay for detecting Sporothrix in clinical specimens. Results Primer-BLAST searches revealed candidate sequences that were conserved within a single species. Species-specific primers showed no significant homology with human, mouse, or microorganisms outside the Sporothrix genus. The detection limit was 10–100 fg of DNA in a single round of PCR for identifying S. brasiliensis, S. schenckii, S. globosa, S. mexicana, and S. pallida. A simple, direct PCR assay, with conidia as a source of DNA, was effective for rapid, low-cost genotyping. Samples from a murine model of disseminated sporotrichosis confirmed the feasibility of detecting S. brasiliensis and S. schenckii DNA in spleen, liver, lungs, heart, brain, kidney, tail, and feces of infected animals. Conclusions This PCR-based method could successfully detect and identify a single species in samples

  9. Atomic Oxygen Abundance in Molecular Clouds: Absorption Toward Sagittarius B2

    NASA Technical Reports Server (NTRS)

    Lis, D. C.; Keene, Jocelyn; Phillips, T. G.; Schilke, P.; Werner, M. W.; Zmuidzinas, J.

    2001-01-01

    We have obtained high-resolution (approximately 35 km/s) spectra toward the molecular cloud Sgr B2 at 63 micrometers, the wavelength of the ground-state fine-structure line of atomic oxygen (O(I)), using the ISO-LWS instrument. Four separate velocity components are seen in the deconvolved spectrum, in absorption against the dust continuum emission of Sgr B2. Three of these components, corresponding to foreground clouds, are used to study the O(I) content of the cool molecular gas along the line of sight. In principle, the atomic oxygen that produces a particular velocity component could exist in any, or all, of three physically distinct regions: inside a dense molecular cloud, in the UV illuminated surface layer (PDR) of a cloud, and in an atomic (H(I)) gas halo. For each of the three foreground clouds, we estimate, and subtract from the observed O(I) column density, the oxygen content of the H(I) halo gas, by scaling from a published high-resolution 21 cm spectrum. We find that the remaining O(I) column density is correlated with the observed (13)CO column density. From the slope of this correlation, an average [O(I)]/[(13)CO] ratio of 270 +/- 120 (3-sigma) is derived, which corresponds to [O(I)]/[(13)CO] = 9 for a CO to (13)CO abundance ratio of 30. Assuming a (13)CO abundance of 1x10(exp -6) with respect to H nuclei, we derive an atomic oxygen abundance of 2.7x10(exp -4) in the dense gas phase, corresponding to a 15% oxygen depletion compared to the diffuse ISM in our Galactic neighborhood. The presence of multiple, spectrally resolved velocity components in the Sgr B2 absorption spectrum allows, for the first time, a direct determination of the PDR contribution to the O(I) column density. The PDR regions should contain O(I) but not (13)CO, and would thus be expected to produce an offset in the O(I)-(13)CO correlation. Our data do not show such an offset, suggesting that within our beam O(I) is spatially coexistent with the molecular gas, as traced by (13)CO

  10. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    PubMed Central

    Heffernan, Natalie; Brunton, Nigel P.; FitzGerald, Richard J.; Smyth, Thomas J.

    2015-01-01

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds. PMID:25603345

  11. Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

    PubMed

    Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

    2015-01-16

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  12. Species composition and seasonal abundance of sandflies (Diptera: Psychodidae: Phlebotominae) in coffee agroecosystems.

    PubMed

    Pérez, Jeanneth; Virgen, Armando; Rojas, Julio Cesar; Rebollar-Téllez, Eduardo Alfonso; Alfredo, Castillo; Infante, Francisco; Mikery, Oscar; Marina, Carlos Felix; Ibáñez-Bernal, Sergio

    2014-02-01

    The composition and seasonal occurrence of sandflies were investigated in coffee agroecosystems in the Soconusco region of Chiapas, Mexico. Insect sampling was performed on three plantations located at different altitudes: Finca Guadalupe Zajú [1,000 m above sea level (a.s.l.)], Finca Argovia (613 m a.s.l.) and Teotihuacán del Valle (429 m a.s.l.). Sandflies were sampled monthly from August 2007-July 2008 using three sampling methods: Shannon traps, CDC miniature light traps and Disney traps. Sampling was conducted for 3 h during three consecutive nights, beginning at sunset. A total of 4,387 sandflies were collected during the course of the study: 2,718 individuals in Finca Guadalupe Zajú, 605 in Finca Argovia and 1,064 in Teotihuacán del Valle. The Shannon traps captured 94.3% of the total sandflies, while the CDC light traps and Disney traps captured 4.9% and 0.8%, respectively. More females than males were collected at all sites. While the number of sandflies captured was positively correlated with temperature and relative humidity, a negative correlation was observed between sandfly numbers and rainfall. Five species of sandflies were captured: Lutzomyia cruciata , Lutzomyia texana , Lutzomyia ovallesi , Lutzomyia cratifer / undulata and Brumptomyia sp. Lu. cruciata , constituting 98.8% of the total, was the most abundant species. None of the captured sandflies was infected with Leishmania spp. PMID:24271002

  13. Species composition and seasonal abundance of sandflies (Diptera: Psychodidae: Phlebotominae) in coffee agroecosystems.

    PubMed

    Pérez, Jeanneth; Virgen, Armando; Rojas, Julio Cesar; Rebollar-Téllez, Eduardo Alfonso; Alfredo, Castillo; Infante, Francisco; Mikery, Oscar; Marina, Carlos Felix; Ibáñez-Bernal, Sergio

    2014-02-01

    The composition and seasonal occurrence of sandflies were investigated in coffee agroecosystems in the Soconusco region of Chiapas, Mexico. Insect sampling was performed on three plantations located at different altitudes: Finca Guadalupe Zajú [1,000 m above sea level (a.s.l.)], Finca Argovia (613 m a.s.l.) and Teotihuacán del Valle (429 m a.s.l.). Sandflies were sampled monthly from August 2007-July 2008 using three sampling methods: Shannon traps, CDC miniature light traps and Disney traps. Sampling was conducted for 3 h during three consecutive nights, beginning at sunset. A total of 4,387 sandflies were collected during the course of the study: 2,718 individuals in Finca Guadalupe Zajú, 605 in Finca Argovia and 1,064 in Teotihuacán del Valle. The Shannon traps captured 94.3% of the total sandflies, while the CDC light traps and Disney traps captured 4.9% and 0.8%, respectively. More females than males were collected at all sites. While the number of sandflies captured was positively correlated with temperature and relative humidity, a negative correlation was observed between sandfly numbers and rainfall. Five species of sandflies were captured: Lutzomyia cruciata , Lutzomyia texana , Lutzomyia ovallesi , Lutzomyia cratifer / undulata and Brumptomyia sp. Lu. cruciata , constituting 98.8% of the total, was the most abundant species. None of the captured sandflies was infected with Leishmania spp.

  14. Seasonal abundance of livestock-associated Culicoides species in northeastern Brazil.

    PubMed

    Carvalho, L P C; Silva, F S

    2014-06-01

    Culicoides biting midges (Diptera: Ceratopogonidae) are of great medical and veterinary importance because the haematophagous females of some species can transmit diseases to humans and animals. In order to determine the presence and seasonal abundance of the bluetongue virus (BTV) vector Culicoides insignis Lutz at domestic animal sheds in northeastern Brazil, insects were collected once a month between January and December 2010. Light traps were set from 18.00 to 06.00 hours at a pigsty, chicken coop and bovine corral. Culicoides insignis accounted for 81% of the 22,316 specimens collected. Other well-represented species were: Culicoides paucienfuscatus Barbosa (3246 individuals), Culicoides diabolicus Hoffman (308), Culicoides leopoldoi Ortiz (224) and Culicoides duartei Tavares and Luna Dias (221). The remainder accounted for 4% of the total sample. Culicoides insignis occurred mostly at the cattle corral, 98.2% in the rainy season. This study confirms the presence and close association of C. insignis with cattle in Maranhão state, northeastern Brazil and emphasizes the risk of bluetongue infections spreading in the area. PMID:24382216

  15. Historical abundance and morphology of Didymosphenia species in Naknek Lake, Alaska

    USGS Publications Warehouse

    Pite, D.P.; Lane, K.A.; Hermann, A.K.; Spaulding, S.A.; Finney, B.P.

    2009-01-01

    Since the 1980s, nuisance blooms of Didymosphenia geminata (Lyngbye) M. Schmidt have been documented in sites that are warmer and more mesotrophic than historical records indicate. While the invasion of D. geminata in New Zealand is well documented, it is less clear whether nuisance blooms in North America are a new phenomenon. In order to test the hypothesis that D. geminata blooms have increased in recent years, we examined the historical record of this species in sediments of Naknek Lake, in Katmai National Park, Alaska. Chronological control was established by relating the presence of two ash layers to known volcanic eruptions. We identified two species of Didymosphenia within the sediment record: D. geminata and D. clavaherculis (Ehrenberg) Metzeltin et Lange-Bertalot. This is the first published record of D. clavaherculis in North America. We found no statistically significant change in the numerical presence of D. geminata or D. clavaherculis, as a group, in Naknek Lake between the years 1218 and 2003. While there has been no sudden, or recent, increase in abundance of Didymosphenia in Naknek Lake, morphological features of D. geminata populations in Naknek Lake are distinct compared to morphological features of D. geminata in streams containing nuisance blooms from sites in North America and New Zealand. Variance in the morphology of Didymosphenia cells may help determine relationships between distinct sub-populations and establish the history of habitat invasion.

  16. Species composition and seasonal abundance of sandflies (Diptera: Psychodidae: Phlebotominae) in coffee agroecosystems

    PubMed Central

    Pérez, Jeanneth; Virgen, Armando; Rojas, Julio Cesar; Rebollar-Téllez, Eduardo Alfonso; Alfredo, Castillo; Infante, Francisco; Mikery, Oscar; Marina, Carlos Felix; Ibáñez-Bernal, Sergio

    2013-01-01

    The composition and seasonal occurrence of sandflies were investigated in coffee agroecosystems in the Soconusco region of Chiapas, Mexico. Insect sampling was performed on three plantations located at different altitudes: Finca Guadalupe Zajú [1,000 m above sea level (a.s.l.)], Finca Argovia (613 m a.s.l.) and Teotihuacán del Valle (429 m a.s.l.). Sandflies were sampled monthly from August 2007-July 2008 using three sampling methods: Shannon traps, CDC miniature light traps and Disney traps. Sampling was conducted for 3 h during three consecutive nights, beginning at sunset. A total of 4,387 sandflies were collected during the course of the study: 2,718 individuals in Finca Guadalupe Zajú, 605 in Finca Argovia and 1,064 in Teotihuacán del Valle. The Shannon traps captured 94.3% of the total sandflies, while the CDC light traps and Disney traps captured 4.9% and 0.8%, respectively. More females than males were collected at all sites. While the number of sandflies captured was positively correlated with temperature and relative humidity, a negative correlation was observed between sandfly numbers and rainfall. Five species of sandflies were captured: Lutzomyia cruciata , Lutzomyia texana , Lutzomyia ovallesi , Lutzomyia cratifer / undulata and Brumptomyia sp. Lu. cruciata , constituting 98.8% of the total, was the most abundant species. None of the captured sandflies was infected with Leishmania spp. PMID:24271002

  17. ABUNDANCE OF {sup 26}Al AND {sup 60}Fe IN EVOLVING GIANT MOLECULAR CLOUDS

    SciTech Connect

    Vasileiadis, Aristodimos; Nordlund, Ake; Bizzarro, Martin

    2013-05-20

    The nucleosynthesis and ejection of radioactive {sup 26}Al (t{sub 1/2} {approx} 0.72 Myr) and {sup 60}Fe, (t{sub 1/2} {approx} 2.5 Myr) into the interstellar medium is dominated by the stellar winds of massive stars and supernova type II explosions. Studies of meteorites and their components indicate that the initial abundances of these short-lived radionuclides in the solar protoplanetary disk were higher than the background levels of the galaxy inferred from {gamma}-ray astronomy and models of the galactic chemical evolution. This observation has been used to argue for a late-stage addition of stellar debris to the solar system's parental molecular cloud or, alternatively, the solar protoplanetary disk, thereby requiring a special scenario for the formation of our solar system. Here, we use supercomputers to model-from first principles-the production, transport, and admixing of freshly synthesized {sup 26}Al and {sup 60}Fe in star-forming regions within giant molecular clouds. Under typical star formation conditions, the levels of {sup 26}Al in most star-forming regions are comparable to that deduced from meteorites, suggesting that the presence of short-lived radionuclides in the early solar system is a generic feature of the chemical evolution of giant molecular clouds. The {sup 60}Fe/{sup 26}Al yield ratio of Almost-Equal-To 0.2 calculated from our simulations is consistent with the galactic value of 0.15 {+-} 0.06 inferred from {gamma}-ray astronomy but is significantly higher than most current solar system measurements indicate. We suggest that estimates based on differentiated meteorites and some chondritic components may not be representative of the initial {sup 60}Fe abundance of the bulk solar system.

  18. DNA barcode-based molecular identification system for fish species.

    PubMed

    Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

    2010-12-01

    In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

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

    PubMed Central

    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

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

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; 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

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

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; 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.

  2. Models of Experimentally Derived Competitive Effects Predict Biogeographical Differences in the Abundance of Invasive and Native Plant Species

    PubMed Central

    Xiao, Sa; Ni, Guangyan; Callaway, Ragan M.

    2013-01-01

    Mono-dominance by invasive species provides opportunities to explore determinants of plant distributions and abundance; however, linking mechanistic results from small scale experiments to patterns in nature is difficult. We used experimentally derived competitive effects of an invader in North America, Acroptilon repens, on species with which it co-occurs in its native range of Uzbekistan and on species with which it occurs in its non-native ranges in North America, in individual-based models. We found that competitive effects yielded relative abundances of Acroptilon and other species in models that were qualitatively similar to those observed in the field in the two ranges. In its non-native range, Acroptilon can occur in nearly pure monocultures at local scales, whereas such nearly pure stands of Acroptilon appear to be much less common in its native range. Experimentally derived competitive effects of Acroptilon on other species predicted Acroptilon to be 4–9 times more proportionally abundant than natives in the North American models, but proportionally equal to or less than the abundance of natives in the Eurasian models. Our results suggest a novel way to integrate complex combinations of interactions simultaneously, and that biogeographical differences in the competitive effects of an invader correspond well with biogeographical differences in abundance and impact. PMID:24265701

  3. ANALYTICAL FORMULAE OF MOLECULAR ION ABUNDANCES AND THE N{sub 2}H{sup +} RING IN PROTOPLANETARY DISKS

    SciTech Connect

    Aikawa, Yuri; Furuya, Kenji; Nomura, Hideko; Qi, Chunhua

    2015-07-10

    We investigate the chemistry of ion molecules in protoplanetary disks, motivated by the detection of the N{sub 2}H{sup +} ring around TW Hya. While the ring inner radius coincides with the CO snow line, it is not apparent why N{sub 2}H{sup +} is abundant outside the CO snow line in spite of the similar sublimation temperatures of CO and N{sub 2}. Using the full gas-grain network model, we reproduced the N{sub 2}H{sup +} ring in a disk model with millimeter grains. The chemical conversion of CO and N{sub 2} to less volatile species (sink effect hereinafter) is found to affect the N{sub 2}H{sup +} distribution. Since the efficiency of the sink depends on various parameters such as activation barriers of grain-surface reactions, which are not well constrained, we also constructed the no-sink model; the total (gas and ice) CO and N{sub 2} abundances are set constant, and their gaseous abundances are given by the balance between adsorption and desorption. Abundances of molecular ions in the no-sink model are calculated by analytical formulae, which are derived by analyzing the full-network model. The N{sub 2}H{sup +} ring is reproduced by the no-sink model, as well. The 2D (R-Z) distribution of N{sub 2}H{sup +}, however, is different among the full-network model and no-sink model. The column density of N{sub 2}H{sup +} in the no-sink model depends sensitively on the desorption rate of CO and N{sub 2} and the cosmic-ray flux. We also found that N{sub 2}H{sup +} abundance can peak at the temperature slightly below the CO sublimation, even if the desorption energies of CO and N{sub 2} are the same.

  4. Characterization of Capsicum species using anatomical and molecular data.

    PubMed

    Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

    2013-02-28

    Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features.

  5. Plankton studies in San Francisco Bay; VI, Zooplankton species composition and abundance in the North Bay, 1979-1980

    USGS Publications Warehouse

    Hutchinson, Anne

    1982-01-01

    Data are presented that summarize zooplankton species composition and abundance in North San Francisco Bay during 1979 and 1980. Sampling was conducted once monthly at six stations during 1979 and twice monthly at sixteen stations during 1980. Samples were collected by pump at three depths in the shipping channel and at one depth over the shoals. Subsamples were enumerated while alive. Total zooplankton biomass, as carbon, was calculated from estimated carbon quotas and abundances of each organism enumerated.

  6. Phospholipid molecular species of frog rod outer segment membranes.

    PubMed

    Wiegand, R D; Anderson, R E

    1983-08-01

    Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were isolated from frog retinal rod outer segment (ROS) membranes and their major molecular species determined. Saturated fatty acids are predominantly located on position-1 and polyunsaturates on position-2, although this assignment is not absolute. One-fifth of the species of PC are of the saturated and monoenoic type, compared to only trace amounts of these species in PE. On the other hand, PE contains at least 50% dipolyunsaturated species, while PC has 6%. The predominant molecular species of frog PC are: 18:0-22:6 omega 3 (39%), 16:0-22:6 omega 3 (17%), 16:0-16:1 (6%), 16:0-18:1 (5%) and 16:0-16:0 (4%). The major molecular species of frog PE are: 22:6 omega 3-22:6 omega 3 (21%), 18:0-22:6 omega 3 (18%), 18:1-22:6 omega 3 (14%), 22:4 omega 6-22:6 omega 3 (10%), 22:5 omega (3 + 6)-22:6 omega 3 (10%), 16:0-22:6 omega 3 (7%) and 20:4 omega 6-22:6 omega 3 (5%). The specific molecular species are discussed in relation to their effect on fluidity and asymmetry of ROS disc membranes.

  7. Modelling the Abundances of Two Major Culicoides (Diptera: Ceratopogonidae) Species in the Niayes Area of Senegal

    PubMed Central

    Diarra, Maryam; Fall, Moussa; Lancelot, Renaud; Diop, Aliou; Fall, Assane G.; Dicko, Ahmadou; Seck, Momar Talla; Garros, Claire; Allène, Xavier; Rakotoarivony, Ignace; Bakhoum, Mame Thierno; Bouyer, Jérémy; Guis, Hélène

    2015-01-01

    In Senegal, considerable mortality in the equine population and hence major economic losses were caused by the African horse sickness (AHS) epizootic in 2007. Culicoides oxystoma and Culicoides imicola, known or suspected of being vectors of bluetongue and AHS viruses are two predominant species in the vicinity of horses and are present all year-round in Niayes area, Senegal. The aim of this study was to better understand the environmental and climatic drivers of the dynamics of these two species. Culicoides collections were obtained using OVI (Onderstepoort Veterinary Institute) light traps at each of the 5 sites for three nights of consecutive collection per month over one year. Cross Correlation Map analysis was performed to determine the time-lags for which environmental variables and abundance data were the most correlated. C. oxystoma and C. imicola count data were highly variable and overdispersed. Despite modelling large Culicoides counts (over 220,000 Culicoides captured in 354 night-traps), using on-site climate measures, overdispersion persisted in Poisson, negative binomial, Poisson regression mixed-effect with random effect at the site of capture models. The only model able to take into account overdispersion was the Poisson regression mixed-effect model with nested random effects at the site and date of capture levels. According to this model, meteorological variables that contribute to explaining the dynamics of C. oxystoma and C. imicola abundances were: mean temperature and relative humidity of the capture day, mean humidity between 21 and 19 days prior a capture event, density of ruminants, percentage cover of water bodies within a 2 km radius and interaction between temperature and humidity for C. oxystoma; mean rainfall and NDVI of the capture day and percentage cover of water bodies for C. imicola. Other variables such as soil moisture, wind speed, degree days, land cover or landscape metrics could be tested to improve the models. Further work

  8. Dynamic relationships between body size, species richness, abundance, and energy use in a shallow marine epibenthic faunal community

    PubMed Central

    Labra, Fabio A; Hernández-Miranda, Eduardo; Quiñones, Renato A

    2015-01-01

    We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species-averaged values with individual-based estimates which allow species to potentially occupy multiple size classes. For individual-based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species-based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual-based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species-based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic

  9. Dynamic relationships between body size, species richness, abundance, and energy use in a shallow marine epibenthic faunal community.

    PubMed

    Labra, Fabio A; Hernández-Miranda, Eduardo; Quiñones, Renato A

    2015-01-01

    We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species-averaged values with individual-based estimates which allow species to potentially occupy multiple size classes. For individual-based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species-based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual-based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species-based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic

  10. Dynamic relationships between body size, species richness, abundance, and energy use in a shallow marine epibenthic faunal community.

    PubMed

    Labra, Fabio A; Hernández-Miranda, Eduardo; Quiñones, Renato A

    2015-01-01

    We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species-averaged values with individual-based estimates which allow species to potentially occupy multiple size classes. For individual-based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species-based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual-based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species-based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic

  11. Dietary flavonoid fisetin increases abundance of high-molecular-mass hyaluronan conferring resistance to prostate oncogenesis.

    PubMed

    Lall, Rahul K; Syed, Deeba N; Khan, Mohammad Imran; Adhami, Vaqar M; Gong, Yuansheng; Lucey, John A; Mukhtar, Hasan

    2016-09-01

    We and others have shown previously that fisetin, a plant flavonoid, has therapeutic potential against many cancer types. Here, we examined the probable mechanism of its action in prostate cancer (PCa) using a global metabolomics approach. HPLC-ESI-MS analysis of tumor xenografts from fisetin-treated animals identified several metabolic targets with hyaluronan (HA) as the most affected. Efficacy of fisetin on HA was then evaluated in vitro and also in vivo in the transgenic TRAMP mouse model of PCa. Size exclusion chromatography-multiangle laser light scattering (SEC-MALS) was performed to analyze the molar mass (Mw) distribution of HA. Fisetin treatment downregulated intracellular and secreted HA levels both in vitro and in vivo Fisetin inhibited HA synthesis and degradation enzymes, which led to cessation of HA synthesis and also repressed the degradation of the available high-molecular-mass (HMM)-HA. SEC-MALS analysis of intact HA fragment size revealed that cells and animals have more abundance of HMM-HA and less of low-molecular-mass (LMM)-HA upon fisetin treatment. Elevated HA levels have been shown to be associated with disease progression in certain cancer types. Biological responses triggered by HA mainly depend on the HA polymer length where HMM-HA represses mitogenic signaling and has anti-inflammatory properties whereas LMM-HA promotes proliferation and inflammation. Similarly, Mw analysis of secreted HA fragment size revealed less HMM-HA is secreted that allowed more HMM-HA to be retained within the cells and tissues. Our findings establish that fisetin is an effective, non-toxic, potent HA synthesis inhibitor, which increases abundance of antiangiogenic HMM-HA and could be used for the management of PCa.

  12. Dietary flavonoid fisetin increases abundance of high-molecular-mass hyaluronan conferring resistance to prostate oncogenesis.

    PubMed

    Lall, Rahul K; Syed, Deeba N; Khan, Mohammad Imran; Adhami, Vaqar M; Gong, Yuansheng; Lucey, John A; Mukhtar, Hasan

    2016-09-01

    We and others have shown previously that fisetin, a plant flavonoid, has therapeutic potential against many cancer types. Here, we examined the probable mechanism of its action in prostate cancer (PCa) using a global metabolomics approach. HPLC-ESI-MS analysis of tumor xenografts from fisetin-treated animals identified several metabolic targets with hyaluronan (HA) as the most affected. Efficacy of fisetin on HA was then evaluated in vitro and also in vivo in the transgenic TRAMP mouse model of PCa. Size exclusion chromatography-multiangle laser light scattering (SEC-MALS) was performed to analyze the molar mass (Mw) distribution of HA. Fisetin treatment downregulated intracellular and secreted HA levels both in vitro and in vivo Fisetin inhibited HA synthesis and degradation enzymes, which led to cessation of HA synthesis and also repressed the degradation of the available high-molecular-mass (HMM)-HA. SEC-MALS analysis of intact HA fragment size revealed that cells and animals have more abundance of HMM-HA and less of low-molecular-mass (LMM)-HA upon fisetin treatment. Elevated HA levels have been shown to be associated with disease progression in certain cancer types. Biological responses triggered by HA mainly depend on the HA polymer length where HMM-HA represses mitogenic signaling and has anti-inflammatory properties whereas LMM-HA promotes proliferation and inflammation. Similarly, Mw analysis of secreted HA fragment size revealed less HMM-HA is secreted that allowed more HMM-HA to be retained within the cells and tissues. Our findings establish that fisetin is an effective, non-toxic, potent HA synthesis inhibitor, which increases abundance of antiangiogenic HMM-HA and could be used for the management of PCa. PMID:27335141

  13. Determinants of distribution and abundance of two shrub species, Guiera senegalensis and Piliostigma reticulatum, in Peanut Basin, Senegal

    NASA Astrophysics Data System (ADS)

    Lufafa, A.; Diédhiou, I.; Ndiaye, N.; Kizito, F.; Dick, R.; Noller, J. S.

    2005-05-01

    The ability to predict and manage the course of landscape-level ecological change and its longer-term consequences on ecosystem functions (e.g. carbon stabilization and soil degradation mitigation) depends on the ability to understand how a particular ecosystem functions and the mechanisms that control the distribution, configuration and abundance of key species. Guiera senegalensis and Piliostigma reticulatum are two native shrub species that are widely found in Sub-Saharan Africa but unrecognized in their potential role in regulating hydrological and carbon cycles in both natural and agro-ecosystems. Our objective was to conduct a study on the determinants of landscape-level distribution and abundance of these shrub species as a basis for ecological modeling and management of this fragile semiarid environment. Formal Recursive Inference Modeling was used to adduce determinants of species presence while logistic regression and geostatistical approaches were used to estimate shrub abundance within their communities. The results showed that distribution of the shrubs is controlled by four factors: geological substrate, mean annual temperature, mean annual rainfall and landform (profile convexity). Relative abundance within the shrub communities is under the influence of mean annual rainfall, maximum annual temperature and elevation (for G. senegalensis) and mean annual rainfall, mean annual temperature, elevation and landform (profile convexity) (for P. reticulatum). Predictive models for shrub distribution and abundance were generally poor, probably highlighting the weakness of statistical models in analysis and quantification of the spatial structure of ecosystems.

  14. Species Diversity, Abundance, and Host Preferences of Mosquitoes (Diptera: Culicidae) in Two Different Ecotypes of Madagascar With Recent RVFV Transmission.

    PubMed

    Jean Jose Nepomichene, Thiery Nirina; Elissa, Nohal; Cardinale, Eric; Boyer, Sebastien

    2015-09-01

    Mosquito diversity and abundance were examined in six Madagascan villages in either arid (Toliary II district) or humid (Mampikony district) ecotypes, each with a history of Rift Valley fever virus transmission. Centers for Disease Control and Prevention light traps without CO2 (LT) placed near ruminant parks and animal-baited net trap (NT) baited with either zebu or sheep/goat were used to sample mosquitoes, on two occasions between March 2011 and October 2011. Culex tritaeniorhynchus (Giles) was the most abundant species, followed by Culex antennatus (Becker) and Anopheles squamosus/cydippis (Theobald/de Meillon). These three species comprised more than half of all mosquitoes collected. The NT captured more mosquitoes in diversity and in abundance than the LT, and also caught more individuals of each species, except for An. squamosus/cydippis. Highest diversity and abundance were observed in the humid and warm district of Mampikony. No host preference was highlighted, except for Cx. tritaeniorhynchus presenting a blood preference for zebu baits. The description of species diversity, abundance, and host preference described herein can inform the development of control measures to reduce the risk of mosquito-borne diseases in Madagascar.

  15. Species Diversity, Abundance, and Host Preferences of Mosquitoes (Diptera: Culicidae) in Two Different Ecotypes of Madagascar With Recent RVFV Transmission.

    PubMed

    Jean Jose Nepomichene, Thiery Nirina; Elissa, Nohal; Cardinale, Eric; Boyer, Sebastien

    2015-09-01

    Mosquito diversity and abundance were examined in six Madagascan villages in either arid (Toliary II district) or humid (Mampikony district) ecotypes, each with a history of Rift Valley fever virus transmission. Centers for Disease Control and Prevention light traps without CO2 (LT) placed near ruminant parks and animal-baited net trap (NT) baited with either zebu or sheep/goat were used to sample mosquitoes, on two occasions between March 2011 and October 2011. Culex tritaeniorhynchus (Giles) was the most abundant species, followed by Culex antennatus (Becker) and Anopheles squamosus/cydippis (Theobald/de Meillon). These three species comprised more than half of all mosquitoes collected. The NT captured more mosquitoes in diversity and in abundance than the LT, and also caught more individuals of each species, except for An. squamosus/cydippis. Highest diversity and abundance were observed in the humid and warm district of Mampikony. No host preference was highlighted, except for Cx. tritaeniorhynchus presenting a blood preference for zebu baits. The description of species diversity, abundance, and host preference described herein can inform the development of control measures to reduce the risk of mosquito-borne diseases in Madagascar. PMID:26336259

  16. [Species-abundance distribution patterns along succession series of Phyllostachys glauca forest in a limestone mountain].

    PubMed

    Shi, Jian-min; Fan, Cheng-fang; Liu, Yang; Yang, Qing-pei; Fang, Kai; Fan, Fang-li; Yang, Guang-yao

    2015-12-01

    To detect the ecological process of the succession series of Phyllostachys glauca forest in a limestone mountain, five niche models, i.e., broken stick model (BSM), niche preemption model (NPM), dominance preemption model (DPM), random assortment model (RAM) and overlap- ping niche model (ONM) were employed to describe the species-abundance distribution patterns (SDPs) of 15 samples. χ² test and Akaike information criterion (AIC) were used to test the fitting effects of the five models. The results showed that the optimal SDP models for P. glauca forest, bamboo-broadleaved mixed forest and broadleaved forest were DPM (χ² = 35.86, AIC = -69.77), NPM (χ² = 1.60, AIC = -94.68) and NPM (χ² = 0.35, AIC = -364.61), respectively. BSM also well fitted the SDP of bamboo-broadleaved mixed forest and broad-leaved forest, while it was unsuitable to describe the SDP of P. glauca forest. The fittings of RAM and ONM in the three forest types were all rejected by the χ² test and AIC. With the development of community succession from P. glauca forest to broadleaved forest, the species richness and evenness increased, and the optimal SDP model changed from DPM to NPM. It was inferred that the change of ecological process from habitat filtration to interspecific competition was the main driving force of the forest succession. The results also indicated that the application of multiple SDP models and test methods would be beneficial to select the best model and deeply understand the ecological process of community succession. PMID:27111994

  17. Environmental factors influence both abundance and genetic diversity in a widespread bird species

    PubMed Central

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-01-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

  18. [Species-abundance distribution patterns along succession series of Phyllostachys glauca forest in a limestone mountain].

    PubMed

    Shi, Jian-min; Fan, Cheng-fang; Liu, Yang; Yang, Qing-pei; Fang, Kai; Fan, Fang-li; Yang, Guang-yao

    2015-12-01

    To detect the ecological process of the succession series of Phyllostachys glauca forest in a limestone mountain, five niche models, i.e., broken stick model (BSM), niche preemption model (NPM), dominance preemption model (DPM), random assortment model (RAM) and overlap- ping niche model (ONM) were employed to describe the species-abundance distribution patterns (SDPs) of 15 samples. χ² test and Akaike information criterion (AIC) were used to test the fitting effects of the five models. The results showed that the optimal SDP models for P. glauca forest, bamboo-broadleaved mixed forest and broadleaved forest were DPM (χ² = 35.86, AIC = -69.77), NPM (χ² = 1.60, AIC = -94.68) and NPM (χ² = 0.35, AIC = -364.61), respectively. BSM also well fitted the SDP of bamboo-broadleaved mixed forest and broad-leaved forest, while it was unsuitable to describe the SDP of P. glauca forest. The fittings of RAM and ONM in the three forest types were all rejected by the χ² test and AIC. With the development of community succession from P. glauca forest to broadleaved forest, the species richness and evenness increased, and the optimal SDP model changed from DPM to NPM. It was inferred that the change of ecological process from habitat filtration to interspecific competition was the main driving force of the forest succession. The results also indicated that the application of multiple SDP models and test methods would be beneficial to select the best model and deeply understand the ecological process of community succession.

  19. Environmental factors influence both abundance and genetic diversity in a widespread bird species.

    PubMed

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-11-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations.

  20. Sulphur-bearing species in molecular clouds

    NASA Astrophysics Data System (ADS)

    Bilalbegović, G.; Baranović, G.

    2015-01-01

    We study several molecules that could help in the solution of the missing sulphur problem in dense clouds and circumstellar regions, as well as in the clarification of the sulphur chemistry in comets. These sulphur molecules are the trimer (CH2S)3 and the tetramer (CH2S)4 of thioformaldehyde, pentathian S5CH2, hexathiepan S6CH2, thiirane C2H4S, trisulfane HSSSH, and thioacetone (CH3)2CS. Infrared spectra of these species are calculated using the density functional theory methods. The majority of calculated bands belong to the mid-infrared, with some of them occurring in the near- and far-infrared region. We suggest that some of unidentified spectral features measured by Infrared Space Observatory in several active galactic nuclei and starburst galaxies could be caused by 1,3,5-trithiane ((CH2S)3), 1,3,5,7-tetrathiocane ((CH2S)4), and thiirane (C2H4S). The objects whose unidentified infrared features we compare with calculated bands are NGC 253, M82, NGC 1068, Circinus, Arp 220, 30 Doradus, Orion KL, and Sgr B2.

  1. A database of marine phytoplankton abundance, biomass and species composition in Australian waters

    PubMed Central

    Davies, Claire H.; Coughlan, Alex; Hallegraeff, Gustaaf; Ajani, Penelope; Armbrecht, Linda; Atkins, Natalia; Bonham, Prudence; Brett, Steve; Brinkman, Richard; Burford, Michele; Clementson, Lesley; Coad, Peter; Coman, Frank; Davies, Diana; Dela-Cruz, Jocelyn; Devlin, Michelle; Edgar, Steven; Eriksen, Ruth; Furnas, Miles; Hassler, Christel; Hill, David; Holmes, Michael; Ingleton, Tim; Jameson, Ian; Leterme, Sophie C.; Lønborg, Christian; McLaughlin, James; McEnnulty, Felicity; McKinnon, A. David; Miller, Margaret; Murray, Shauna; Nayar, Sasi; Patten, Renee; Pritchard, Tim; Proctor, Roger; Purcell-Meyerink, Diane; Raes, Eric; Rissik, David; Ruszczyk, Jason; Slotwinski, Anita; Swadling, Kerrie M.; Tattersall, Katherine; Thompson, Peter; Thomson, Paul; Tonks, Mark; Trull, Thomas W.; Uribe-Palomino, Julian; Waite, Anya M.; Yauwenas, Rouna; Zammit, Anthony; Richardson, Anthony J.

    2016-01-01

    There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels. PMID:27328409

  2. Semiparametric bivariate zero-inflated Poisson models with application to studies of abundance for multiple species

    USGS Publications Warehouse

    Arab, Ali; Holan, Scott H.; Wikle, Christopher K.; Wildhaber, Mark L.

    2012-01-01

    Ecological studies involving counts of abundance, presence–absence or occupancy rates often produce data having a substantial proportion of zeros. Furthermore, these types of processes are typically multivariate and only adequately described by complex nonlinear relationships involving externally measured covariates. Ignoring these aspects of the data and implementing standard approaches can lead to models that fail to provide adequate scientific understanding of the underlying ecological processes, possibly resulting in a loss of inferential power. One method of dealing with data having excess zeros is to consider the class of univariate zero-inflated generalized linear models. However, this class of models fails to address the multivariate and nonlinear aspects associated with the data usually encountered in practice. Therefore, we propose a semiparametric bivariate zero-inflated Poisson model that takes into account both of these data attributes. The general modeling framework is hierarchical Bayes and is suitable for a broad range of applications. We demonstrate the effectiveness of our model through a motivating example on modeling catch per unit area for multiple species using data from the Missouri River Benthic Fishes Study, implemented by the United States Geological Survey.

  3. A database of marine phytoplankton abundance, biomass and species composition in Australian waters.

    PubMed

    Davies, Claire H; Coughlan, Alex; Hallegraeff, Gustaaf; Ajani, Penelope; Armbrecht, Linda; Atkins, Natalia; Bonham, Prudence; Brett, Steve; Brinkman, Richard; Burford, Michele; Clementson, Lesley; Coad, Peter; Coman, Frank; Davies, Diana; Dela-Cruz, Jocelyn; Devlin, Michelle; Edgar, Steven; Eriksen, Ruth; Furnas, Miles; Hassler, Christel; Hill, David; Holmes, Michael; Ingleton, Tim; Jameson, Ian; Leterme, Sophie C; Lønborg, Christian; McLaughlin, James; McEnnulty, Felicity; McKinnon, A David; Miller, Margaret; Murray, Shauna; Nayar, Sasi; Patten, Renee; Pritchard, Tim; Proctor, Roger; Purcell-Meyerink, Diane; Raes, Eric; Rissik, David; Ruszczyk, Jason; Slotwinski, Anita; Swadling, Kerrie M; Tattersall, Katherine; Thompson, Peter; Thomson, Paul; Tonks, Mark; Trull, Thomas W; Uribe-Palomino, Julian; Waite, Anya M; Yauwenas, Rouna; Zammit, Anthony; Richardson, Anthony J

    2016-06-21

    There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels.

  4. A database of marine phytoplankton abundance, biomass and species composition in Australian waters.

    PubMed

    Davies, Claire H; Coughlan, Alex; Hallegraeff, Gustaaf; Ajani, Penelope; Armbrecht, Linda; Atkins, Natalia; Bonham, Prudence; Brett, Steve; Brinkman, Richard; Burford, Michele; Clementson, Lesley; Coad, Peter; Coman, Frank; Davies, Diana; Dela-Cruz, Jocelyn; Devlin, Michelle; Edgar, Steven; Eriksen, Ruth; Furnas, Miles; Hassler, Christel; Hill, David; Holmes, Michael; Ingleton, Tim; Jameson, Ian; Leterme, Sophie C; Lønborg, Christian; McLaughlin, James; McEnnulty, Felicity; McKinnon, A David; Miller, Margaret; Murray, Shauna; Nayar, Sasi; Patten, Renee; Pritchard, Tim; Proctor, Roger; Purcell-Meyerink, Diane; Raes, Eric; Rissik, David; Ruszczyk, Jason; Slotwinski, Anita; Swadling, Kerrie M; Tattersall, Katherine; Thompson, Peter; Thomson, Paul; Tonks, Mark; Trull, Thomas W; Uribe-Palomino, Julian; Waite, Anya M; Yauwenas, Rouna; Zammit, Anthony; Richardson, Anthony J

    2016-01-01

    There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels. PMID:27328409

  5. [Seasonal evaluation of mammal species richness and abundance in the "Mário Viana" municipal reserve, Mato Grosso, Brasil].

    PubMed

    Rocha, Ednaldo Cândido; Silva, Elias; Martins, Sebastião Venâncio; Barreto, Francisco Cândido Cardoso

    2006-09-01

    We evaluated seasonal species presence and richness, and abundance of medium and large sized mammalian terrestrial fauna in the "Mário Viana" Municipal Biological Reserve, Nova Xavantina, Mato Grosso, Brazil. During 2001, two monthly visits were made to an established transect, 2,820 m in length. Records of 22 mammal species were obtained and individual footprint sequences quantified for seasonal calculation of species richness and relative abundance index (x footprints/km traveled). All 22 species occurred during the rainy season, but only 18 during the dry season. Pseudalopex vetulus (Lund, 1842) (hoary fox), Eira barbara (Linnaeus, 1758) (tayra), Puma concolor (Linnaeus, 1771) (cougar) and Hydrochaeris hydrochaeris (Linnaeus, 1766) (capybara) were only registered during the rainy season. The species diversity estimated using the Jackknife procedure in the dry season (19.83, CI = 2.73) was smaller than in the rainy season (25.67, CI = 3.43). Among the 18 species common in the two seasons, only four presented significantly different abundance indexes: Dasypus novemcinctus Linnaeus, 1758 (nine-banded armadillo), Euphractus sexcinctus (Linnaeus, 1758) (six-banded armadillo), Dasyprocta azarae Lichtenstein, 1823 (Azara's Agouti) and Tapirus terrestris (Linnaeus, 1758) (tapir). On the other hand, Priodontes maximus (Kerr, 1792) (giant armadillo) and Leopardus pardalis (Linnaeus, 1758) (ocelot) had identical abundance index over the two seasons. Distribution of species abundance in the sampled area followed the expected pattern for communities in equilibrium, especially in the rainy season, suggesting that the environment still maintains good characteristics for mammal conservation. The present study shows that the reserve, although only 470 ha in size, plays an important role for conservation of mastofauna of the area as a refuge in an environment full of anthropic influence (mainly cattle breeding in exotic pasture). PMID:18491629

  6. [Seasonal evaluation of mammal species richness and abundance in the "Mário Viana" municipal reserve, Mato Grosso, Brasil].

    PubMed

    Rocha, Ednaldo Cândido; Silva, Elias; Martins, Sebastião Venâncio; Barreto, Francisco Cândido Cardoso

    2006-09-01

    We evaluated seasonal species presence and richness, and abundance of medium and large sized mammalian terrestrial fauna in the "Mário Viana" Municipal Biological Reserve, Nova Xavantina, Mato Grosso, Brazil. During 2001, two monthly visits were made to an established transect, 2,820 m in length. Records of 22 mammal species were obtained and individual footprint sequences quantified for seasonal calculation of species richness and relative abundance index (x footprints/km traveled). All 22 species occurred during the rainy season, but only 18 during the dry season. Pseudalopex vetulus (Lund, 1842) (hoary fox), Eira barbara (Linnaeus, 1758) (tayra), Puma concolor (Linnaeus, 1771) (cougar) and Hydrochaeris hydrochaeris (Linnaeus, 1766) (capybara) were only registered during the rainy season. The species diversity estimated using the Jackknife procedure in the dry season (19.83, CI = 2.73) was smaller than in the rainy season (25.67, CI = 3.43). Among the 18 species common in the two seasons, only four presented significantly different abundance indexes: Dasypus novemcinctus Linnaeus, 1758 (nine-banded armadillo), Euphractus sexcinctus (Linnaeus, 1758) (six-banded armadillo), Dasyprocta azarae Lichtenstein, 1823 (Azara's Agouti) and Tapirus terrestris (Linnaeus, 1758) (tapir). On the other hand, Priodontes maximus (Kerr, 1792) (giant armadillo) and Leopardus pardalis (Linnaeus, 1758) (ocelot) had identical abundance index over the two seasons. Distribution of species abundance in the sampled area followed the expected pattern for communities in equilibrium, especially in the rainy season, suggesting that the environment still maintains good characteristics for mammal conservation. The present study shows that the reserve, although only 470 ha in size, plays an important role for conservation of mastofauna of the area as a refuge in an environment full of anthropic influence (mainly cattle breeding in exotic pasture).

  7. Physical factors affecting the abundance and species richness of fishes in the shallow waters of the southern Bothnian Sea (Sweden)

    NASA Astrophysics Data System (ADS)

    Thorman, Staffan

    1986-03-01

    The relationship between the composition of the fish assemblages and the abiotic environment in seven shallow areas within the same geographical range in the southern Bothnian Sea were studied in May, July, September and November 1982. Eighteen species were found in the areas and the major species were Pungitius pungitius (L.), Pomatoschistus minutus (Pallas), Gasterosteus aculeatus (L.), Phoxinus phoxinus (L.), Pomatoschistus microps (Krøyer) and Gobius niger L. The main purpose of the study was to examine the possible effects of exposure, organic contents in sediments and habitat heterogeneity on species richness and abundance of the assemblages. There was a negative correlation between the organic contents of the sediment and exposure. There were no significant correlations between exposure, organic contents, size of the areas and species numbers but habitat heterogeneity was positively correlated with species number. There were no correlations between fish abundance and heterogeneity of the areas. Negative correlations occurred between the exposure of the areas and fish abundance. The amounts of the pooled benthic fauna were negatively correlated to the exposure. The species/area hypothesis finds no support in the results, because there was no correlation between habitat heterogeneity of an area and its size. The effective fetch combined with the heterogeneity measurement of the areas seemed to be useful indicators of the species composition and fish abundance. Habitat heterogeneity and exposure were the most important structuring factors of these shallow water fish assemblages during the ice-free period and within the local geographical range. The assemblages consist of a mixture of species with marine or limnic origin and they have probably not evolved in the Bothnian Sea or together. They are most likely regulated by their physiological plasticity and not by interactions with other species.

  8. Relationship between Reproductive Allocation and Relative Abundance among 32 Species of a Tibetan Alpine Meadow: Effects of Fertilization and Grazing

    PubMed Central

    Niu, Kechang; Schmid, Bernhard; Choler, Philippe; Du, Guozhen

    2012-01-01

    Background Understanding the relationship between species traits and species abundance is an important goal in ecology and biodiversity science. Although theoretical studies predict that traits related to performance (e.g. reproductive allocation) are most directly linked to species abundance within a community, empirical investigations have rarely been done. It also remains unclear how environmental factors such as grazing or fertilizer application affect the predicted relationship. Methodology We conducted a 3-year field experiment in a Tibetan alpine meadow to assess the relationship between plant reproductive allocation (RA) and species relative abundance (SRA) on control, grazed and fertilized plots. Overall, the studied plant community contained 32 common species. Principal Findings At the treatment level, (i) RA was negatively correlated with SRA on control plots and during the first year on fertilized plots. (ii) No negative RA–SRA correlations were observed on grazed plots and during the second and third year on fertilized plots. (iii) Seed size was positively correlated with SRA on control plots. At the plot level, the correlation between SRA and RA were not affected by treatment, year or species composition. Conclusions/Significance Our study shows that the performance-related trait RA can negatively affect SRA within communities, which is possibly due to the tradeoffs between clonal growth (for space occupancy) and sexual reproduction. We propose that if different species occupy different positions along these tradeoffs it will contribute to biodiversity maintenance in local communities or even at lager scale. PMID:22536385

  9. Dynamics of the abundance of some bivalve species in Russian waters of the Sea of Japan and its prognosis

    NASA Astrophysics Data System (ADS)

    Gabaev, D. D.

    2009-04-01

    The abundance dynamics of several species of bivalve mollusks spats were studied on scallop collectors situated in Minonosok bay of Pos’eta Gulf for 27 years and for 4 years in Kit bay of the Sea of Japan (Russia). A significant positive relation was found between the species having similar thermopathy: the Japanese scallop Mizuhopecten yessoensis and Swift’s scallop Swiftopecten swifti, as well as between the wrinkled rock borer Hiatella arctica and Swift’s scallop Swiftopecten swifti. A significant reverse relation was found between the bay mussel Mytilus trossulus and the Northern Pacific seastar Asterias amurensis. Some of the studied mollusks of Minonosok bay and the remote Kit bay display a significant reversed interrelation in their abundance dynamics caused by the precipitation regime. The one-way dispersion analysis a revealed significant influence of the water temperature in June and the precipitation abundance in the summer on Swift’s scallop’s dynamic abundance. The two-way dispersion analysis showed a significant influence of the ice period duration and the solar activity expressed in Wolf’s numbers on the Japanese scallop abundance dynamics. The uneven years in the period from 1977 to 1984 were usually productive for M. yessoensis and S. swifti spat. After 1985, the even years became more productive (there was asynchronicity in the abundance dynamics compared with 1977-1984). Such asynchronicity appeared with the advent of the new 22-year solar cycle, which caused a change in the magnet polarity in 1986.

  10. Current methods for molecular typing of Campylobacter species.

    PubMed

    Taboada, Eduardo N; Clark, Clifford G; Sproston, Emma L; Carrillo, Catherine D

    2013-10-01

    Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many molecular subtyping methods have been developed to characterize Campylobacter species, but only a few are commonly used in molecular epidemiology studies. This review examines the applicability of these methods, as well as the role that emerging whole genome sequencing technologies will play in tracking sources of Campylobacter spp. infection. PMID:23871858

  11. Climate warming increases biodiversity of small rodents by favoring rare or less abundant species in a grassland ecosystem.

    PubMed

    Jiang, Guangshun; Liu, Jun; Xu, Lei; Yu, Guirui; He, Honglin; Zhang, Zhibin

    2013-06-01

    Our Earth is facing the challenge of accelerating climate change, which imposes a great threat to biodiversity. Many published studies suggest that climate warming may cause a dramatic decline in biodiversity, especially in colder and drier regions. In this study, we investigated the effects of temperature, precipitation and a normalized difference vegetation index on biodiversity indices of rodent communities in the current or previous year for both detrended and nondetrended data in semi-arid grassland of Inner Mongolia during 1982-2006. Our results demonstrate that temperature showed predominantly positive effects on the biodiversity of small rodents; precipitation showed both positive and negative effects; a normalized difference vegetation index showed positive effects; and cross-correlation function values between rodent abundance and temperature were negatively correlated with rodent abundance. Our results suggest that recent climate warming increased the biodiversity of small rodents by providing more benefits to population growth of rare or less abundant species than that of more abundant species in Inner Mongolia grassland, which does not support the popular view that global warming would decrease biodiversity in colder and drier regions. We hypothesized that higher temperatures might benefit rare or less abundant species (with smaller populations and more folivorous diets) by reducing the probability of local extinction and/or by increasing herbaceous food resources.

  12. Predicting foundation bunchgrass species abundances: Model-assisted decision-making in protected-area sagebrush steppe

    USGS Publications Warehouse

    Rodhouse, Thomas J.; Irvine, Kathryn M.; Sheley, Roger L.; Smith, Brenda S.; Hoh, Shirley; Esposito, Daniel M.; Mata-Gonzalez, Ricardo

    2014-01-01

    Foundation species are structurally dominant members of ecological communities that can stabilize ecological processes and influence resilience to disturbance and resistance to invasion. Being common, they are often overlooked for conservation but are increasingly threatened from land use change, biological invasions, and over-exploitation. The pattern of foundation species abundances over space and time may be used to guide decision-making, particularly in protected areas for which they are iconic. We used ordinal logistic regression to identify the important environmental influences on the abundance patterns of bluebunch wheatgrass (Pseudoroegneria spicata), Thurber's needlegrass (Achnatherum thurberianum), and Sandberg bluegrass (Poa secunda) in protected-area sagebrush steppe. We then predicted bunchgrass abundances along gradients of topography, disturbance, and invasive annual grass abundance. We used model predictions to prioritize the landscape for implementation of a management and restoration decision-support tool. Models were fit to categorical estimates of grass cover obtained from an extensive ground-based monitoring dataset. We found that remnant stands of abundant wheatgrass and bluegrass were associated with steep north-facing slopes in higher and more remote portions of the landscape outside of recently burned areas where invasive annual grasses were less abundant. These areas represented only 25% of the landscape and were prioritized for protection efforts. Needlegrass was associated with south-facing slopes, but in low abundance and in association with invasive cheatgrass (Bromus tectorum). Abundances of all three species were strongly negatively correlated with occurrence of another invasive annual grass, medusahead (Taeniatherum caput-medusae). The rarity of priority bunchgrass stands underscored the extent of degradation and the need for prioritization. We found no evidence that insularity reduced invasibility; annual grass invasion represents

  13. Low molecular weight species in humic and fulvic fractions

    USGS Publications Warehouse

    Wilson, M.A.; Collin, P.J.; Malcolm, R.L.; Perdue, E.M.; Cresswell, P.

    1988-01-01

    Fourier transform solution 1H nuclear magnetic resonance (NMR) spectrometry with homogated water peak irradiation is a useful method for detecting low molecular weight substances in humic extracts. Succinate, acetate, methanol, formate, lactate and some aryl methoxyl compounds have been detected in extracts from a wide range of sources. In view of the controversy over whether low molecular weight substances are contaminants in humic extracts introduced by the concentration procedure, we report that some of these materials are not contaminants since 1H-NMR can be used to follow their formation from higher molecular weight species. ?? 1988.

  14. Anomalous 13C isotope abundances in C3S and C4H observed toward the cold interstellar cloud, Taurus Molecular Cloud-1.

    PubMed

    Sakai, Nami; Takano, Shuro; Sakai, Takeshi; Shiba, Shoichi; Sumiyoshi, Yoshihiro; Endo, Yasuki; Yamamoto, Satoshi

    2013-10-01

    We have studied the abundances of the (13)C isotopic species of C3S and C4H in the cold molecular cloud, Taurus Molecular Cloud-1 (Cyanopolyyne Peak), by radioastronomical observations of their rotational emission lines. The CCCS/(13)CCCS and CCCS/C(13)CCS ratios are determined to be >206 and 48 ± 15, respectively. The CC(13)CS line is identified with the aid of laboratory microwave spectroscopy, and the range of the CCCS/CC(13)CS ratio is found to be from 30 to 206. The abundances of at least two (13)C isotopic species of C3S are thus found to be different. Similarly, it is found that the abundances of the four (13)C isotopic species of C4H are not equivalent. The CCCCH/(13)CCCCH, CCCCH/C(13)CCCH, CCCCH/CC(13)CCH, and CCCCH/CCC(13)CH ratios are evaluated to be 141 ± 44, 97 ± 27, 82 ± 15, and 118 ± 23, respectively. Here the errors denote 3 times the standard deviation. These results will constrain the formation pathways of C3S and C4H, if the nonequivalence is caused during the formation processes of these molecules. The exchange reactions after the formation of these two molecules may also contribute to the nonequivalence. In addition, we have confirmed that the (12)C/(13)C ratio of some species are significantly higher than the interstellar elemental (12)C/(13)C ratio of 60-70. The observations of the (13)C isotopic species provide us with rich information on chemical processes in cold interstellar clouds.

  15. Ecological effects of cell-level processes: genome size, functional traits and regional abundance of herbaceous plant species

    PubMed Central

    Herben, Tomáš; Suda, Jan; Klimešová, Jitka; Mihulka, Stanislav; Říha, Pavel; Šímová, Irena

    2012-01-01

    Background and Aims Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate. Methods Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis. Key Results Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R2 = 0·145) than for perennials (R2 = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance. Conclusions The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes. PMID:22628380

  16. Molecular characterization of the species Salvinia (Salviniaceae) from the upper Paraná River floodplain.

    PubMed

    Machado, S A; Oliveira, A V; Fabrin, T M C; Prioli, S M A P; Prioli, A J

    2016-08-12

    The pteridophytes Salvinia minima, S. herzogii, and S. auriculata are among the most abundant aquatic macrophytes in the upper Paraná River floodplain. Since some species have highly similar morphological features, it is very difficult to identify members of this genus to the species level. An indication of this difficulty is a set of poorly differentiated taxa comprising S. auriculata and S. herzogii known as the 'S. auriculata complex', which is found in the Paraná River together with other Salvinia species such as S. biloba and S. molesta. Some authors have reported the existence of inter-species hybrids. Despite the complex Salvinia taxonomy, few genetic studies have been performed on purported species within the genus to resolve this complexity. The present study was conducted to determine useful molecular sequences for the discrimination of Salvinia species of the upper Paraná River floodplain. Molecular data were compared with data of other species of the genus to clarify phylogenetic relationships, employing the nucleotide sequence trnL-trnF from the chloroplast DNA. The results revealed that Salvinia populations in the upper Paraná River floodplain belong to different species and indicated that species of the S. auriculata complex may be distinguished from one another after the division of the S. minima group, corroborating results by other researchers. Although the taxonomic position of S. oblongifolia was clarified, as high closeness between S. oblongifolia and the S. auriculata complex was reported, Salvinia kinship is still not thoroughly established and further investigations in morphology and molecular diversity are required.

  17. New Molecular Species In Comet C/1995 (Hale-Bopp) Observed with the Caltech Submillimeter Observatory

    NASA Technical Reports Server (NTRS)

    Lis, D. C.; Mehringer, D. M.; Benford, D.; Gardner, M.; Phillips, T. G.; Bockelee-Morvan, D.; Biver, N.; Colom, P.; Crovisier, J.; Despois, D.; Rauer, H.

    1998-01-01

    We present millimeter-wave observations of HNCO, HC3N, SO, NH2CHO, H(13)CN, and H3O(+) in comet C/1995 O1 (Hale-Bopp) obtained in February-April, 1997 with the Caltech Submillimeter Observatory (CSO). HNCO, first detected at the CSO in comet C/1996 B2 (Hyakutake), is securely confirmed in comet Hale-Bopp via observations of three rotational transitions. The derived abundance with respect to H2O is (4-13) x 10(exp -4). HC3N, SO, and NH2CHO are detected for the first time in a comet. The fractional abundance of HC3N based on observations of three rotational lines is (1.9 +/- 0.2) x 10(exp -4). Four transitions of SO are detected and the derived fractional abundance, (2-8) x 10(exp -3), is higher than the upper limits derived from UV observations of previous comets. Observations of NH2CHO imply a fractional abundance of (1-8) x 10(exp -4). H3O(+) is detected for the first time from the ground. The H(13)CN (3-2) transition is also detected and the derived HCN/H(13)CN abundance ratio is 90 +/- 15, consistent with the terrestrial C-13/C-12 ratio. in addition, a number of other molecular species are detected, including HNC, OCS, HCO(+), CO(+), and CN (the last two are first detections in a comet at radio wavelengths).

  18. The Impact of Land Abandonment on Species Richness and Abundance in the Mediterranean Basin: A Meta-Analysis

    PubMed Central

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no “one-size-fits-all” conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity. PMID:24865979

  19. The impact of land abandonment on species richness and abundance in the Mediterranean Basin: a meta-analysis.

    PubMed

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no "one-size-fits-all" conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity.

  20. The impact of land abandonment on species richness and abundance in the Mediterranean Basin: a meta-analysis.

    PubMed

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no "one-size-fits-all" conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity. PMID:24865979

  1. MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample

    PubMed Central

    Wang, Yi; Leung, Henry C.M.; Yiu, S.M.; Chin, Francis Y.L.

    2012-01-01

    Motivation: Metagenomic binning remains an important topic in metagenomic analysis. Existing unsupervised binning methods for next-generation sequencing (NGS) reads do not perform well on (i) samples with low-abundance species or (ii) samples (even with high abundance) when there are many extremely low-abundance species. These two problems are common for real metagenomic datasets. Binning methods that can solve these problems are desirable. Results: We proposed a two-round binning method (MetaCluster 5.0) that aims at identifying both low-abundance and high-abundance species in the presence of a large amount of noise due to many extremely low-abundance species. In summary, MetaCluster 5.0 uses a filtering strategy to remove noise from the extremely low-abundance species. It separate reads of high-abundance species from those of low-abundance species in two different rounds. To overcome the issue of low coverage for low-abundance species, multiple w values are used to group reads with overlapping w-mers, whereas reads from high-abundance species are grouped with high confidence based on a large w and then binning expands to low-abundance species using a relaxed (shorter) w. Compared to the recent tools, TOSS and MetaCluster 4.0, MetaCluster 5.0 can find more species (especially those with low abundance of say 6× to 10×) and can achieve better sensitivity and specificity using less memory and running time. Availability: http://i.cs.hku.hk/~alse/MetaCluster/ Contact: chin@cs.hku.hk PMID:22962452

  2. Valuing the recreational benefits of wetland adaptation to climate change: a trade-off between species' abundance and diversity.

    PubMed

    Faccioli, Michela; Riera Font, Antoni; Torres Figuerola, Catalina M

    2015-03-01

    Climate change will further exacerbate wetland deterioration, especially in the Mediterranean region. On the one side, it will accelerate the decline in the populations and species of plants and animals, this resulting in an impoverishment of biological abundance. On the other one, it will also promote biotic homogenization, resulting in a loss of species' diversity. In this context, different climate change adaptation policies can be designed: those oriented to recovering species' abundance and those aimed at restoring species' diversity. Based on the awareness that knowledge about visitors' preferences is crucial to better inform policy makers and secure wetlands' public use and conservation, this paper assesses the recreational benefits of different adaptation options through a choice experiment study carried out in S'Albufera wetland (Mallorca). Results show that visitors display positive preferences for an increase in both species' abundance and diversity, although they assign a higher value to the latter, thus suggesting a higher social acceptability of policies pursuing wetlands' differentiation. This finding acquires special relevance not only for adaptation management in wetlands but also for tourism planning, as most visitors to S'Albufera are tourists. Thus, given the growing competition to attract visitors and the increasing demand for high environmental quality and unique experiences, promoting wetlands' differentiation could be a good strategy to gain competitive advantage over other wetland areas and tourism destinations.

  3. Effects of habitat-forming species richness, evenness, identity, and abundance on benthic intertidal community establishment and productivity.

    PubMed

    Lemieux, Julie; Cusson, Mathieu

    2014-01-01

    In a context of reduced global biodiversity, the potential impacts from the loss of habitat-forming species (HFS) on ecosystem structure and functioning must be established. These species are often the main community primary producers and have a major role in the establishment of organisms through facilitation processes. This study focuses on macroalgae and mussels as HFS within an intertidal zone along the St. Lawrence estuary (Quebec, Canada). Over a 16-week period, we manipulated the in situ diversity profile (richness, evenness, identity, and abundance) of the dominant HFS (Fucus distichus edentatus, F. vesiculosus, and Mytilus spp.) in order to define their role in both the establishment of associated species and community primary production. Contrary to expectation, no general change in HFS richness, evenness, abundance, or identity on associated species community establishment was observed. However, over the study period, the HFS diversity profile modified the structure within the trophic guilds, which may potentially affect further community functions. Also, our results showed that the low abundance of HFS had a negative impact on the primary productivity of the community. Our results suggest that HFS diversity profiles have a limited short-term role in our study habitat and may indicate that biological forcing in these intertidal communities is less important than environmental conditions. As such, there was an opportunistic establishment of species that ensured rapid colonization regardless of the absence, or the diversity profile, of facilitators such as HFS. PMID:25313459

  4. Effects of Habitat-Forming Species Richness, Evenness, Identity, and Abundance on Benthic Intertidal Community Establishment and Productivity

    PubMed Central

    Lemieux, Julie; Cusson, Mathieu

    2014-01-01

    In a context of reduced global biodiversity, the potential impacts from the loss of habitat-forming species (HFS) on ecosystem structure and functioning must be established. These species are often the main community primary producers and have a major role in the establishment of organisms through facilitation processes. This study focuses on macroalgae and mussels as HFS within an intertidal zone along the St. Lawrence estuary (Quebec, Canada). Over a 16-week period, we manipulated the in situ diversity profile (richness, evenness, identity, and abundance) of the dominant HFS (Fucus distichus edentatus, F. vesiculosus, and Mytilus spp.) in order to define their role in both the establishment of associated species and community primary production. Contrary to expectation, no general change in HFS richness, evenness, abundance, or identity on associated species community establishment was observed. However, over the study period, the HFS diversity profile modified the structure within the trophic guilds, which may potentially affect further community functions. Also, our results showed that the low abundance of HFS had a negative impact on the primary productivity of the community. Our results suggest that HFS diversity profiles have a limited short-term role in our study habitat and may indicate that biological forcing in these intertidal communities is less important than environmental conditions. As such, there was an opportunistic establishment of species that ensured rapid colonization regardless of the absence, or the diversity profile, of facilitators such as HFS. PMID:25313459

  5. Valuing the Recreational Benefits of Wetland Adaptation to Climate Change: A Trade-off Between Species' Abundance and Diversity

    NASA Astrophysics Data System (ADS)

    Faccioli, Michela; Riera Font, Antoni; Torres Figuerola, Catalina M.

    2015-03-01

    Climate change will further exacerbate wetland deterioration, especially in the Mediterranean region. On the one side, it will accelerate the decline in the populations and species of plants and animals, this resulting in an impoverishment of biological abundance. On the other one, it will also promote biotic homogenization, resulting in a loss of species' diversity. In this context, different climate change adaptation policies can be designed: those oriented to recovering species' abundance and those aimed at restoring species' diversity. Based on the awareness that knowledge about visitors' preferences is crucial to better inform policy makers and secure wetlands' public use and conservation, this paper assesses the recreational benefits of different adaptation options through a choice experiment study carried out in S'Albufera wetland (Mallorca). Results show that visitors display positive preferences for an increase in both species' abundance and diversity, although they assign a higher value to the latter, thus suggesting a higher social acceptability of policies pursuing wetlands' differentiation. This finding acquires special relevance not only for adaptation management in wetlands but also for tourism planning, as most visitors to S'Albufera are tourists. Thus, given the growing competition to attract visitors and the increasing demand for high environmental quality and unique experiences, promoting wetlands' differentiation could be a good strategy to gain competitive advantage over other wetland areas and tourism destinations.

  6. Valuing the recreational benefits of wetland adaptation to climate change: a trade-off between species' abundance and diversity.

    PubMed

    Faccioli, Michela; Riera Font, Antoni; Torres Figuerola, Catalina M

    2015-03-01

    Climate change will further exacerbate wetland deterioration, especially in the Mediterranean region. On the one side, it will accelerate the decline in the populations and species of plants and animals, this resulting in an impoverishment of biological abundance. On the other one, it will also promote biotic homogenization, resulting in a loss of species' diversity. In this context, different climate change adaptation policies can be designed: those oriented to recovering species' abundance and those aimed at restoring species' diversity. Based on the awareness that knowledge about visitors' preferences is crucial to better inform policy makers and secure wetlands' public use and conservation, this paper assesses the recreational benefits of different adaptation options through a choice experiment study carried out in S'Albufera wetland (Mallorca). Results show that visitors display positive preferences for an increase in both species' abundance and diversity, although they assign a higher value to the latter, thus suggesting a higher social acceptability of policies pursuing wetlands' differentiation. This finding acquires special relevance not only for adaptation management in wetlands but also for tourism planning, as most visitors to S'Albufera are tourists. Thus, given the growing competition to attract visitors and the increasing demand for high environmental quality and unique experiences, promoting wetlands' differentiation could be a good strategy to gain competitive advantage over other wetland areas and tourism destinations. PMID:25472830

  7. Improved Molecular Technique for the Differentiation of Neotropical Anopheline Species

    PubMed Central

    Matson, Ryan; Rios, Carlos Tong; Chavez, Cesar Banda; Gilman, Robert H.; Florin, David; Sifuentes, Victor Lopez; Greffa, Roldan Cardenas; Yori, Pablo Peñataro; Fernandez, Roberto; Portocarrero, Daniel Velasquez; Vinetz, Joseph M.; Kosek, Margaret

    2008-01-01

    We evaluated a PCR-RFLP of the ribosomal internal transcribed spacer 2 region (ITS2) to distinguish species of Anopheles commonly reported in the Amazon and validated this method using reared F1 offspring. The following species of Anopheles were used for molecular analysis: An. (Nys.) benarrochi, An. (Nys.) darlingi, An. (Nys.) nuneztovari, An. (Nys.) konderi, An. (Nys.) rangeli, and An. (Nys.) triannulatus sensu lato (s.l.). In addition, three species of the subgenus Anopheles, An. (Ano.) forattini, An. (Ano.) mattogrossensis, and An. (Ano.) peryassui were included for testing. Each of the nine species tested yielded diagnostic banding patterns. The PCR-RFLP method was successful in identifying all life stages including exuviae with small fractions of the sample. The assay is rapid and can be applied as an unbiased confirmatory method for identification of morphologic variants, disputed samples, imperfectly preserved specimens, and life stages from which taxonomic keys do not allow for definitive species determination. PMID:18337348

  8. Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

    PubMed

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

    2015-09-01

    The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent.

  9. Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

    PubMed

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

    2015-09-01

    The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. PMID:26277215

  10. Abundant molecular oxygen in the coma of comet 67P/Churyumov-Gerasimenko.

    PubMed

    Bieler, A; Altwegg, K; Balsiger, H; Bar-Nun, A; Berthelier, J-J; Bochsler, P; Briois, C; Calmonte, U; Combi, M; De Keyser, J; van Dishoeck, E F; Fiethe, B; Fuselier, S A; Gasc, S; Gombosi, T I; Hansen, K C; Hässig, M; Jäckel, A; Kopp, E; Korth, A; Le Roy, L; Mall, U; Maggiolo, R; Marty, B; Mousis, O; Owen, T; Rème, H; Rubin, M; Sémon, T; Tzou, C-Y; Waite, J H; Walsh, C; Wurz, P

    2015-10-29

    The composition of the neutral gas comas of most comets is dominated by H2O, CO and CO2, typically comprising as much as 95 per cent of the total gas density. In addition, cometary comas have been found to contain a rich array of other molecules, including sulfuric compounds and complex hydrocarbons. Molecular oxygen (O2), however, despite its detection on other icy bodies such as the moons of Jupiter and Saturn, has remained undetected in cometary comas. Here we report in situ measurement of O2 in the coma of comet 67P/Churyumov-Gerasimenko, with local abundances ranging from one per cent to ten per cent relative to H2O and with a mean value of 3.80 ± 0.85 per cent. Our observations indicate that the O2/H2O ratio is isotropic in the coma and does not change systematically with heliocentric distance. This suggests that primordial O2 was incorporated into the nucleus during the comet's formation, which is unexpected given the low upper limits from remote sensing observations. Current Solar System formation models do not predict conditions that would allow this to occur. PMID:26511578

  11. Abundant molecular oxygen in the coma of comet 67P/Churyumov-Gerasimenko.

    PubMed

    Bieler, A; Altwegg, K; Balsiger, H; Bar-Nun, A; Berthelier, J-J; Bochsler, P; Briois, C; Calmonte, U; Combi, M; De Keyser, J; van Dishoeck, E F; Fiethe, B; Fuselier, S A; Gasc, S; Gombosi, T I; Hansen, K C; Hässig, M; Jäckel, A; Kopp, E; Korth, A; Le Roy, L; Mall, U; Maggiolo, R; Marty, B; Mousis, O; Owen, T; Rème, H; Rubin, M; Sémon, T; Tzou, C-Y; Waite, J H; Walsh, C; Wurz, P

    2015-10-29

    The composition of the neutral gas comas of most comets is dominated by H2O, CO and CO2, typically comprising as much as 95 per cent of the total gas density. In addition, cometary comas have been found to contain a rich array of other molecules, including sulfuric compounds and complex hydrocarbons. Molecular oxygen (O2), however, despite its detection on other icy bodies such as the moons of Jupiter and Saturn, has remained undetected in cometary comas. Here we report in situ measurement of O2 in the coma of comet 67P/Churyumov-Gerasimenko, with local abundances ranging from one per cent to ten per cent relative to H2O and with a mean value of 3.80 ± 0.85 per cent. Our observations indicate that the O2/H2O ratio is isotropic in the coma and does not change systematically with heliocentric distance. This suggests that primordial O2 was incorporated into the nucleus during the comet's formation, which is unexpected given the low upper limits from remote sensing observations. Current Solar System formation models do not predict conditions that would allow this to occur.

  12. Where to nest? Ecological determinants of chimpanzee nest abundance and distribution at the habitat and tree species scale.

    PubMed

    Carvalho, Joana S; Meyer, Christoph F J; Vicente, Luis; Marques, Tiago A

    2015-02-01

    Conversion of forests to anthropogenic land-uses increasingly subjects chimpanzee populations to habitat changes and concomitant alterations in the plant resources available to them for nesting and feeding. Based on nest count surveys conducted during the dry season, we investigated nest tree species selection and the effect of vegetation attributes on nest abundance of the western chimpanzee, Pan troglodytes verus, at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau, a forest-savannah mosaic widely disturbed by humans. Further, we assessed patterns of nest height distribution to determine support for the anti-predator hypothesis. A zero-altered generalized linear mixed model showed that nest abundance was negatively related to floristic diversity (exponential form of the Shannon index) and positively with the availability of smaller-sized trees, reflecting characteristics of dense-canopy forest. A positive correlation between nest abundance and floristic richness (number of plant species) and composition indicated that species-rich open habitats are also important in nest site selection. Restricting this analysis to feeding trees, nest abundance was again positively associated with the availability of smaller-sized trees, further supporting the preference for nesting in food tree species from dense forest. Nest tree species selection was non-random, and oil palms were used at a much lower proportion (10%) than previously reported from other study sites in forest-savannah mosaics. While this study suggests that human disturbance may underlie the exclusive arboreal nesting at LCNP, better quantitative data are needed to determine to what extent the construction of elevated nests is in fact a response to predators able to climb trees. Given the importance of LCNP as refuge for Pan t. verus our findings can improve conservation decisions for the management of this important umbrella species as well as its remaining suitable habitats. PMID:25224379

  13. Corroborating molecular species discovery: Four new pine-feeding species of Chionaspis (Hemiptera, Diaspididae)

    PubMed Central

    Vea, Isabelle M.; Gwiazdowski, Rodger A.; Normark, Benjamin B.

    2013-01-01

    Abstract The genus Chionaspis (Hemiptera, Diaspididae) includes two North American species of armored scale insects feeding on Pinaceae: Chionaspis heterophyllae Cooley, and Chionaspis pinifoliae (Fitch). Despite the economic impact of conifer-feeding Chionaspis on horticulture, the species diversity in this group has only recently been systematically investigated using samples from across the group’s geographic and host range. This paper provides morphological recognition characters for four new species that were recently hypothesized to exist on the basis of molecular evidence. The new species, here described, are Chionaspis brachycephalon Vea sp. n., Chionaspis caudata Vea sp. n., Chionaspis sonorae Vea sp. n. and Chionaspis torreyanae Vea sp. n.  One of the new species, Chionaspis caudata Vea, has a gland spine at the apex of the pygidium, between the median lobes, unlike any other species of Chionaspis. An identification key to the species of Chionaspis feeding on pine in North America is provided. PMID:23717184

  14. Generalized Additive Models Used to Predict Species Abundance in the Gulf of Mexico: An Ecosystem Modeling Tool

    PubMed Central

    Drexler, Michael; Ainsworth, Cameron H.

    2013-01-01

    Spatially explicit ecosystem models of all types require an initial allocation of biomass, often in areas where fisheries independent abundance estimates do not exist. A generalized additive modelling (GAM) approach is used to describe the abundance of 40 species groups (i.e. functional groups) across the Gulf of Mexico (GoM) using a large fisheries independent data set (SEAMAP) and climate scale oceanographic conditions. Predictor variables included in the model are chlorophyll a, sediment type, dissolved oxygen, temperature, and depth. Despite the presence of a large number of zeros in the data, a single GAM using a negative binomial distribution was suitable to make predictions of abundance for multiple functional groups. We present an example case study using pink shrimp (Farfantepenaeus duroarum) and compare the results to known distributions. The model successfully predicts the known areas of high abundance in the GoM, including those areas where no data was inputted into the model fitting. Overall, the model reliably captures areas of high and low abundance for the large majority of functional groups observed in SEAMAP. The result of this method allows for the objective setting of spatial distributions for numerous functional groups across a modeling domain, even where abundance data may not exist. PMID:23691223

  15. Chilean blue whales as a case study to illustrate methods to estimate abundance and evaluate conservation status of rare species.

    PubMed

    Williams, Rob; Hedley, Sharon L; Branch, Trevor A; Bravington, Mark V; Zerbini, Alexandre N; Findlay, Ken P

    2011-06-01

    Often abundance of rare species cannot be estimated with conventional design-based methods, so we illustrate with a population of blue whales (Balaenoptera musculus) a spatial model-based method to estimate abundance. We analyzed data from line-transect surveys of blue whales off the coast of Chile, where the population was hunted to low levels. Field protocols allowed deviation from planned track lines to collect identification photographs and tissue samples for genetic analyses, which resulted in an ad hoc sampling design with increased effort in areas of higher densities. Thus, we used spatial modeling methods to estimate abundance. Spatial models are increasingly being used to analyze data from surveys of marine, aquatic, and terrestrial species, but estimation of uncertainty from such models is often problematic. We developed a new, broadly applicable variance estimator that showed there were likely 303 whales (95% CI 176-625) in the study area. The survey did not span the whales' entire range, so this is a minimum estimate. We estimated current minimum abundance relative to pre-exploitation abundance (i.e., status) with a population dynamics model that incorporated our minimum abundance estimate, likely population growth rates from a meta-analysis of rates of increase in large baleen whales, and two alternative assumptions about historic catches. From this model, we estimated that the population was at a minimum of 9.5% (95% CI 4.9-18.0%) of pre-exploitation levels in 1998 under one catch assumption and 7.2% (CI 3.7-13.7%) of pre-exploitation levels under the other. Thus, although Chilean blue whales are probably still at a small fraction of pre-exploitation abundance, even these minimum abundance estimates demonstrate that their status is better than that of Antarctic blue whales, which are still <1% of pre-exploitation population size. We anticipate our methods will be broadly applicable in aquatic and terrestrial surveys for rarely encountered species

  16. Chilean blue whales as a case study to illustrate methods to estimate abundance and evaluate conservation status of rare species.

    PubMed

    Williams, Rob; Hedley, Sharon L; Branch, Trevor A; Bravington, Mark V; Zerbini, Alexandre N; Findlay, Ken P

    2011-06-01

    Often abundance of rare species cannot be estimated with conventional design-based methods, so we illustrate with a population of blue whales (Balaenoptera musculus) a spatial model-based method to estimate abundance. We analyzed data from line-transect surveys of blue whales off the coast of Chile, where the population was hunted to low levels. Field protocols allowed deviation from planned track lines to collect identification photographs and tissue samples for genetic analyses, which resulted in an ad hoc sampling design with increased effort in areas of higher densities. Thus, we used spatial modeling methods to estimate abundance. Spatial models are increasingly being used to analyze data from surveys of marine, aquatic, and terrestrial species, but estimation of uncertainty from such models is often problematic. We developed a new, broadly applicable variance estimator that showed there were likely 303 whales (95% CI 176-625) in the study area. The survey did not span the whales' entire range, so this is a minimum estimate. We estimated current minimum abundance relative to pre-exploitation abundance (i.e., status) with a population dynamics model that incorporated our minimum abundance estimate, likely population growth rates from a meta-analysis of rates of increase in large baleen whales, and two alternative assumptions about historic catches. From this model, we estimated that the population was at a minimum of 9.5% (95% CI 4.9-18.0%) of pre-exploitation levels in 1998 under one catch assumption and 7.2% (CI 3.7-13.7%) of pre-exploitation levels under the other. Thus, although Chilean blue whales are probably still at a small fraction of pre-exploitation abundance, even these minimum abundance estimates demonstrate that their status is better than that of Antarctic blue whales, which are still <1% of pre-exploitation population size. We anticipate our methods will be broadly applicable in aquatic and terrestrial surveys for rarely encountered species

  17. Estimating number of species and relative abundances in stream-fish communities: effects of sampling effort and discontinuous spatial distributions

    USGS Publications Warehouse

    Angermeier, Paul L.; Smogor, Roy A.

    1995-01-01

    We sampled fishes and measured microhabitat in series of contiguous habitat units (riffles, runs, pools) in three Virginia streams. We used Monte Carlo simulations to construct hypothetical series of habitat units, then examined how number of species, similarity in relative abundances, and number of microhabitats accumulated with increasing number of habitat units (i.e., sampling effort). Proportions of all species and microhabitats represented were relatively low and variable at low sampling effort, but increased asymptotically and became less variable with greater sampling effort. To facilitate comparisons among streams, we fitted simulation results to negative exponential curves. The curves indicated that 90% of the species present were usually found by sampling 5 to 14 habitat units (stream length of 22–67 stream widths). Estimates of species relative abundances required less sampling effort for a given accuracy than estimates of number of species. Rates of species accumulation (with effort) varied among streams and reflected discontinuity in species distributions among habitat units. Most discontinuity seemed to be due to low population density rather than to habitat selectivity. Results from an Illinois stream corroborated our findings from Virginia, and suggested that greater sampling effort is needed to characterize fish community structure in more homogeneous stream reaches.

  18. Statistical analysis of polychaete population density: dynamics of dominant species and scaling properties in relative abundance fluctuations

    NASA Astrophysics Data System (ADS)

    Quiroz-Martinez, B.; Schmitt, F. G.; Dauvin, J.-C.

    2012-01-01

    We consider here the dynamics of two polychaete populations based on a 20 yr temporal benthic survey of two muddy fine sand communities in the Bay of Morlaix, Western English Channel. These populations display high temporal variability, which is analyzed here using scaling approaches. We find that population densities have heavy tailed probability density functions. We analyze the dynamics of relative species abundance in two different communities of polychaetes by estimating in a novel way a "mean square drift" coefficient which characterizes their fluctuations in relative abundance over time. We show the usefulness of using new tools to approach and model such highly variable population dynamics in marine ecosystems.

  19. Plankton studies in San Francisco Bay; V, Zooplankton species composition and abundance in the South Bay, 1980-1981

    USGS Publications Warehouse

    Hutchinson, Anne

    1982-01-01

    Data are presented that summarize zooplankton species composition and abundance in South San Francisco Bay during 1980 and 1981. Sampling was conducted at least twice monthly at thirteen stations, from the southern extremity of the South Bay to the Golden Gate Bridge between January 1980 and May 1981. Samples were collected by pump at three depths in the shipping channel and one depth over the shoals. Subsamples were enumerated while alive. Total zooplankton biomass as carbon was calculated from estimated carbon quotas and abundances of each organism enumerated.

  20. Mosquito species diversity and abundance in relation to land use in a riceland agroecosystem in Mwea, Kenya.

    PubMed

    Muturi, Ephantus J; Shililu, Josephat; Jacob, Benjamin; Gu, Weidong; Githure, John; Novak, Robert

    2006-06-01

    We conducted an entomological survey to determine the mosquito species diversity and abundance in relation to land use in the Mwea rice scheme, Kenya. Adult mosquitoes were collected by indoor spraying of houses and outdoors by CDC light traps in three villages representing planned (Mbuinjeru) and unplanned (Kiamachiri) rice agroecosystems and a non-irrigated agroecosystem (Murinduko). During the 12-month sampling period, a total of 98,708 mosquitoes belonging to five genera and 25 species were collected. The five most common species collected during this study were Anopheles arabiensis Patton (52.5%), Culex quinquefasciatus Say (36.7%), Anopheles pharoensis Theobald (5.2%), Anopheles coustani Laveran (1.4%), and Anopheles funestus Giles (1.3%). Anopheles arabiensis, Cx quinquefasciatus, and An. pharoensis were more abundant in rice agroecosystems than in the non-irrigated agroecosystem, and in planned than in the unplanned rice agroecosystems. In contrast, An. funestus was more abundant in the non-irrigated agroecosystem. The mosquito species diversity (H) and evenness (E(H)) in the non-irrigated agroecosystem (Shannon diversity Index, H = 1.507, EH = 0.503) was significantly higher than in the rice agroecosystems (H) = 0.968, E(H) = 0.313, unplanned; and H= 1.040, E(H) = 0.367 planned). Results of lag cross correlation analysis revealed a strong relationship between rainfall and the abundance of An. arabiensis, and C. quinquefasciatus in the non-irrigated agroecosystem but not in the rice agroecosystems. It is inferred from the data that different levels of habitat perturbations with regard to rice cultivation have different effects on mosquito diversity and abundance. This provides an understanding of how mosquito diversity is impacted by different habitat management and rice cropping strategies.

  1. Power to detect trends in abundance of secretive marsh birds: effects of species traits and sampling effort

    USGS Publications Warehouse

    Steidl, Robert J.; Conway, Courtney J.; Litt, Andrea R.

    2013-01-01

    Standardized protocols for surveying secretive marsh birds have been implemented across North America, but the efficacy of surveys to detect population trends has not been evaluated. We used survey data collected from populations of marsh birds across North America and simulations to explore how characteristics of bird populations (proportion of survey stations occupied, abundance at occupied stations, and detection probability) and aspects of sampling effort (numbers of survey routes, stations/route, and surveys/station/year) affect statistical power to detect trends in abundance of marsh bird populations. In general, the proportion of survey stations along a route occupied by a species had a greater relative effect on power to detect trends than did the number of birds detected per survey at occupied stations. Uncertainty introduced by imperfect detection during surveys reduced power to detect trends considerably, but across the range of detection probabilities for most species of marsh birds, variation in detection probability had only a minor influence on power. For species that occupy a relatively high proportion of survey stations (0.20), have relatively high abundances at occupied stations (2.0 birds/station), and have high detection probability (0.50), ≥40 routes with 10 survey stations per route surveyed 3 times per year would provide an 80% chance of detecting a 3% annual decrease in abundance after 20 years of surveys. Under the same assumptions but for species that are less common, ≥100 routes would be needed to achieve the same power. Our results can help inform the design of programs to monitor trends in abundance of marsh bird populations, especially with regards to the amount of sampling effort necessary to meet programmatic goals.

  2. Determining the Diversity and Species Abundance Patterns in Arctic Soils using Rational Methods for Exploring Microbial Diversity

    NASA Astrophysics Data System (ADS)

    Ovreas, L.; Quince, C.; Sloan, W.; Lanzen, A.; Davenport, R.; Green, J.; Coulson, S.; Curtis, T.

    2012-12-01

    Arctic microbial soil communities are intrinsically interesting and poorly characterised. We have inferred the diversity and species abundance distribution of 6 Arctic soils: new and mature soil at the foot of a receding glacier, Arctic Semi Desert, the foot of bird cliffs and soil underlying Arctic Tundra Heath: all near Ny-Ålesund, Spitsbergen. Diversity, distribution and sample sizes were estimated using the rational method of Quince et al., (Isme Journal 2 2008:997-1006) to determine the most plausible underlying species abundance distribution. A log-normal species abundance curve was found to give a slightly better fit than an inverse Gaussian curve if, and only if, sequencing error was removed. The median estimates of diversity of operational taxonomic units (at the 3% level) were 3600-5600 (lognormal assumed) and 2825-4100 (inverse Gaussian assumed). The nature and origins of species abundance distributions are poorly understood but may yet be grasped by observing and analysing such distributions in the microbial world. The sample size required to observe the distribution (by sequencing 90% of the taxa) varied between ~ 106 and ~105 for the lognormal and inverse Gaussian respectively. We infer that between 5 and 50 GB of sequencing would be required to capture 90% or the metagenome. Though a principle components analysis clearly divided the sites into three groups there was a high (20-45%) degree of overlap in between locations irrespective of geographical proximity. Interestingly, the nearest relatives of the most abundant taxa at a number of most sites were of alpine or polar origin. Samples plotted on first two principal components together with arbitrary discriminatory OTUs

  3. Artificial nanomachines based on interlocked molecular species: recent advances.

    PubMed

    Balzani, Vincenzo; Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2006-11-01

    The bottom-up construction and operation of nanoscale machines and motors, that is, supramolecular systems wherein the molecular components can be set in motion in a controlled manner for ultimately accomplishing a function, is a topic of great interest in nanoscience and a fascinating challenge of nanotechnology. The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest. Research in the last decade has shown that species made of interlocked molecular components like rotaxanes, catenanes and related systems are most attractive candidates. In recent times, the evolution of the structural and functional design of such systems has led to the construction and operation of complex molecular machines that, in some cases, are able to do specific tasks. This tutorial review is intended to discuss the design principles for nanomachines based on interlocked molecules, and to provide a timely overview on representative prototype systems.

  4. Predicting changes in the distribution and abundance of species under environmental change

    PubMed Central

    Ehrlén, Johan; Morris, William F

    2015-01-01

    Environmental changes are expected to alter both the distribution and the abundance of organisms. A disproportionate amount of past work has focused on distribution only, either documenting historical range shifts or predicting future occurrence patterns. However, simultaneous predictions of abundance and distribution across landscapes would be far more useful. To critically assess which approaches represent advances towards the goal of joint predictions of abundance and distribution, we review recent work on changing distributions and on effects of environmental drivers on single populations. Several methods have been used to predict changing distributions. Some of these can be easily modified to also predict abundance, but others cannot. In parallel, demographers have developed a much better understanding of how changing abiotic and biotic drivers will influence growth rate and abundance in single populations. However, this demographic work has rarely taken a landscape perspective and has largely ignored the effects of intraspecific density. We advocate a synthetic approach in which population models accounting for both density dependence and effects of environmental drivers are used to make integrated predictions of equilibrium abundance and distribution across entire landscapes. Such predictions would constitute an important step forward in assessing the ecological consequences of environmental changes. PMID:25611188

  5. Predicting changes in the distribution and abundance of species under environmental change.

    PubMed

    Ehrlén, Johan; Morris, William F

    2015-03-01

    Environmental changes are expected to alter both the distribution and the abundance of organisms. A disproportionate amount of past work has focused on distribution only, either documenting historical range shifts or predicting future occurrence patterns. However, simultaneous predictions of abundance and distribution across landscapes would be far more useful. To critically assess which approaches represent advances towards the goal of joint predictions of abundance and distribution, we review recent work on changing distributions and on effects of environmental drivers on single populations. Several methods have been used to predict changing distributions. Some of these can be easily modified to also predict abundance, but others cannot. In parallel, demographers have developed a much better understanding of how changing abiotic and biotic drivers will influence growth rate and abundance in single populations. However, this demographic work has rarely taken a landscape perspective and has largely ignored the effects of intraspecific density. We advocate a synthetic approach in which population models accounting for both density dependence and effects of environmental drivers are used to make integrated predictions of equilibrium abundance and distribution across entire landscapes. Such predictions would constitute an important step forward in assessing the ecological consequences of environmental changes.

  6. Predicting changes in the distribution and abundance of species under environmental change.

    PubMed

    Ehrlén, Johan; Morris, William F

    2015-03-01

    Environmental changes are expected to alter both the distribution and the abundance of organisms. A disproportionate amount of past work has focused on distribution only, either documenting historical range shifts or predicting future occurrence patterns. However, simultaneous predictions of abundance and distribution across landscapes would be far more useful. To critically assess which approaches represent advances towards the goal of joint predictions of abundance and distribution, we review recent work on changing distributions and on effects of environmental drivers on single populations. Several methods have been used to predict changing distributions. Some of these can be easily modified to also predict abundance, but others cannot. In parallel, demographers have developed a much better understanding of how changing abiotic and biotic drivers will influence growth rate and abundance in single populations. However, this demographic work has rarely taken a landscape perspective and has largely ignored the effects of intraspecific density. We advocate a synthetic approach in which population models accounting for both density dependence and effects of environmental drivers are used to make integrated predictions of equilibrium abundance and distribution across entire landscapes. Such predictions would constitute an important step forward in assessing the ecological consequences of environmental changes. PMID:25611188

  7. The abundance of CH(+) in translucent molecular clouds - Further tests of shock models

    NASA Technical Reports Server (NTRS)

    Gredel, R.; Van Dishoeck, E. F.; Black, J. H.

    1993-01-01

    Observations of interstellar absorption lines of CH(+) in the (0, 0) and (1, 0) bands of the A 1Pi - X 1Sigma(+) system are presented for 17 stars with reddenings up to E(B-V) about 1.5 mag. Complementary data on interstellar CH in the (0, 0) bands of the A 2Delta - X 2Pi and B 2Sigma(-) - X 2Pi systems and C2 in the A 1Pi(u) - X 1Sigma(g)(+) red system have been obtained as well. The derived CH(+) column densities continue to increase with total column density, and values up to 10 exp 14/sq cm are reported for highly-reddened lines of sight. In most cases, the CH(+) and CH absorptions are dominated by a single strong component, with weaker features displaced by a few km/s. No significant velocity difference is found between CH(+) and neutral species such as CH and CN for this sample of randomly oriented lines of sight. In contrast with CN, the CH(+) abundance does not increase with the density in the cloud as derived from the observed C2 excitation. For the two clouds with the largest density, HD 62542 and HD 94413, no CH(+) absorption is found with CH(+)/CH less than 0.03 and 0.14, respectively. The CH(+) findings do not support a single-shock origin for the formation of the ion.

  8. [Abundance and species diversity of tabanids (Diptera) in the biosphere reserve Ipassa-Makokou (Gabon) during the rainy season].

    PubMed

    Mavoungou, J F; Makanga, B K; Acapovi-Yao, G; Desquesnes, M; M'Batchi, B

    2012-05-01

    The abundance and species diversity of tabanids were evaluated by trapping of insects using Vavoua traps, during the rainy season, from October 4 to November 30, 2009, in three different habitats: primary forest, secondary forest and village, in the biosphere reserve Ipassa-IRET Makokou in Gabon. Eight species belonging to three genera of tabanids have been identified for a total of 402 specimens caught. The tabanid species numerically the most abundant were: Tabanus secedens Walker, 1854 (55.2%), Tabanus obscurehirtus Ricardo, 1908 (13.9%), Chrysops dimidiatus Wulp, 1885 (11.2%) and Chrysops silaceus Austen, 1907 (10.7%). The less abundant species were Tabanus par Walker, 1854 (3.2%), Tabanus besti arbucklei Austen, 1912 (3%), Tabanus marmorosus congoicola Bequaert, 1930 (1%) and Ancala fasciata fasciata (Fabricius, 1775) (0.5%). Specimens of the genera Tabanus and Chrysops could not be identified, these insects represented respectively 0.7% and 0.5% of the insects trapped. The highest proportion of tabanids was trapped in secondary forest (75.1%) and the lower in primary forest (4.5%).

  9. Molecular identification of Malassezia species isolated from dermatitis affections.

    PubMed

    Affes, M; Ben Salah, S; Makni, F; Sellami, H; Ayadi, A

    2009-05-01

    The lipophilic yeast of the genus Malassezia are opportunistic microorganisms of the skin microflora but they can be agents of various dermatomycoses. The aim of this study was to perform molecular identification of the commonly isolated Malassezia species from various dermatomycoses in our region. Thirty strains of Malassezia were isolated from different dermatologic affections: pityriasis versicolor (17), dandruff (5), seborrheic dermatitis (4), onyxis (2), folliculitis (1) and blepharitis (1). These species were identified by their morphological features and biochemical characterisation. The molecular identification was achieved by amplification of the internal transcribed spacer region by simple PCR. PCR technique was used for molecular characterisation of four Malassezia species: Malassezia globosa (270 bp), Malassezia furfur (230 bp), Malassezia sympodialis (190 bp) and Malassezia restricta (320 bp). We have detected the association between M. furfur and M. sympodialis in 16% and confirmed presumptive identification in 70% of the cases. The phenotypic identification based on microscopic and physiological method is difficult and time consuming. The application of a simple PCR method provides a sensitive and rapid identification system for Malassezia species, which may be applied in epidemiological surveys and routine practice. PMID:18643889

  10. Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling.

    PubMed

    Bode, Antonio; Estévez, M Graciela; Varela, Manuel; Vilar, José A

    2015-09-01

    Phytoplankton is a sentinel of marine ecosystem change. Composed by many species with different life-history strategies, it rapidly responds to environment changes. An analysis of the abundance of 54 phytoplankton species in Galicia (NW Spain) between 1989 and 2008 to determine the main components of temporal variability in relation to climate and upwelling showed that most of this variability was stochastic, as seasonality and long term trends contributed to relatively small fractions of the series. In general, trends appeared as non linear, and species clustered in 4 groups according to the trend pattern but there was no defined pattern for diatoms, dinoflagellates or other groups. While, in general, total abundance increased, no clear trend was found for 23 species, 14 species decreased, 4 species increased during the early 1990s, and only 13 species showed a general increase through the series. In contrast, series of local environmental conditions (temperature, stratification, nutrients) and climate-related variables (atmospheric pressure indices, upwelling winds) showed a high fraction of their variability in deterministic seasonality and trends. As a result, each species responded independently to environmental and climate variability, measured by generalized additive models. Most species showed a positive relationship with nutrient concentrations but only a few showed a direct relationship with stratification and upwelling. Climate variables had only measurable effects on some species but no common response emerged. Because its adaptation to frequent disturbances, phytoplankton communities in upwelling ecosystems appear less sensitive to changes in regional climate than other communities characterized by short and well defined productive periods.

  11. Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling.

    PubMed

    Bode, Antonio; Estévez, M Graciela; Varela, Manuel; Vilar, José A

    2015-09-01

    Phytoplankton is a sentinel of marine ecosystem change. Composed by many species with different life-history strategies, it rapidly responds to environment changes. An analysis of the abundance of 54 phytoplankton species in Galicia (NW Spain) between 1989 and 2008 to determine the main components of temporal variability in relation to climate and upwelling showed that most of this variability was stochastic, as seasonality and long term trends contributed to relatively small fractions of the series. In general, trends appeared as non linear, and species clustered in 4 groups according to the trend pattern but there was no defined pattern for diatoms, dinoflagellates or other groups. While, in general, total abundance increased, no clear trend was found for 23 species, 14 species decreased, 4 species increased during the early 1990s, and only 13 species showed a general increase through the series. In contrast, series of local environmental conditions (temperature, stratification, nutrients) and climate-related variables (atmospheric pressure indices, upwelling winds) showed a high fraction of their variability in deterministic seasonality and trends. As a result, each species responded independently to environmental and climate variability, measured by generalized additive models. Most species showed a positive relationship with nutrient concentrations but only a few showed a direct relationship with stratification and upwelling. Climate variables had only measurable effects on some species but no common response emerged. Because its adaptation to frequent disturbances, phytoplankton communities in upwelling ecosystems appear less sensitive to changes in regional climate than other communities characterized by short and well defined productive periods. PMID:26283032

  12. A Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and the Complement Pathway

    PubMed Central

    Hajishengallis, George; Liang, Shuang; Payne, Mark A.; Hashim, Ahmed; Jotwani, Ravi; Eskan, Mehmet A.; McIntosh, Megan L.; Alsam, Asil; Kirkwood, Keith L.; Lambris, John D.; Darveau, Richard P.; Curtis, Michael A.

    2011-01-01

    SUMMARY Porphyromonas gingivalis is a low-abundance oral anaerobic bacterium implicated in periodontitis, a polymicrobial inflammatory disease, and the associated systemic conditions. However, the mechanism by which P. gingivalis contributes to inflammation and disease has remained elusive. Here we show that P. gingivalis, at very low colonization levels, triggers changes to the amount and composition of the oral commensal microbiota leading to inflammatory periodontal bone loss. The commensal microbiota and the complement pathway were both required for P. gingivalis-induced bone loss as germ-free mice or conventionally raised C3a and C5a receptor deficient mice did not develop bone loss after inoculation with P. gingivalis. These findings demonstrate that a single, low-abundance species can disrupt host-microbial homeostasis to cause inflammatory disease. The identification and targeting of similar low-abundance pathogens with community-wide impact may be important for treating inflammatory diseases of polymicrobial etiology. PMID:22036469

  13. The abundance of Ixodes ricinus ticks depends on tree species composition and shrub cover.

    PubMed

    Tack, W; Madder, M; Baeten, L; De Frenne, P; Verheyen, K

    2012-09-01

    The mainstream forestry policy in many European countries is to convert coniferous plantations into (semi-natural) deciduous woodlands. However, woodlands are the main habitat for Ixodes ricinus ticks. Therefore, assessing to what extent tick abundance and infection with Borrelia spirochetes are affected by forest composition and structure is a prerequisite for effective prevention of Lyme borreliosis. We selected a total of 25 pine and oak stands, both with and without an abundant shrub layer, in northern Belgium and estimated tick abundance between April and October 2008-2010. Additionally, the presence of deer beds was used as an indicator of relative deer habitat use. Borrelia infections in questing nymphs were determined by polymerase chain reactions. The abundance of larvae, nymphs, and adults was higher in oak stands compared to pine stands and increased with increasing shrub cover, most likely due to differences in habitat use by the ticks' main hosts. Whereas tick abundance was markedly higher in structure-rich oak stands compared to homogeneous pine stands, the Borrelia infection rates in nymphs did not differ significantly. Our results indicate that conversion towards structure-rich deciduous forests might create more suitable tick habitats, but we were unable to detect an effect on the infection rate.

  14. Molecular characterization of DSC1 orthologs in invertebrate species.

    PubMed

    Cui, Ying-Jun; Yu, Lin-Lin; Xu, Hai-Jun; Dong, Ke; Zhang, Chuan-Xi

    2012-05-01

    DSC1 and BSC1 are two founding members of a novel family of invertebrate voltage-gated cation channels with close structural and evolutionary relationships to voltage-gated sodium and calcium channels. In this study, we searched the published genome sequences for DSC1 orthologs. DSC1 orthologs were found in all 48 insect species, and in other invertebrate species belonging to phyla Mollusca, Cnidaria, Hemichordata and Echinodermata. However, DSC1 orthologs were not found in four arachnid species, Ixodes scapularis, Rhipicephalus microplus, Tetranychus urticae and Varroa destructor, two species in Annelida or any vertebrate species. We then cloned and sequenced NlSC1 and BmSC1 full-length cDNAs from the brown planthopper (Nilaparvata lugens) and the silkworm (Bombyx mori), respectively. NlSC1 and BmSC1 share about 50% identity with DSC1, and the expression of NlSC1 and BmSC1 transcripts was most abundant in the head and antenna in adults. All DSC1 orthologs contain a unique and conserved DEEA motif, instead of the EEEE or EEDD motif in classical calcium channels or the DEKA motif in sodium channels. Phylogenetic analyses revealed that DSC1 and its orthologs form a separate group distinct from the classical voltage-gated sodium and calcium channels and constitute a unique family of cation channels. The DSC1/BSC1-family channels could be potential targets of new and safe insecticides for pest control. PMID:22321571

  15. Molecular characterization of DSC1 orthologs in invertebrate species.

    PubMed

    Cui, Ying-Jun; Yu, Lin-Lin; Xu, Hai-Jun; Dong, Ke; Zhang, Chuan-Xi

    2012-05-01

    DSC1 and BSC1 are two founding members of a novel family of invertebrate voltage-gated cation channels with close structural and evolutionary relationships to voltage-gated sodium and calcium channels. In this study, we searched the published genome sequences for DSC1 orthologs. DSC1 orthologs were found in all 48 insect species, and in other invertebrate species belonging to phyla Mollusca, Cnidaria, Hemichordata and Echinodermata. However, DSC1 orthologs were not found in four arachnid species, Ixodes scapularis, Rhipicephalus microplus, Tetranychus urticae and Varroa destructor, two species in Annelida or any vertebrate species. We then cloned and sequenced NlSC1 and BmSC1 full-length cDNAs from the brown planthopper (Nilaparvata lugens) and the silkworm (Bombyx mori), respectively. NlSC1 and BmSC1 share about 50% identity with DSC1, and the expression of NlSC1 and BmSC1 transcripts was most abundant in the head and antenna in adults. All DSC1 orthologs contain a unique and conserved DEEA motif, instead of the EEEE or EEDD motif in classical calcium channels or the DEKA motif in sodium channels. Phylogenetic analyses revealed that DSC1 and its orthologs form a separate group distinct from the classical voltage-gated sodium and calcium channels and constitute a unique family of cation channels. The DSC1/BSC1-family channels could be potential targets of new and safe insecticides for pest control.

  16. Molecular Identification of Cryptosporidium Species from Pet Snakes in Thailand

    PubMed Central

    Yimming, Benjarat; Pattanatanang, Khampee; Sanyathitiseree, Pornchai; Inpankaew, Tawin; Kamyingkird, Ketsarin; Pinyopanuwat, Nongnuch; Chimnoi, Wissanuwat; Phasuk, Jumnongjit

    2016-01-01

    Cryptosporidium is an important pathogen causing gastrointestinal disease in snakes and is distributed worldwide. The main objectives of this study were to detect and identify Cryptosporidium species in captive snakes from exotic pet shops and snake farms in Thailand. In total, 165 fecal samples were examined from 8 snake species, boa constrictor (Boa constrictor constrictor), corn snake (Elaphe guttata), ball python (Python regius), milk snake (Lampropeltis triangulum), king snake (Lampropeltis getula), rock python (Python sebae), rainbow boa (Epicrates cenchria), and carpet python (Morelia spilota). Cryptosporidium oocysts were examined using the dimethyl sulfoxide (DMSO)-modified acid-fast staining and a molecular method based on nested-PCR, PCR-RFLP analysis, and sequencing amplification of the SSU rRNA gene. DMSO-modified acid-fast staining revealed the presence of Cryptosporidium oocysts in 12 out of 165 (7.3%) samples, whereas PCR produced positive results in 40 (24.2%) samples. Molecular characterization indicated the presence of Cryptosporidium parvum (mouse genotype) as the most common species in 24 samples (60%) from 5 species of snake followed by Cryptosporidium serpentis in 9 samples (22.5%) from 2 species of snake and Cryptosporidium muris in 3 samples (7.5%) from P. regius. PMID:27658593

  17. Molecular Identification of Cryptosporidium Species from Pet Snakes in Thailand.

    PubMed

    Yimming, Benjarat; Pattanatanang, Khampee; Sanyathitiseree, Pornchai; Inpankaew, Tawin; Kamyingkird, Ketsarin; Pinyopanuwat, Nongnuch; Chimnoi, Wissanuwat; Phasuk, Jumnongjit

    2016-08-01

    Cryptosporidium is an important pathogen causing gastrointestinal disease in snakes and is distributed worldwide. The main objectives of this study were to detect and identify Cryptosporidium species in captive snakes from exotic pet shops and snake farms in Thailand. In total, 165 fecal samples were examined from 8 snake species, boa constrictor (Boa constrictor constrictor), corn snake (Elaphe guttata), ball python (Python regius), milk snake (Lampropeltis triangulum), king snake (Lampropeltis getula), rock python (Python sebae), rainbow boa (Epicrates cenchria), and carpet python (Morelia spilota). Cryptosporidium oocysts were examined using the dimethyl sulfoxide (DMSO)-modified acid-fast staining and a molecular method based on nested-PCR, PCR-RFLP analysis, and sequencing amplification of the SSU rRNA gene. DMSO-modified acid-fast staining revealed the presence of Cryptosporidium oocysts in 12 out of 165 (7.3%) samples, whereas PCR produced positive results in 40 (24.2%) samples. Molecular characterization indicated the presence of Cryptosporidium parvum (mouse genotype) as the most common species in 24 samples (60%) from 5 species of snake followed by Cryptosporidium serpentis in 9 samples (22.5%) from 2 species of snake and Cryptosporidium muris in 3 samples (7.5%) from P. regius.

  18. Molecular Identification of Cryptosporidium Species from Pet Snakes in Thailand.

    PubMed

    Yimming, Benjarat; Pattanatanang, Khampee; Sanyathitiseree, Pornchai; Inpankaew, Tawin; Kamyingkird, Ketsarin; Pinyopanuwat, Nongnuch; Chimnoi, Wissanuwat; Phasuk, Jumnongjit

    2016-08-01

    Cryptosporidium is an important pathogen causing gastrointestinal disease in snakes and is distributed worldwide. The main objectives of this study were to detect and identify Cryptosporidium species in captive snakes from exotic pet shops and snake farms in Thailand. In total, 165 fecal samples were examined from 8 snake species, boa constrictor (Boa constrictor constrictor), corn snake (Elaphe guttata), ball python (Python regius), milk snake (Lampropeltis triangulum), king snake (Lampropeltis getula), rock python (Python sebae), rainbow boa (Epicrates cenchria), and carpet python (Morelia spilota). Cryptosporidium oocysts were examined using the dimethyl sulfoxide (DMSO)-modified acid-fast staining and a molecular method based on nested-PCR, PCR-RFLP analysis, and sequencing amplification of the SSU rRNA gene. DMSO-modified acid-fast staining revealed the presence of Cryptosporidium oocysts in 12 out of 165 (7.3%) samples, whereas PCR produced positive results in 40 (24.2%) samples. Molecular characterization indicated the presence of Cryptosporidium parvum (mouse genotype) as the most common species in 24 samples (60%) from 5 species of snake followed by Cryptosporidium serpentis in 9 samples (22.5%) from 2 species of snake and Cryptosporidium muris in 3 samples (7.5%) from P. regius. PMID:27658593

  19. Morphological and molecular evidence for the occurrence of three Hippocampus species (Teleostei: Syngnathidae) in Brazil.

    PubMed

    Silveira, Rosana Beatriz; Siccha-Ramirez, Raquel; Silva, José Rodrigo Santos; Oliveira, Claudio

    2014-09-16

    For many decades only two species of seahorses were recognized from Brazil: Hippocampus reidi Ginsburg, 1933, the long snout seahorse, and H. erectus Perry, 1810, the lined seahorse. The presence of a possible third species, recognized in 2002, brought about the need for a broad revision of the genus in Brazilian waters. A total of 335 specimens of seahorses, obtained from Brazilian and other collections, representing the three putative species from Brazil were analyzed: H. reidi, the species of greatest abundance and occurs in estuaries and the sea; H. erectus, which occurs only in the sea, and Hippocampus patagonicus was also determined to be present based on multiple specimens. Our morphometric / numerical and molecular analysis showed that the species currently identified as H. erectus in Brazil is actually H. patagonicus Piacentino & Luzatto, 2004. The existence of a possible third species, was instead based on the true H. erectus, as confirmed in the present study by the study of classical systematic and mitochondrial analysis. Thus, we recognize three species of seahorses in Brazil: H. erectus, H. reidi and H. patagonicus.

  20. Change in abundance of three phytophagous mite species (Acari: Eriophyidae, Tetranychidae) on quackgrass in the presence of choke disease.

    PubMed

    Rector, Brian G; Czarnoleski, Marcin; Skoracka, Anna; Lembicz, Marlena

    2016-09-01

    Phytophagous mites and endophytic fungi may interact when sharing a host plant, potentially influencing one another's growth or population dynamics; however, interactions between them are poorly known and remain largely unexplored. In this study, quantitative associations between three species of phytophagous mites and the endophytic fungus Epichloë bromicola Leuchtm. & Schardl (Clavicipitaceae, Ascomycotina) on quackgrass, Elymus repens (L.) Gould are reported. The mites' abundance was assessed on field-collected grass shoots that were either exhibiting choke disease symptoms or without the fungus. Overall, the abundance of Tetranychus urticae and Aculodes mckenziei was significantly lower on quackgrass plants infected by E. bromicola compared to plants without the fungus. Conversely, populations of Abacarus hystrix were significantly larger on plants colonised by the fungus than on uninfected plants. Thus, the presence of this endophytic fungus may have divergent effects on different phytophagous mite species although the basis of these effects is not yet known. PMID:27388448

  1. Change in abundance of three phytophagous mite species (Acari: Eriophyidae, Tetranychidae) on quackgrass in the presence of choke disease.

    PubMed

    Rector, Brian G; Czarnoleski, Marcin; Skoracka, Anna; Lembicz, Marlena

    2016-09-01

    Phytophagous mites and endophytic fungi may interact when sharing a host plant, potentially influencing one another's growth or population dynamics; however, interactions between them are poorly known and remain largely unexplored. In this study, quantitative associations between three species of phytophagous mites and the endophytic fungus Epichloë bromicola Leuchtm. & Schardl (Clavicipitaceae, Ascomycotina) on quackgrass, Elymus repens (L.) Gould are reported. The mites' abundance was assessed on field-collected grass shoots that were either exhibiting choke disease symptoms or without the fungus. Overall, the abundance of Tetranychus urticae and Aculodes mckenziei was significantly lower on quackgrass plants infected by E. bromicola compared to plants without the fungus. Conversely, populations of Abacarus hystrix were significantly larger on plants colonised by the fungus than on uninfected plants. Thus, the presence of this endophytic fungus may have divergent effects on different phytophagous mite species although the basis of these effects is not yet known.

  2. Tanaidacean fauna of the Kuril-Kamchatka Trench and adjacent abyssal plain - abundance, diversity and rare species

    NASA Astrophysics Data System (ADS)

    Błażewicz-Paszkowycz, Magdalena; Pabis, Krzysztof; Jóźwiak, Piotr

    2015-01-01

    Here we examine the distribution patterns, abundance, and species richness of tanaidacean peracarids in the abyssal-hadal transition zone. Material was collected in the region of Kuril-Kamchatka Trench during the German-Russian KuramBio Expedition with use of a giant boxcorer (GKG) of sampling area 0.25 m2. In the 23 samples collected from depths 4900 to 5800 m 48 species of Tanaidacea belonging to 11 families have been identified; most of the species (80%) are new to science. There was no evidence of a distribution pattern associated with depth or geographic location of stations in the nMDS analysis. Frequency of occurrence of twelve species was high (at 34-78% of stations) although the stations were distributed along a distance of about 1000 km. This observation is rationalized by the uniform environmental conditions of temperature, hydrostatic pressure, salinity, conductivity, and character of bottom deposits in the investigated area. Mean tanaidacean densities were 25.0±18.0 ind./0.25 m2, with mean values of species richness (number of species per sample) and diversity (Shannon Index) as high as 9.7±4.6 and 1.9±0.3 respectively. Singletons constituted about 20% of all species and more than one third of the species occurred as low counts per sample. The species accumulation curve did not reach the asymptotic level suggesting under-sampling of the studied area.

  3. Snow cover and extreme winter warming events control flower abundance of some, but not all species in high arctic Svalbard.

    PubMed

    Semenchuk, Philipp R; Elberling, Bo; Cooper, Elisabeth J

    2013-08-01

    The High Arctic winter is expected to be altered through ongoing and future climate change. Winter precipitation and snow depth are projected to increase and melt out dates change accordingly. Also, snow cover and depth will play an important role in protecting plant canopy from increasingly more frequent extreme winter warming events. Flower production of many Arctic plants is dependent on melt out timing, since season length determines resource availability for flower preformation. We erected snow fences to increase snow depth and shorten growing season, and counted flowers of six species over 5 years, during which we experienced two extreme winter warming events. Most species were resistant to snow cover increase, but two species reduced flower abundance due to shortened growing seasons. Cassiope tetragona responded strongly with fewer flowers in deep snow regimes during years without extreme events, while Stellaria crassipes responded partly. Snow pack thickness determined whether winter warming events had an effect on flower abundance of some species. Warming events clearly reduced flower abundance in shallow but not in deep snow regimes of Cassiope tetragona, but only marginally for Dryas octopetala. However, the affected species were resilient and individuals did not experience any long term effects. In the case of short or cold summers, a subset of species suffered reduced reproductive success, which may affect future plant composition through possible cascading competition effects. Extreme winter warming events were shown to expose the canopy to cold winter air. The following summer most of the overwintering flower buds could not produce flowers. Thus reproductive success is reduced if this occurs in subsequent years. We conclude that snow depth influences flower abundance by altering season length and by protecting or exposing flower buds to cold winter air, but most species studied are resistant to changes. Winter warming events, often occurring

  4. Snow cover and extreme winter warming events control flower abundance of some, but not all species in high arctic Svalbard

    PubMed Central

    Semenchuk, Philipp R; Elberling, Bo; Cooper, Elisabeth J

    2013-01-01

    Abstract The High Arctic winter is expected to be altered through ongoing and future climate change. Winter precipitation and snow depth are projected to increase and melt out dates change accordingly. Also, snow cover and depth will play an important role in protecting plant canopy from increasingly more frequent extreme winter warming events. Flower production of many Arctic plants is dependent on melt out timing, since season length determines resource availability for flower preformation. We erected snow fences to increase snow depth and shorten growing season, and counted flowers of six species over 5 years, during which we experienced two extreme winter warming events. Most species were resistant to snow cover increase, but two species reduced flower abundance due to shortened growing seasons. Cassiope tetragona responded strongly with fewer flowers in deep snow regimes during years without extreme events, while Stellaria crassipes responded partly. Snow pack thickness determined whether winter warming events had an effect on flower abundance of some species. Warming events clearly reduced flower abundance in shallow but not in deep snow regimes of Cassiope tetragona, but only marginally for Dryas octopetala. However, the affected species were resilient and individuals did not experience any long term effects. In the case of short or cold summers, a subset of species suffered reduced reproductive success, which may affect future plant composition through possible cascading competition effects. Extreme winter warming events were shown to expose the canopy to cold winter air. The following summer most of the overwintering flower buds could not produce flowers. Thus reproductive success is reduced if this occurs in subsequent years. We conclude that snow depth influences flower abundance by altering season length and by protecting or exposing flower buds to cold winter air, but most species studied are resistant to changes. Winter warming events, often

  5. Seasonal variations of species composition and abundance of zooplankton in Ehoma Lake, a floodplain lake in Nigeria.

    PubMed

    Okogwu, Okechukwu I

    2010-03-01

    Ehoma Lake is among the important breeding sites of the major fishes in the Mid-Cross River, Nigeria. The juveniles of these fishes are solely dependent on zooplankton, which has not been studied previously. I studied monthly the lake's physico-chemical variables and zooplankton composition in three stations (littoral, sub-littoral and pelagic) from March 2005 to August 2006. Sixty-seven zooplankton species (42 rotifers, 19 cladocerans and 6 copepods) were identified. Daphnia obtusa Kurz, Keratella valga Ehrenberg, Keratella ticinensis Callerrio, Keratella hiemalis Carlin, Brachionus dimidiatus Bryce and Lecane candida Hauer and Murray are new records for Nigeria The dominant zooplankters were Diaphanosoma excisum Kurz and Moina micrura Kurz. There was an inverse relationship between species richness and abundance. Richness was highest in the dry season while peak zooplankton abundance was recorded in the rainy season. Zooplankton abundance and species richness decreased progressively from the littoral to the pelagic station while the Shannon-Weaver diversity index varied from 0.68 to 1.28 without a clear seasonal trend. There is a succession pattern: rotifers that are dominant in the dry season are replaced by cladocerans in the rainy season. This succession was greatly influenced by seasonal flooding of the lake. As no previous information on the zooplankton of the lake is available, this study provides baseline data on the lake's zooplankton. PMID:20411715

  6. Characterization of the most abundant Lactobacillus species in chicken gastrointestinal tract and potential use as probiotics for genetic engineering.

    PubMed

    Wang, Lei; Fang, Mingjian; Hu, Yanping; Yang, Yuxin; Yang, Mingming; Chen, Yulin

    2014-07-01

    The count and diffusion of Lactobacilli species in the different gastrointestinal tract (GI) regions of broilers were investigated by quantitative real-time polymerase chain reaction, and the probiotic characteristics of six L. reuteri species isolated from broilers' GI tract were also investigated to obtain the potential target for genetic engineering. Lactobacilli had the highest diversity in the crop and the lowest one in the cecum. Compared with the lower GI tract, more Lactobacilli were found in the upper GI tract. Lactobacillus reuteri, L. johnsonii, L. acidophilus, L. crispatus, L. salivarius, and L. aviarius were the predominant Lactobacillus species and present throughout the GI tract of chickens. Lactobacillus reuteri was the most abundant Lactobacillus species. Lactobacillus reuteri XC1 had good probiotic characteristics that would be a potential and desirable target for genetic engineering. PMID:24850302

  7. Species richness and abundance of ectomycorrhizal basidiomycete sporocarps on a moisture gradient in the Tsuga heterophylla zone

    USGS Publications Warehouse

    O'Dell, Thomas E.; Ammirati, Joseph F.; Schreiner, Edward G.

    1999-01-01

    Sporocarps of epigeous ectomycorrhizal fungi and vegetation data were collected from eight Tsuga heterophylla (Raf.) Sarg. - Pseudotsuga menziesii (Mirb.) Franco stands along a wet to dry gradient in Olympic National Park, Washington, U.S.A. One hundred and fifty species of ectomycorrhizal fungi were collected from a total sample area of 2.08 ha. Over 2 years, fungal species richness ranged from 19 to 67 taxa per stand. Sporocarp standing crop ranged from 0 to 3.8 kg/ha, averaging 0.58 kg/ha, 0.06 kg/ha in spring and 0.97 kg/ha in fall. Sporocarp standing crop and fungal species richness were correlated with precipitation. These results demonstrated that ectomycorrhizal fungal sporocarp abundance and species richness can be partly explained in terms of an environmental gradient.

  8. Molecular characterization of Ephedra species found in Pakistan.

    PubMed

    Ghafoor, S; Shah, M M; Ahmad, H; Swati, Z A; Shah, S H; Pervez, A; Farooq, U

    2007-12-11

    Ephedra, also known as "ma huang", is a dioecious, drought- and frost-resistant, perennial, evergreen shrub with compelling medicinal value. The genus is represented by 42 species around the world, 9 of which were provisionally reported from Pakistan. Species of the genus have a controversial taxonomy due to their overlapping morphological features. Conventional tools alone are not sufficient for characterizing the species. The objective of present study was to assess the genetic variability present in different biotypes of Ephedra growing in Pakistan using molecular markers. A total of six genotypes collected from diverse geographic zones of Pakistan were used. The DNA of all genotypes was amplified using nine randomly amplified polymorphic DNA (RAPD) primers to study genetic variability at the molecular level. The dissimilarity coefficient matrix based on the data of 9 RAPD primers was used to construct a dendrogram which was then used to group the genotypes in clusters. Based on the dendrogram and dissimilarity coefficient matrix, the RAPD markers used here revealed a moderate to high level of genetic polymorphism (6 to 49%) among the genotypes. It was found that the collection of genotype accessions from Swat Valley in northwestern Pakistan was most distantly related to the other five collections. More molecular markers including functional genes and ribosomal spacer regions are suggested to find a better estimate of the genetic diversity present in Ephedra growing in Pakistan. The information provided here is useful for identifying valuable Ephedra variants which will be used for medicinal purposes and earning foreign currency.

  9. Presence and abundance of non-native plant species associated with recent energy development in the Williston Basin

    USGS Publications Warehouse

    Preston, Todd M.

    2015-01-01

    The Williston Basin, located in the Northern Great Plains, is experiencing rapid energy development with North Dakota and Montana being the epicenter of current and projected development in the USA. The average single-bore well pad is 5 acres with an estimated 58,485 wells in North Dakota alone. This landscape-level disturbance may provide a pathway for the establishment of non-native plants. To evaluate potential influences of energy development on the presence and abundance of non-native species, vegetation surveys were conducted at 30 oil well sites (14 ten-year-old and 16 five-year-old wells) and 14 control sites in native prairie environments across the Williston Basin. Non-native species richness and cover were recorded in four quadrats, located at equal distances, along four transects for a total of 16 quadrats per site. Non-natives were recorded at all 44 sites and ranged from 5 to 13 species, 7 to 15 species, and 2 to 8 species at the 10-year, 5-year, and control sites, respectively. Respective non-native cover ranged from 1 to 69, 16 to 76, and 2 to 82 %. Total, forb, and graminoid non-native species richness and non-native forb cover were significantly greater at oil well sites compared to control sites. At oil well sites, non-native species richness and forb cover were significantly greater adjacent to the well pads and decreased with distance to values similar to control sites. Finally, non-native species whose presence and/or abundance were significantly greater at oil well sites relative to control sites were identified to aid management efforts.

  10. Presence and abundance of non-native plant species associated with recent energy development in the Williston Basin.

    PubMed

    Preston, Todd M

    2015-04-01

    The Williston Basin, located in the Northern Great Plains, is experiencing rapid energy development with North Dakota and Montana being the epicenter of current and projected development in the USA. The average single-bore well pad is 5 acres with an estimated 58,485 wells in North Dakota alone. This landscape-level disturbance may provide a pathway for the establishment of non-native plants. To evaluate potential influences of energy development on the presence and abundance of non-native species, vegetation surveys were conducted at 30 oil well sites (14 ten-year-old and 16 five-year-old wells) and 14 control sites in native prairie environments across the Williston Basin. Non-native species richness and cover were recorded in four quadrats, located at equal distances, along four transects for a total of 16 quadrats per site. Non-natives were recorded at all 44 sites and ranged from 5 to 13 species, 7 to 15 species, and 2 to 8 species at the 10-year, 5-year, and control sites, respectively. Respective non-native cover ranged from 1 to 69, 16 to 76, and 2 to 82%. Total, forb, and graminoid non-native species richness and non-native forb cover were significantly greater at oil well sites compared to control sites. At oil well sites, non-native species richness and forb cover were significantly greater adjacent to the well pads and decreased with distance to values similar to control sites. Finally, non-native species whose presence and/or abundance were significantly greater at oil well sites relative to control sites were identified to aid management efforts. PMID:25797884

  11. Thysanoptera (Thrips) Within Citrus Orchards in Florida: Species Distribution, Relative and Seasonal Abundance Within Trees, and Species on Vines and Ground Cover Plants

    PubMed Central

    Childers, Carl C.; Nakahara, Sueo

    2006-01-01

    crops in Florida. The five most abundant thrips species collected within citrus tree canopies were: A. fasciapennis, F. bispinosa, C. orchidii, K. flavipes, and D. trifasciatus. In comparison, the following five thrips species were most abundant on vines or ground cover plants: F. bispinosa, H. gowdeyi, F. cephalica, M. abdominalis, and F. gossypiana. Fifty-eight species of vines or ground cover plants in 26 families were infested with one or more of 27 species of thrips. PMID:20233100

  12. Species differences and molecular determinant of TRPA1 cold sensitivity

    PubMed Central

    Chen, Jun; Kang, Dawon; Xu, Jing; Lake, Marc; Hogan, James O.; Sun, Chaohong; Walter, Karl; Yao, Betty; Kim, Donghee

    2013-01-01

    TRPA1 is an ion channel and has been proposed as a thermosensor across species. In invertebrate and ancestral vertebrates such as fly, mosquito, frog, lizard and snakes, TRPA1 serves as a heat receptor, a sensory input utilized for heat avoidance or infrared detection. However, in mammals, whether TRPA1 is a receptor for noxious cold is highly controversial, as channel activation by cold was observed by some groups but disputed by others. Here we attribute the discrepancy to species differences. We show that cold activates rat and mouse TRPA1 but not human or rhesus monkey TRPA1. At the molecular level, a single residue within the S5 transmembrane domain (G878 in rodent but V875 in primate) accounts for the observed difference in cold sensitivity. This residue difference also underlies the species-specific effects of menthol. Together, our findings identify the species-specific cold activation of TRPA1 and reveal a molecular determinant of cold-sensitive gating. PMID:24071625

  13. Mosquito species richness, composition, and abundance along habitat-climate-elevation gradients in the northern Colorado Front Range.

    PubMed

    Eisen, Lars; Bolling, Bethany G; Blair, Carol D; Beaty, Barry J; Moore, Chester G

    2008-07-01

    We exploited elevation gradients (1,500-2,400 m) ranging from plains to montane areas along the Poudre River and Big Thompson River in the northern Colorado Front Range to determine how mosquito species richness, composition, and abundance change along natural habitat-climate-elevation gradients. Mosquito collections in 26 sites in 2006 by using CO2-baited CDC light traps yielded a total of 7,136 identifiable mosquitoes of 27 species. Commonly collected species included Aedes vexans (Meigen) (n = 4,722), Culex tarsalis Coquillett (n = 825), Ochlerotatus increpitus (Dyar) (n = 546), Ochlerotatus trivittatus (Coquillett) (n = 303), Aedes cinereus Meigen (n = 280), Ochlerotatus melanimon (Dyar) (n = 146), Ochlerotatus dorsalis (Meigen) (n = 67), Culiseta inornata (Williston) (n = 52), Ochlerotatus pullatus (Coquillett) (n = 38), Ochlerotatus spencerii idahoensis (Theobald) (n = 37), and Culex pipiens L. (n = 29). Species richness was highest in plains habitats at elevations below 1,600 m. Numerous species were found exclusively or predominantly at low elevations below 1,700 m [Anopheles earlei Vargas, Anophelesfreeborni Aitken, Coquilletidia perturbans (Walker), Culex erythrothorax (Dyar), Cx. pipiens, Culex territans Walker, Oc. dorsalis, Ochlerotatus hendersoni (Cockerell), Oc. melanimon, and Oc. trivittatus], whereas others occurred predominantly at high elevations above 2,300 m [Ae. cinereus, Culiseta incidens (Thomson), Culiseta morsitans (Theoblad), Ochlerotatus cataphylla (Dyar), Ochlerotatus intrudens (Dyar), Oc. pullatus, and Ochlerotatus punctor (Kirby)]. Ae. vexans and Cx. tarsalis were abundant in the plains (< 1,600 m; mean June-August temperature > 19.5 degrees C), occurred at low abundances in foothills and low montane areas (1,610-1,730 m; 18.0-19.5 degrees C), and they were collected only sporadically in montane areas above 1,750 m (mean June-August temperature < 17.5 degrees C). These findings suggest that future climate warming may lead to shifts in

  14. Using ecological niche models to predict the abundance and impact of invasive species: application to the common carp.

    PubMed

    Kulhanek, Stefanie A; Leung, Brian; Ricciardi, Anthony

    2011-01-01

    In order to efficiently manage nonindigenous species (NIS), predictive tools are needed to prioritize locations where they are likely to become established and where their impacts will be most severe. While predicting the impact of a NIS has generally proved challenging, forecasting its abundance patterns across potential recipient locations should serve as a useful surrogate method of estimating the relative severity of the impacts to be expected. Yet such approaches have rarely been applied in invasion biology. We used long-term monitoring data for lakes within the state of Minnesota and artificial neural networks to model both the occurrence as well as the abundance of a widespread aquatic NIS, common carp (Cyprinus carpio). We then tested the ability of the resulting models to (1) interpolate to new sites within our main study region, (2) extrapolate to lakes in the neighboring state of South Dakota, and (3) assessed the relative contribution of each variable to model predictions. Our models correctly identified over 83% of sites where carp are either present or absent and explained 73% of the variation in carp abundance for validation lakes in Minnesota (i.e., lakes not used to build the model). When extrapolated to South Dakota, our models correctly classified carp occurrence in 79% of lakes and explained 32% of the variation in carp abundance. Variables related to climate and water quality were found to be the most important predictors of carp distribution. These results demonstrate that ecological niche-based modeling techniques can be used to forecast both the occurrence and abundance patterns of invasive species at a regional scale. Models also yielded sensible predictions when extrapolated to neighboring regions. Such predictions, when combined, should provide more useful estimates of the overall risk posed by NIS on potential recipient systems.

  15. Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

    PubMed Central

    Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

    2016-01-01

    The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

  16. Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae).

    PubMed

    Šašić, Ljiljana; Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

    2016-01-01

    The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

  17. Multigene Molecular Systematics Confirm Species Status of Morphologically Convergent Pagurus Hermit Crabs

    PubMed Central

    Matzen da Silva, Joana; dos Santos, Antonina; Cunha, Marina R.; Costa, Filipe O.; Creer, Simon; Carvalho, Gary R.

    2011-01-01

    Introduction In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone. Methodology/Principal Findings To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea. Conclusions/Significance Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea. PMID:22174780

  18. Distribution of nekton species and abundance within and among four Oregon estuaries

    EPA Science Inventory

    Crabs, shrimps and fishes provide valued ecosystem goods and services to communities of the Pacific Northwest, including species that are fished for food and recreation and those that serve as prey for fished species. In the face of increasing use of these services and potential...

  19. Dilaton and off-shell (non-critical string) effects in Boltzmann equation for species abundances

    NASA Astrophysics Data System (ADS)

    Lahanas, Ab; Mavromatos, Ne; Nanopoulos, Dv

    In this work we derive the modifications to the Boltzmann equation governing the cosmic evolution of relic abundances induced by dilaton dissipative-source and non-critical-string terms in dilaton-driven non-equilibrium string Cosmologies. We also discuss briefly the most important phenomenological consequences, including modifications of the constraints on the available parameter space of cosmologically appealing particle physics models, imposed by recent precision data of astrophysical measurements.

  20. Refuge habitats for fishes during seasonal drying in an intermittent stream: movement, survival and abundance of three minnow species

    USGS Publications Warehouse

    Hodges, S.W.; Magoulick, Daniel D.

    2011-01-01

    Drought and summer drying can be important disturbance events in many small streams leading to intermittent or isolated habitats. We examined what habitats act as refuges for fishes during summer drying, hypothesizing that pools would act as refuge habitats. We predicted that during drying fish would show directional movement into pools from riffle habitats, survival rates would be greater in pools than in riffles, and fish abundance would increase in pool habitats. We examined movement, survival and abundance of three minnow species, bigeye shiner (Notropis boops), highland stoneroller (Campostoma spadiceum) and creek chub (Semotilus atromaculatus), during seasonal stream drying in an Ozark stream using a closed robust multi-strata mark-recapture sampling. Population parameters were estimated using plausible models within program MARK, where a priori models are ranked using Akaike's Information Criterion. Creek chub showed directional movement into pools and increased survival and abundance in pools during drying. Highland stonerollers showed strong directional movement into pools and abundance increased in pools during drying, but survival rates were not significantly greater in pools than riffles. Bigeye shiners showed high movement rates during drying, but the movement was non-directional, and survival rates were greater in riffles than pools. Therefore, creek chub supported our hypothesis and pools appear to act as refuge habitats for this species, whereas highland stonerollers partly supported the hypothesis and bigeye shiners did not support the pool refuge hypothesis. Refuge habitats during drying are species dependent. An urgent need exists to further understand refuge habitats in streams given projected changes in climate and continued alteration of hydrological regimes.

  1. Refuge habitats for fishes during seasonal drying in an intermittent stream: Movement, survival and abundance of three minnow species

    USGS Publications Warehouse

    Hodges, S.W.; Magoulick, D.D.

    2011-01-01

    Drought and summer drying can be important disturbance events in many small streams leading to intermittent or isolated habitats. We examined what habitats act as refuges for fishes during summer drying, hypothesizing that pools would act as refuge habitats. We predicted that during drying fish would show directional movement into pools from riffle habitats, survival rates would be greater in pools than in riffles, and fish abundance would increase in pool habitats. We examined movement, survival and abundance of three minnow species, bigeye shiner (Notropis boops), highland stoneroller (Campostoma spadiceum) and creek chub (Semotilus atromaculatus), during seasonal stream drying in an Ozark stream using a closed robust multi-strata mark-recapture sampling. Population parameters were estimated using plausible models within program MARK, where a priori models are ranked using Akaike's Information Criterion. Creek chub showed directional movement into pools and increased survival and abundance in pools during drying. Highland stonerollers showed strong directional movement into pools and abundance increased in pools during drying, but survival rates were not significantly greater in pools than riffles. Bigeye shiners showed high movement rates during drying, but the movement was non-directional, and survival rates were greater in riffles than pools. Therefore, creek chub supported our hypothesis and pools appear to act as refuge habitats for this species, whereas highland stonerollers partly supported the hypothesis and bigeye shiners did not support the pool refuge hypothesis. Refuge habitats during drying are species dependent. An urgent need exists to further understand refuge habitats in streams given projected changes in climate and continued alteration of hydrological regimes. ?? 2011 Springer Basel AG (outside the USA).

  2. The shark assemblage at French Frigate Shoals atoll, Hawai'i: species composition, abundance and habitat use.

    PubMed

    Dale, Jonathan J; Stankus, Austin M; Burns, Michael S; Meyer, Carl G

    2011-01-01

    Empirical data on the abundance and habitat preferences of coral reef top predators are needed to evaluate their ecological impacts and guide management decisions. We used longline surveys to quantify the shark assemblage at French Frigate Shoals (FFS) atoll from May to August 2009. Fishing effort consisted of 189 longline sets totaling 6,862 hook hours of soak time. A total of 221 sharks from 7 species were captured, among which Galapagos (Carcharhinus galapagensis, 36.2%), gray reef (Carcharhinus amblyrhynchos, 25.8%) and tiger (Galeocerdo cuvier, 20.4%) sharks were numerically dominant. A lack of blacktip reef sharks (Carcharhinus melanopterus) distinguished the FFS shark assemblage from those at many other atolls in the Indo-Pacific. Compared to prior underwater visual survey estimates, longline methods more accurately represented species abundance and composition for the majority of shark species. Sharks were significantly less abundant in the shallow lagoon than adjacent habitats. Recaptures of Galapagos sharks provided the first empirical estimate of population size for any Galapagos shark population. The overall recapture rate was 5.4%. Multiple closed population models were evaluated, with Chao M(h) ranking best in model performance and yielding a population estimate of 668 sharks with 95% confidence intervals ranging from 289-1720. Low shark abundance in the shallow lagoon habitats suggests removal of a small number of sharks from the immediate vicinity of lagoonal islets may reduce short-term predation on endangered monk seal (Monachus schauinslandi) pups, but considerable fishing effort would be required to catch even a small number of sharks. Additional data on long-term movements and habitat use of sharks at FFS are required to better assess the likely ecological impacts of shark culling. PMID:21347321

  3. The Shark Assemblage at French Frigate Shoals Atoll, Hawai‘i: Species Composition, Abundance and Habitat Use

    PubMed Central

    Dale, Jonathan J.; Stankus, Austin M.; Burns, Michael S.; Meyer, Carl G.

    2011-01-01

    Empirical data on the abundance and habitat preferences of coral reef top predators are needed to evaluate their ecological impacts and guide management decisions. We used longline surveys to quantify the shark assemblage at French Frigate Shoals (FFS) atoll from May to August 2009. Fishing effort consisted of 189 longline sets totaling 6,862 hook hours of soak time. A total of 221 sharks from 7 species were captured, among which Galapagos (Carcharhinus galapagensis, 36.2%), gray reef (Carcharhinus amblyrhynchos, 25.8%) and tiger (Galeocerdo cuvier, 20.4%) sharks were numerically dominant. A lack of blacktip reef sharks (Carcharhinus melanopterus) distinguished the FFS shark assemblage from those at many other atolls in the Indo-Pacific. Compared to prior underwater visual survey estimates, longline methods more accurately represented species abundance and composition for the majority of shark species. Sharks were significantly less abundant in the shallow lagoon than adjacent habitats. Recaptures of Galapagos sharks provided the first empirical estimate of population size for any Galapagos shark population. The overall recapture rate was 5.4%. Multiple closed population models were evaluated, with Chao Mh ranking best in model performance and yielding a population estimate of 668 sharks with 95% confidence intervals ranging from 289–1720. Low shark abundance in the shallow lagoon habitats suggests removal of a small number of sharks from the immediate vicinity of lagoonal islets may reduce short-term predation on endangered monk seal (Monachus schauinslandi) pups, but considerable fishing effort would be required to catch even a small number of sharks. Additional data on long-term movements and habitat use of sharks at FFS are required to better assess the likely ecological impacts of shark culling. PMID:21347321

  4. The shark assemblage at French Frigate Shoals atoll, Hawai'i: species composition, abundance and habitat use.

    PubMed

    Dale, Jonathan J; Stankus, Austin M; Burns, Michael S; Meyer, Carl G

    2011-02-10

    Empirical data on the abundance and habitat preferences of coral reef top predators are needed to evaluate their ecological impacts and guide management decisions. We used longline surveys to quantify the shark assemblage at French Frigate Shoals (FFS) atoll from May to August 2009. Fishing effort consisted of 189 longline sets totaling 6,862 hook hours of soak time. A total of 221 sharks from 7 species were captured, among which Galapagos (Carcharhinus galapagensis, 36.2%), gray reef (Carcharhinus amblyrhynchos, 25.8%) and tiger (Galeocerdo cuvier, 20.4%) sharks were numerically dominant. A lack of blacktip reef sharks (Carcharhinus melanopterus) distinguished the FFS shark assemblage from those at many other atolls in the Indo-Pacific. Compared to prior underwater visual survey estimates, longline methods more accurately represented species abundance and composition for the majority of shark species. Sharks were significantly less abundant in the shallow lagoon than adjacent habitats. Recaptures of Galapagos sharks provided the first empirical estimate of population size for any Galapagos shark population. The overall recapture rate was 5.4%. Multiple closed population models were evaluated, with Chao M(h) ranking best in model performance and yielding a population estimate of 668 sharks with 95% confidence intervals ranging from 289-1720. Low shark abundance in the shallow lagoon habitats suggests removal of a small number of sharks from the immediate vicinity of lagoonal islets may reduce short-term predation on endangered monk seal (Monachus schauinslandi) pups, but considerable fishing effort would be required to catch even a small number of sharks. Additional data on long-term movements and habitat use of sharks at FFS are required to better assess the likely ecological impacts of shark culling.

  5. Molecular Phylogenetics of Exophiala Species Isolated from Korea

    PubMed Central

    Lee, Ho Chung; Kim, Dong Min; Ha, Gyoung Yim; Choi, Jong Soo

    2012-01-01

    Background Recently, identification of fungi have been supplemented by molecular tools, such as ribosomal internal transcribed spacer (ITS) sequence analysis. According to these tools, morphological Exophiala species was newly introduced or redefined. Objective This study was designed to investigate the phylogenetics based on ribosomal ITS sequence analysis from clinical Exophiala species isolated in Korea. Methods The strains of Exophiala species were 4 clinical isolates of phaeohyphomycosis agents kept in the department of dermatology, Dongguk University Medical Center(DUMC), Gyeongju, Korea. The DNAs of total 5 strains of Exophiala species were extracted by bead-beating method. Polymerase chain reaction of ITS region using the primer pairs ITS1-ITS4, was done and phylogenetic tree contributed from sequences of ITS region from 5 Korean isolates including E. dermatitidis CBS 109154 and comparative related strains deposited in GenBank. Results The strains of Exophiala species were 3 strains of E. dermatitidis, 1 strain of E. jeanselmei and 1 strain of Exophiala new species. Among the 3 subtypes (type A, B, C) of E. jeanselmei, E. jeanselmei DUMC 9901 belonged to type B. Of the 2 main types of E. dermatitidis (type A, B) and 3 subtypes of E. dermatitidis type A (A0, A1 and A2), two strains (E. dermatitidis CBS 709.95, E. dermatitidis CBS 109154) belonged to A0 subtypes, 1 strain (E. dermatitidis DUMC 9902) A1 subtype, respectively. Conclusion Phylogenetic analysis of ITS region sequence provided useful information not only for new species identification but for the subtyping and origin of Exophiala species. PMID:22879712

  6. Regional Variation in Parasite Species Richness and Abundance in the Introduced Range of the Invasive Lionfish, Pterois volitans.

    PubMed

    Sellers, Andrew J; Ruiz, Gregory M; Leung, Brian; Torchin, Mark E

    2015-01-01

    Parasites can play an important role in biological invasions. While introduced species often lose parasites from their native range, they can also accumulate novel parasites in their new range. The accumulation of parasites by introduced species likely varies spatially, and more parasites may shift to new hosts where parasite diversity is high. Considering that parasitism and disease are generally more prevalent at lower latitudes, the accumulation of parasites by introduced hosts may be greater in tropical regions. The Indo-Pacific lionfish (Pterois volitans) has become widely distributed across the Western Atlantic. In this study, we compared parasitism across thirteen locations in four regions, spanning seventeen degrees of latitude in the lionfish's introduced range to examine potential spatial variation in parasitism. In addition, as an initial step to explore how indirect effects of parasitism might influence interactions between lionfish and ecologically similar native hosts, we also compared parasitism in lionfish and two co-occurring native fish species, the graysby grouper, Cephalopholis cruentata, and the lizardfish, Synodus intermedius, in the southernmost region, Panama. Our results show that accumulation of native parasites on lionfish varies across broad spatial scales, and that colonization by ectoparasites was highest in Panama, relative to the other study sites. Endoparasite richness and abundance, on the other hand, were highest in Belize where lionfish were infected by twice as many endoparasite species as lionfish in other regions. The prevalence of all but two parasite species infecting lionfish was below 25%, and we did not detect an association between parasite abundance and host condition, suggesting a limited direct effect of parasites on lionfish, even where parasitism was highest. Further, parasite species richness and abundance were significantly higher in both native fishes compared to lionfish, and parasite abundance was negatively

  7. Regional Variation in Parasite Species Richness and Abundance in the Introduced Range of the Invasive Lionfish, Pterois volitans.

    PubMed

    Sellers, Andrew J; Ruiz, Gregory M; Leung, Brian; Torchin, Mark E

    2015-01-01

    Parasites can play an important role in biological invasions. While introduced species often lose parasites from their native range, they can also accumulate novel parasites in their new range. The accumulation of parasites by introduced species likely varies spatially, and more parasites may shift to new hosts where parasite diversity is high. Considering that parasitism and disease are generally more prevalent at lower latitudes, the accumulation of parasites by introduced hosts may be greater in tropical regions. The Indo-Pacific lionfish (Pterois volitans) has become widely distributed across the Western Atlantic. In this study, we compared parasitism across thirteen locations in four regions, spanning seventeen degrees of latitude in the lionfish's introduced range to examine potential spatial variation in parasitism. In addition, as an initial step to explore how indirect effects of parasitism might influence interactions between lionfish and ecologically similar native hosts, we also compared parasitism in lionfish and two co-occurring native fish species, the graysby grouper, Cephalopholis cruentata, and the lizardfish, Synodus intermedius, in the southernmost region, Panama. Our results show that accumulation of native parasites on lionfish varies across broad spatial scales, and that colonization by ectoparasites was highest in Panama, relative to the other study sites. Endoparasite richness and abundance, on the other hand, were highest in Belize where lionfish were infected by twice as many endoparasite species as lionfish in other regions. The prevalence of all but two parasite species infecting lionfish was below 25%, and we did not detect an association between parasite abundance and host condition, suggesting a limited direct effect of parasites on lionfish, even where parasitism was highest. Further, parasite species richness and abundance were significantly higher in both native fishes compared to lionfish, and parasite abundance was negatively

  8. Regional Variation in Parasite Species Richness and Abundance in the Introduced Range of the Invasive Lionfish, Pterois volitans

    PubMed Central

    2015-01-01

    Parasites can play an important role in biological invasions. While introduced species often lose parasites from their native range, they can also accumulate novel parasites in their new range. The accumulation of parasites by introduced species likely varies spatially, and more parasites may shift to new hosts where parasite diversity is high. Considering that parasitism and disease are generally more prevalent at lower latitudes, the accumulation of parasites by introduced hosts may be greater in tropical regions. The Indo-Pacific lionfish (Pterois volitans) has become widely distributed across the Western Atlantic. In this study, we compared parasitism across thirteen locations in four regions, spanning seventeen degrees of latitude in the lionfish's introduced range to examine potential spatial variation in parasitism. In addition, as an initial step to explore how indirect effects of parasitism might influence interactions between lionfish and ecologically similar native hosts, we also compared parasitism in lionfish and two co-occurring native fish species, the graysby grouper, Cephalopholis cruentata, and the lizardfish, Synodus intermedius, in the southernmost region, Panama. Our results show that accumulation of native parasites on lionfish varies across broad spatial scales, and that colonization by ectoparasites was highest in Panama, relative to the other study sites. Endoparasite richness and abundance, on the other hand, were highest in Belize where lionfish were infected by twice as many endoparasite species as lionfish in other regions. The prevalence of all but two parasite species infecting lionfish was below 25%, and we did not detect an association between parasite abundance and host condition, suggesting a limited direct effect of parasites on lionfish, even where parasitism was highest. Further, parasite species richness and abundance were significantly higher in both native fishes compared to lionfish, and parasite abundance was negatively

  9. Effects of advection on the seasonal abundance patterns of three species of planktonic calanoid copepods in Dabob Bay, Washington

    NASA Astrophysics Data System (ADS)

    Osgood, Kenric E.; Frost, Bruce W.

    1996-08-01

    The copepodid stage abundances of Calanus marshallae, Calanus pacificus and Metridia pacifica in Dabob Bay, Washington were followed through two years. Based on the species' life histories, vertical distributions, abundances inside and outside the bay, and the hydrographic setting, times when advection was important were explored. During the first study-year, 1973, advection acted to keep the copepod concentrations inside and outside Dabob Bay similar through the early summer. During the summer, a period of very little advective exchange, the copepod concentrations diverged at the two stations. In the fall, when advection picked up again, the copepod concentrations at the two stations once again became similar. During the summer of the other study-year, 1982, flow of deep water into Dabob Bay occurred. This may have caused some of the differences observed in the abundances of the copepods during the summer of 1982 vs 1973. Due in part to the advective events, the seasonal abundance patterns of the copepods could not be predicted based upon their locally expressed life history patterns. The most striking example of this was C. pacificus. Its population decreased during the spring and increased during the fall, despite having its major reproductive peak in the spring. Advective effects clearly contributed to this.

  10. Abundance and spatial-temporal distribution of the shrimp Xiphopenaeus kroyeri (Decapoda: Penaeidae): an exploited species in southeast Brazil.

    PubMed

    Silva, E R; Sancinetti, G S; Fransozo, A; Azevedo, A; Costa, R C

    2016-04-19

    This study evaluated the abundance and spatial-temporal distribution of the shrimp Xiphopenaeus kroyeri in the coastal region of Macaé, state of Rio de Janeiro, southeastern Brazil. Monthly samples were obtained from March 2008 to February 2010 in six stations located in Inner (5, 10 and 15m depth) and Outer (25, 35 and 45m depth) areas. It was used a commercial fishery boat equipped with an otter-trawl net (3.5 m mouth width, mesh size 20mm and 15mm in the cod end). Water samples were taken for determination of temperature and salinity, and sediment samples for determination of texture and organic matter content. A total of 7146 shrimps were sampled. About 95% of all shrimps were caught in the shallow area, i.e., depths <20m. Greatest abundances were recorded in winter and spring. No significant correlation was observed between sediment (phi) and abundance. The distribution of X. kroyeri in the studied area was closely related to seasonal cold waterfront of the South Atlantic Central Water (SACW) and temperature was the main factor affecting the species abundance. PMID:27097079

  11. Abundance and spatial-temporal distribution of the shrimp Xiphopenaeus kroyeri (Decapoda: Penaeidae): an exploited species in southeast Brazil.

    PubMed

    Silva, E R; Sancinetti, G S; Fransozo, A; Azevedo, A; Costa, R C

    2016-04-19

    This study evaluated the abundance and spatial-temporal distribution of the shrimp Xiphopenaeus kroyeri in the coastal region of Macaé, state of Rio de Janeiro, southeastern Brazil. Monthly samples were obtained from March 2008 to February 2010 in six stations located in Inner (5, 10 and 15m depth) and Outer (25, 35 and 45m depth) areas. It was used a commercial fishery boat equipped with an otter-trawl net (3.5 m mouth width, mesh size 20mm and 15mm in the cod end). Water samples were taken for determination of temperature and salinity, and sediment samples for determination of texture and organic matter content. A total of 7146 shrimps were sampled. About 95% of all shrimps were caught in the shallow area, i.e., depths <20m. Greatest abundances were recorded in winter and spring. No significant correlation was observed between sediment (phi) and abundance. The distribution of X. kroyeri in the studied area was closely related to seasonal cold waterfront of the South Atlantic Central Water (SACW) and temperature was the main factor affecting the species abundance.

  12. Field study site selection, species abundance and monthly distribution of anopheline mosquitoes in the northern Kruger National Park, South Africa

    PubMed Central

    2014-01-01

    Background Knowledge of the ecology and behaviour of a target species is a prerequisite for the successful development of any vector control strategy. Before the implementation of any strategy it is essential to have comprehensive information on the bionomics of species in the targeted area. The aims of this study were to conduct regular entomological surveillance and to determine the relative abundance of anopheline species in the northern Kruger National Park. In addition to this, the impact of weather conditions on an Anopheles arabiensis population were evaluated and a range of mosquito collection methods were assessed. Methods A survey of Anopheles species was made between July 2010 and December 2012. Mosquitoes were collected from five sites in the northern Kruger National Park, using carbon dioxide-baited traps, human landing and larval collections. Specimens were identified morphologically and polymerase chain reaction assays were subsequently used where appropriate. Results A total of 3,311 specimens belonging to nine different taxa was collected. Species collected were: Anopheles arabiensis (n = 1,352), Anopheles quadriannulatus (n = 870), Anopheles coustani (n = 395), Anopheles merus (n = 349), Anopheles pretoriensis (n = 35), Anopheles maculipalpis (n = 28), Anopheles rivulorum (n = 19), Anopheles squamosus (n = 3) and Anopheles rufipes (n = 2). Members of the Anopheles gambiae species complex were the most abundant and widely distributed, occurring across all collection sites. The highest number of mosquitoes was collected using CO2 baited net traps (58.2%) followed by human landing catches (24.8%). Larval collections (17%) provided an additional method to increase sample size. Mosquito sampling productivity was influenced by prevailing weather conditions and overall population densities fluctuated with seasons. Conclusion Several anopheline species occur in the northern Kruger National Park and their densities

  13. Effects of landscape composition and wetland fragmentation on frog and toad abundance and species richness in Iowa and Wisconsin, USA

    USGS Publications Warehouse

    Knutson, M.G.; Sauer, J.R.; Olsen, D.A.; Mossman, M.J.; Hemesath, L.M.; Lannoo, M.J.

    1999-01-01

    Management of amphibian populations to reverse recent declines will require defining high-quality habitat for individual species or groups of species, followed by efforts to retain or restore these habitats on the landscape. We examined landscape-level habitat relationships for frogs and toads by measuring associations between relative abundance and species richness based on survey data derived from anuran calls and features of land-cover maps for Iowa and Wisconsin. The most consistent result across all anuran guilds was a negative association with the presence of urban land. Upland and wetland forests and emergent wetlands tended to be positively associated with anurans. Landscape metrics that represent edges and patch diversity also had generally positive associations, indicating that anurans benefit from a complex of habitats that include wetlands. In Iowa the most significant associations with relative abundance were the length of the edge between wetland and forest (positive) and the presence of urban land (negative). In Wisconsin the two most significant associations with relative abundance were forest area and agricultural area (both positive). Anurans had positive associations with agriculture in Wisconsin but not in Iowa. Remnant forest patches in agricultural landscapes may be providing refuges for some anuran species. Differences in anuran associations with deep water and permanent wetlands between the two states suggest opportunities for management action. Large-scale maps can contribute to predictive models of amphibian habitat use, but water quality and vegetation information collected from individual wetlands will likely be needed to strengthen those predictions. Landscape habitat analyses provide a framework for future experimental and intensive research on specific factors affecting the health of anurans.

  14. Reliable molecular identification of nine tropical whitefly species

    PubMed Central

    Ovalle, Tatiana M; Parsa, Soroush; Hernández, Maria P; Becerra Lopez-Lavalle, Luis A

    2014-01-01

    The identification of whitefly species in adult stage is problematic. Morphological differentiation of pupae is one of the better methods for determining identity of species, but it may vary depending on the host plant on which they develop which can lead to misidentifications and erroneous naming of new species. Polymerase chain reaction (PCR) fragment amplified from the mitochondrial cytochrome oxidase I (COI) gene is often used for mitochondrial haplotype identification that can be associated with specific species. Our objective was to compare morphometric traits against DNA barcode sequences to develop and implement a diagnostic molecular kit based on a RFLP-PCR method using the COI gene for the rapid identification of whiteflies. This study will allow for the rapid diagnosis of the diverse community of whiteflies attacking plants of economic interest in Colombia. It also provides access to the COI sequence that can be used to develop predator conservation techniques by establishing which predators have a trophic linkage with the focal whitefly pest species. PMID:25614792

  15. Relative importance of phenotypic trait matching and species' abundances in determining plant-avian seed dispersal interactions in a small insular community.

    PubMed

    González-Castro, Aarón; Yang, Suann; Nogales, Manuel; Carlo, Tomás A

    2015-03-05

    Network theory has provided a general way to understand mutualistic plant-animal interactions at the community level. However, the mechanisms responsible for interaction patterns remain controversial. In this study we use a combination of statistical models and probability matrices to evaluate the relative importance of species morphological and nutritional (phenotypic) traits and species abundance in determining interactions between fleshy-fruited plants and birds that disperse their seeds. The models included variables associated with species abundance, a suite of variables associated with phenotypic traits (fruit diameter, bird bill width, fruit nutrient compounds), and the species identity of the avian disperser. Results show that both phenotypic traits and species abundance are important determinants of pairwise interactions. However, when considered separately, fruit diameter and bill width were more important in determining seed dispersal interactions. The effect of fruit compounds was less substantial and only important when considered together with abundance-related variables and/or the factor 'animal species'.

  16. How to link the relative abundances of gas species in coma of comets to their initial chemical composition?

    NASA Astrophysics Data System (ADS)

    Marboeuf, Ulysse; Schmitt, Bernard

    2014-11-01

    Comets are expected to be the most primitive objects in the Solar System. The chemical composition of these objects is frequently assumed to be directly provided by the observations of the abundances of volatile molecules in the coma. The present work aims to determine the relationship between the chemical composition of the coma, the outgassing profile of volatile molecules and the internal chemical composition, and water ice structure of the nucleus, and physical assumptions on comets. To do this, we have developed a quasi 3D model of a cometary nucleus which takes into account all phase changes and water ice structures (amorphous, crystalline, clathrate, and a mixture of them); we have applied this model to the Comet 67P/Churyumov-Gerasimenko, the target of the Rosetta mission. We find that the outgassing profile of volatile molecules is a strong indicator of the physical and thermal properties (water ice structure, thermal inertia, abundances, distribution, physical differentiation) of the solid nucleus. Day/night variations of the rate of production of species helps to distinguish the clathrate structure from other water ice structures in nuclei, implying different thermodynamic conditions of cometary ice formation in the protoplanetary disc. The relative abundance (to H2O) of volatile molecules released from the nucleus interior varies by some orders of magnitude as a function of the distance to the Sun, the volatility of species, their abundance and distribution between the "trapped" and "condensed" states, the structure of water ice, and the thermal inertia and other physical assumptions (dust mantle, …) on the nucleus. For the less volatile molecules such as CO2 and H2S, the relative (to H2O) abundance of species in coma remain similar to the primitive composition of the nucleus (relative deviation less than 25%) only around the perihelion passage (in the range -3 to -2 to +2-3 AU), whatever is the water ice structure and chemical composition, and under

  17. Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†

    PubMed Central

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    Summary: Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination. PMID:21233509

  18. Comparisons among survey methodologies to test for abundance and size of a highly targeted fish species.

    PubMed

    Gardner, J P A; Struthers, C D

    2013-01-01

    Three sampling methods for estimating abundance and size of blue cod Parapercis colias were compared inside and outside Kapiti Marine Reserve, New Zealand (40° 49' 31·77('') S; 174° 55' 02·87('') E). Two baited methods, baited underwater video (BUV) and experimental angling (EA), were more efficient and had lower levels of estimate variation than diver-based underwater visual census (UVC). The BUV and EA recorded more fish and of greater size ranges than UVC, and also had fewer zero count replicates. The BUV and EA methodologies revealed highly significant differences in abundance and size of fish between sites (reserve v. non-reserve), whereas UVC revealed no such differences. These results indicate that BUV is likely to be the most accurate, cost-effective and easy to use methodology for the surveying of carnivorous temperate reef fishes for future monitoring. It is noted, however, that new data acquired using the BUV methodology may need to be compared over a calibration period to data acquired using the UVC methodology to ensure that historical data sets derived from UVC still have validity and application for future monitoring activity.

  19. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution

    PubMed Central

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  20. Distribution species abundance and nesting site use of Atlantic coast colonies of herons and their allies

    USGS Publications Warehouse

    Custer, T.W.; Osborn, R.G.; Stout, W.F.

    1980-01-01

    In 1975 and 1976, 8 teams of investigators located 262 colonies of nesting herons and their allies along the Atlantic coast from Florida to Maine [USA]. Fourteen species [Ajaia ajaja, Plegadis falcinellus, Nycticorax nycticorax, Ardea herodias, Eudocimus albus, Egretta thula, Hydranassa tricolor, Bubulcus ibis, Casmerodius albus, Butorides striatus, Florida caerulea, Dichromanassa rufescens, Nyctanassa violacea and Mycteria americana] were found in Florida, numbers decreasing to 7 in Maine. Colonies censused in the extreme south and north of the study area were lower in number of species and number of adults than those in the intermediate area. More than 90% of the colony sites surveyed in 1975 were active in 1976. The total number of nesting adults per colony, number of species per colony and number of nesting adults of each species per colony in 1976 were significantly correlated with their respective values for 1975. Abandoned and new colonies may be satellites of nearby reused colonies; they had fewer individuals and species than reused colonies and were closer to reused colonies than reused colonies were to each other. [This study was part of an attempt to examine colonially nesting herons as biological indicators of environmental quality.

  1. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution.

    PubMed

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  2. Are parasite richness and abundance linked to prey species richness and individual feeding preferences in fish hosts?

    PubMed

    Cirtwill, Alyssa R; Stouffer, Daniel B; Poulin, Robert; Lagrue, Clément

    2016-01-01

    Variations in levels of parasitism among individuals in a population of hosts underpin the importance of parasites as an evolutionary or ecological force. Factors influencing parasite richness (number of parasite species) and load (abundance and biomass) at the individual host level ultimately form the basis of parasite infection patterns. In fish, diet range (number of prey taxa consumed) and prey selectivity (proportion of a particular prey taxon in the diet) have been shown to influence parasite infection levels. However, fish diet is most often characterized at the species or fish population level, thus ignoring variation among conspecific individuals and its potential effects on infection patterns among individuals. Here, we examined parasite infections and stomach contents of New Zealand freshwater fish at the individual level. We tested for potential links between the richness, abundance and biomass of helminth parasites and the diet range and prey selectivity of individual fish hosts. There was no obvious link between individual fish host diet and helminth infection levels. Our results were consistent across multiple fish host and parasite species and contrast with those of earlier studies in which fish diet and parasite infection were linked, hinting at a true disconnect between host diet and measures of parasite infections in our study systems. This absence of relationship between host diet and infection levels may be due to the relatively low richness of freshwater helminth parasites in New Zealand and high host-parasite specificity. PMID:26573385

  3. Are parasite richness and abundance linked to prey species richness and individual feeding preferences in fish hosts?

    PubMed

    Cirtwill, Alyssa R; Stouffer, Daniel B; Poulin, Robert; Lagrue, Clément

    2016-01-01

    Variations in levels of parasitism among individuals in a population of hosts underpin the importance of parasites as an evolutionary or ecological force. Factors influencing parasite richness (number of parasite species) and load (abundance and biomass) at the individual host level ultimately form the basis of parasite infection patterns. In fish, diet range (number of prey taxa consumed) and prey selectivity (proportion of a particular prey taxon in the diet) have been shown to influence parasite infection levels. However, fish diet is most often characterized at the species or fish population level, thus ignoring variation among conspecific individuals and its potential effects on infection patterns among individuals. Here, we examined parasite infections and stomach contents of New Zealand freshwater fish at the individual level. We tested for potential links between the richness, abundance and biomass of helminth parasites and the diet range and prey selectivity of individual fish hosts. There was no obvious link between individual fish host diet and helminth infection levels. Our results were consistent across multiple fish host and parasite species and contrast with those of earlier studies in which fish diet and parasite infection were linked, hinting at a true disconnect between host diet and measures of parasite infections in our study systems. This absence of relationship between host diet and infection levels may be due to the relatively low richness of freshwater helminth parasites in New Zealand and high host-parasite specificity.

  4. Macroinvertebrate abundance, water chemistry, and wetland characteristics affect use of wetlands by avian species in Maine

    USGS Publications Warehouse

    Longcore, J.R.; McAuley, D.G.; Pendleton, G.W.; Bennatti, C.R.; Mingo, T.M.; Stromborg, K.L.; Hanson, Alan; Kerekes, Joseph; Paquet, Julie

    2006-01-01

    Our objective was to determine use by avian species (e.g., piscivores, marsh birds, waterfowl, selected passerines) of 29 wetlands in areas with low ( 5.51. All years combined use of wetlands by broods was greater on wetlands with pH 5.51 that supported 21.8% of the broods. High mean brood density was associated with mean number of Insecta per wetland. For lentic wetlands created by beaver, those habitats contained vegetative structure and nutrients necessary to provide cover to support invertebrate populations that are prey of omnivore and insectivore species. The fishless status of a few wetlands may have affected use by some waterfowl species and obligate piscivores.

  5. Macroinvertebrate abundance, water chemistry, and wetland characteristics affect use of wetlands by avian species in Maine

    USGS Publications Warehouse

    Longcore, J.R.; McAuley, D.G.; Pendelton, G.W.; Bennatti, C.R.; Mingo, T.M.; Stromborg, K.L.

    2006-01-01

    Our objective was to determine use by avian species (e.g., piscivores, marsh birds, waterfowl, selected passerines) of 29 wetlands in areas with low ( 5.51. All years combined use of wetlands by broods was greater on wetlands with pH ??? 5.51 (77.4%) in contract to wetlands with pH > 5.51 that supported 21.8% of the broods. High mean brood density was associated with mean number of Insecta per wetland. For lentic wetlands created by beaver, those habitats contained vegetative structure and nutrients necessary to provide cover to support invertebrate populations that are prey of omnivore and insectivore species. The fishless status of a few wetlands may have affected use by some waterfowl species and obligate piscivores. ?? Springer 2006.

  6. Assessment of fish abundance and species composition at selected sites in South Dakota: an overview

    USGS Publications Warehouse

    Harwood, Alison

    2010-01-01

    The U.S. Geological Survey (USGS) conducted surveys of streams throughout the State of South Dakota during 2008-09 as part of the U.S. Environmental Protection Agency?s (USEPA) National Rivers and Streams Assessment (NRSA) Program. During 2008-09, as part of the stream assessment, the USGS completed surveys of fish populations and species composition at 64 sites. Fish were inventoried at 60 of the 64 sites, but not at four of the sites because water was too low to sustain fish or specific conductivity was too high to electroshock effectively. Four of the sites were surveyed in 2000-04 during the USEPA's Environmental Monitoring and Assessment Program-West (EMAP-West) project. Two wadeable sites and two boatable sites were revisited for quality-assurance/quality-control requirements. During the study, both wadeable and boatable streams were sampled using electrofishing equipment and methods. Of the 64 sites, 62 were wadeable and 2 were boatable. Procedures for sampling wadeable streams differed slightly from procedures for boatable streams. Backpack electrofishing equipment was used for wadeable streams, whereas boat electrofishing equipment was used for boatable streams. Wadeable streams also were fished in an opposite direction than boatable streams. Several species of fish were collected during the NRSA. Species diversity ranged from 0-11 species in wadeable streams and from 6-26 species in boatable streams. Many common species were sampled during the study. The most frequently sampled fish was the sand shiner (Notropis stramineus), with 609 individuals sampled. In contrast, only one heritage species, the skipjack herring (Alosa chrysochloris), was identified during 2008-09. Common anomalies found in fish caught were parasitic lesions, "black spot disease," and tumors. When comparing the fish sampling results for the four sites visited in both 2000-04 and in 2008-09, more individuals and species were collected during 2008-09 than in 2000-04 at two sites, whereas

  7. The Abundance of Pink-Pigmented Facultative Methylotrophs in the Root Zone of Plant Species in Invaded Coastal Sage Scrub Habitat

    PubMed Central

    Irvine, Irina C.; Brigham, Christy A.; Suding, Katharine N.; Martiny, Jennifer B. H.

    2012-01-01

    Pink-pigmented facultative methylotrophic bacteria (PPFMs) are associated with the roots, leaves and seeds of most terrestrial plants and utilize volatile C1 compounds such as methanol generated by growing plants during cell division. PPFMs have been well studied in agricultural systems due to their importance in crop seed germination, yield, pathogen resistance and drought stress tolerance. In contrast, little is known about the PPFM abundance and diversity in natural ecosystems, let alone their interactions with non-crop species. Here we surveyed PPFM abundance in the root zone soil of 5 native and 5 invasive plant species along ten invasion gradients in Southern California coastal sage scrub habitat. PPFMs were present in every soil sample and ranged in abundance from 102 to 105 CFU/g dry soil. This abundance varied significantly among plant species. PPFM abundance was 50% higher in the root zones of annual or biennial species (many invasives) than perennial species (all natives). Further, PPFM abundance appears to be influenced by the plant community beyond the root zone; pure stands of either native or invasive species had 50% more PPFMs than mixed species stands. In sum, PPFM abundance in the root zone of coastal sage scrub plants is influenced by both the immediate and surrounding plant communities. The results also suggest that PPFMs are a good target for future work on plant-microorganism feedbacks in natural ecosystems. PMID:22383990

  8. Effects of urbanization on the distribution and abundance of amphibians and invasive species in southern California streams

    USGS Publications Warehouse

    Riley, S.P.D.; Busteed, G.T.; Kats, L.B.; Vandergon, T.L.; Lee, L.F.S.; Dagit, R.G.; Kerby, J.L.; Fisher, R.N.; Sauvajot, R.M.

    2005-01-01

    Urbanization negatively affects natural ecosystems in many ways, and aquatic systems in particular. Urbanization is also cited as one of the potential contributors to recent dramatic declines in amphibian populations. From 2000 to 2002 we determined the distribution and abundance of native amphibians and exotic predators and characterized stream habitat and invertebratecommunities in 35 streams in an urbanized landscape north of Los Angeles (U.S.A.). We measured watershed development as the percentage of area within each watershed occupied by urban land uses. Streams in more developed watersheds often had exotic crayfish (Procambarus clarkii) and fish, and had fewer native species such as California newts (Taricha torosa) and California treefrogs (Hyla cadaverina). These effects seemed particularly evident above 8% development, a result coincident with other urban stream studies that show negative impacts beginning at 10-15% urbanization. For Pacific treefrogs (H. regilla), the most widespread native amphibian, abundance was lower in the presence of exotic crayfish, although direct urbanization effects were not found. Benthic macroinvertebrate communities were also less diverse in urban streams, especially for sensitive species. Faunal community changes in urban streams may be related to changes in physical stream habitat, such as fewer pool and more run habitats and increased water depth and flow, leading to more permanent streams. Variation in stream permanence was particularly evident in 2002, a dry year when many natural streams were dry but urban streams were relatively unchanged. Urbanization has significantly altered stream habitat in this region and may enhance invasion by exotic species and negatively affect diversity and abundance of native amphibians. ??2005 Society for Conservation Biology.

  9. Delta smelt: Life history and decline of a once abundant species in the San Francisco Estuary

    USGS Publications Warehouse

    Moyle, Peter B.; Brown, Larry R.; Durand, John R; Hobbs, James A.

    2016-01-01

    This paper reviews what has been learned about Delta Smelt and its status since the publication of The State of Bay-Delta Science, 2008 (Healey et al. 2008). The Delta Smelt is endemic to the upper San Francisco Estuary. Much of its historic habitat is no longer available and remaining habitat is increasingly unable to sustain the population. As a listed species living in the central node of California’s water supply system, Delta Smelt has been the focus of a large research effort to understand causes of decline and identify ways to recover the species. Since 2008, a remarkable record of innovative research on Delta Smelt has been achieved, which is summarized here. Unfortunately, research has not prevented the smelt’s continued decline, which is the result of multiple, interacting factors. A major driver of decline is change to the Delta ecosystem from water exports, resulting in reduced outflows and high levels of entrainment in the large pumps of the South Delta. Invasions of alien species, encouraged by environmental change, have also played a contributing role in the decline. Severe drought effects have pushed Delta Smelt to record low levels in 2014–2015. The rapid decline of the species and failure of recovery efforts demonstrate an inability to manage the Delta for the “co-equal goals” of maintaining a healthy ecosystem and providing a reliable water supply for Californians. Diverse and substantial management actions are needed to preserve Delta Smelt.

  10. Stochastic model for the species abundance problem in an ecological community

    NASA Astrophysics Data System (ADS)

    Pigolotti, Simone; Flammini, Alessandro; Maritan, Amos

    2004-07-01

    We propose a model based on coupled multiplicative stochastic processes to understand the dynamics of competing species in an ecosystem. This process can be conveniently described by a Fokker-Planck equation. We provide an analytical expression for the marginalized stationary distribution. Our solution is found in excellent agreement with numerical simulations and compares rather well with observational data from tropical forests.

  11. Characterising Wetland Properties in Relation to the Abundance of an Invasive Species

    NASA Astrophysics Data System (ADS)

    Yanosik, L. E.; McEnroe, N. A.

    2008-12-01

    Purple loosestrife (Lythrum salicaria) is a colorful but aggressive invasive species found at the Goodyear Swamp Sanctuary in Upstate New York. Flowering from June to September allows a large number of seeds to spread quickly throughout the growing season. This invasive species can alter can alter a wetland's functional properties by impacting the hydrology and soil properties. These modified properties are of concern to wetland scientists and wetland managers as the characterisation of wetland condition becomes more important. Control or eradication of purple loosestrife within the Goodyear Swamp has become regionally important and is carried out by a U.S. Department of Agriculture approved leaf-eating beetle Galerucella calmariensis. A study to investigate the environmental conditions in which purple loosestrife has propagated and changed the native flora of Goodyear Swamp was developed. The aim was to characterize the soil physiochemical properties and hydrological conditions under which the species occurs. These data are relevant to be able to highlight the wetland conditions under which purple loosestrife might invade and to be able to compare treated and untreated wetlands. We highlight key differences in wetland functional properties caused by the invasion of this species.

  12. Associations between regional moisture gradient, tree species dominance, and downed wood abundance

    NASA Astrophysics Data System (ADS)

    Johnson, A. C.; Mills, J.

    2007-12-01

    Downed wood functions as a source of nurse logs, physical structure in streams, food, and carbon. Because downed wood is important in upland and aquatic habitats, an understanding of wood recruitment along a continuum from wet to dry landscapes is critical for both preservation of biodiversity and restoration of natural ecosystem structure and function. We assessed downed wood in public and private forests of Washington and Oregon by using a subset of the Forest Inventory and Analysis (FIA) database including 15,842 sampled conditions. Multivariate regression trees, ANOVA, and t-tests were used to discern environmental conditions most closely associated with abundance of woody debris. Of the 16 parameters included in the analysis, rainfall, forest ownership, number of damaged standing trees, and forest elevation were most indicative of woody debris abundance. The Hemlock/spruce Group, including hemlock, spruce, cedar, and white pine, most associated with wetter soils, had significantly more downed wood than 12 other forest groups. The Ponderosa Pine Group, indicative of drier sites with higher fire frequencies, included ponderosa pine, sugar pine, and incense cedar, and had significantly less downed wood volume. Overall, the amount of woody debris in either the Spruce/hemlock Group or the Ponderosa Pine Group did not change significantly as tree age increased from 5 to 350 years. Plots within the Hemlock/spruce with greater standing tree volume also had significantly greater downed wood volume. In contrast, greater downed wood volume was not associated with greater standing tree volume in the Ponderosa Pine Group. Knowledge of linkages among environmental variables and stand characteristics are useful in development of regional forest models aimed at understanding the effects of climate change and disturbance on forest succession.

  13. Species diversity reduces parasite infection through cross-generational effects on host abundance.

    PubMed

    Johnson, Pieter T J; Preston, Daniel L; Hoverman, Jason T; Henderson, Jeremy S; Paull, Sara H; Richgels, Katherine L D; Redmond, Miranda D

    2012-01-01

    With growing interest in the effects of biodiversity on disease, there is a critical need for studies that empirically identify the mechanisms underlying the diversity-disease relationship. Here, we combined wetland surveys of host community structure with mechanistic experiments involving a multi-host parasite to evaluate competing explanations for the dilution effect. Sampling of 320 wetlands in California indicated that snail host communities were strongly nested, with competent hosts for the trematode Ribeiroia ondatrae predominating in low-richness assemblages and unsuitable hosts increasingly present in more diverse communities. Moreover, competent host density was negatively associated with increases in snail species richness. These patterns in host community assembly support a key prerequisite underlying the dilution effect. Results of multigenerational mesocosm experiments designed to mimic field-observed community assemblages allowed us to evaluate the relative importance of host density and diversity in influencing parasite infection success. Increases in snail species richness (from one to four species) had sharply negative effects on the density of infected hosts (-90% reduction). However, this effect was indirect; competition associated with non-host species led to a 95% reduction in host density (susceptible host regulation), owing primarily to a reduction in host reproduction. Among susceptible hosts, there were no differences in infection prevalence as a function of community structure, indicating a lack of support for a direct effect of diversity on infection (encounter reduction). In monospecific conditions, higher initial host densities increased infection among adult hosts; however, compensatory reproduction in the low-density treatments equalized the final number of infected hosts by the next generation, underscoring the relevance of multigenerational studies in understanding the dilution effect. These findings highlight the role of

  14. Hyperfine excitation of N2H+ by H2: towards a revision of N2H+ abundance in cold molecular clouds

    NASA Astrophysics Data System (ADS)

    Lique, François; Daniel, Fabien; Pagani, Laurent; Feautrier, Nicole

    2015-01-01

    The modelling of emission spectra of molecules seen in interstellar clouds requires the knowledge of collisional rate coefficients. Among the commonly observed species, N2H+ is of particular interest since it was shown to be a good probe of the physical conditions of cold molecular clouds. Thus, we have calculated hyperfine-structure-resolved excitation rate coefficients of N2H+(X1Σ+) by H2(j = 0), the most abundant collisional partner in the cold interstellar medium. The calculations are based on a new potential energy surface, obtained from highly correlated ab initio calculations. State-to-state rate coefficients between the first hyperfine levels were calculated, for temperatures ranging from 5 to 70 K. By comparison with previously published N2H+-He rate coefficients, we found significant differences which cannot be reproduced by a simple scaling relationship. As a first application, we also performed radiative transfer calculations, for physical conditions typical of cold molecular clouds. We found that the simulated line intensities significantly increase when using the new H2 rate coefficients, by comparison with the predictions based on the He rate coefficients. In particular, we revisited the modelling of the N2H+ emission in the LDN 183 core, using the new collisional data, and found that all three of the density, gas kinetic temperature and N2H+ abundance had to be revised.

  15. Species richness, relative abundance, and habitat associations of nocturnal birds along the rio grande in Southern texas

    USGS Publications Warehouse

    Skoruppa, M.K.; Woodin, M.C.; Blacklock, G.

    2009-01-01

    The segment of the Rio Grande between International Falcon Reservoir and Del Rio, Texas (distance ca. 350 km), remains largely unexplored ornithologically. We surveyed nocturnal birds monthly during February-June 1998 at 19 stations along the Rio Grande (n = 6) and at upland stock ponds (n = 13) in Webb County, Texas. We conducted 10-min point counts (n = 89) after sunset and before moonset. Four species of owls and five species of nightjars were detected. Nightjars, as a group, were nearly five limes more abundant (mean number/count = 2.63) than owls (mean number = 0.55). The most, common owl, the great horned owl (Bubo virginianus), had a mean number of 0.25/point count. The mean for elf owls (Micrathene whitneyi) was 0.16/point count. The most common nightjars were the common poorwill (Phalaenoptilus nuttallii; 1.21/point count) and lesser nighthawk (Chordeiles acutipennir, 1.16/point count). Survey sites on the river supported more species (mean = 2.2) than did upland stock ponds (mean = 1.4). However, only one species (common pauraque, Nyctidromus albicollis) showed a preference for the river sites. Our results establish this segment of the Rio Grande in southern Texas as an area of high diversity of nightjars in the United States, matched (in numbers of species) only by southeastern Arizona and southwestern New Mexico.

  16. Multiple Pleistocene refugia and Holocene range expansion of an abundant southwestern American desert plant species (Melampodium leucanthum, Asteraceae).

    PubMed

    Rebernig, Carolin A; Schneeweiss, Gerald M; Bardy, Katharina E; Schönswetter, Peter; Villaseñor, Jose L; Obermayer, Renate; Stuessy, Tod F; Weiss-Schneeweiss, Hanna

    2010-08-01

    Pleistocene climatic fluctuations had major impacts on desert biota in southwestern North America. During cooler and wetter periods, drought-adapted species were isolated into refugia, in contrast to expansion of their ranges during the massive aridification in the Holocene. Here, we use Melampodium leucanthum (Asteraceae), a species of the North American desert and semi-desert regions, to investigate the impact of major aridification in southwestern North America on phylogeography and evolution in a widespread and abundant drought-adapted plant species. The evidence for three separate Pleistocene refugia at different time levels suggests that this species responded to the Quaternary climatic oscillations in a cyclic manner. In the Holocene, once differentiated lineages came into secondary contact and intermixed, but these range expansions did not follow the eastwardly progressing aridification, but instead occurred independently out of separate Pleistocene refugia. As found in other desert biota, the Continental Divide has acted as a major migration barrier for M. leucanthum since the Pleistocene. Despite being geographically restricted to the eastern part of the species' distribution, autotetraploids in M. leucanthum originated multiple times and do not form a genetically cohesive group. PMID:20670366

  17. Molecular abundance profiles characterization of Jupiter'satmosphere using ground-based observations at 5 microns

    NASA Astrophysics Data System (ADS)

    Doriann, Blain; Fouchet, Thierry; Encrenaz, Therese A.; Drossart, Pierre; Greathouse, Thomas K.; Fletcher, Leigh N.; Orton, Glenn S.

    2016-10-01

    We report on early results of an observational campaign to support the Juno mission. At the beginning of this year, using TEXES (Texas Echelon cross-dispersed Echelle Spectrograph), mounted on the NASA Infrared Telescope Facility (IRTF), we obtained maps of Jupiter in several spectral ranges between 1800 and 2200 cm-1 which probes the atmosphere in the 1-4 bar region, with a spectral resolution of R ≈ 7000 and an angular resolution of ≈ 1.5''. This dataset is analyzed by a code which combines a line-by-line radiative transfer model with a non-linear optimal estimation inversion method. The inversion takes into account the abundance profiles of AsH3 , CO, GeH4 and H2O, as well as clouds contribution, in addtion to the abundance profiles of NH3 and PH3 . We will present the inverted abundance profiles, their significance for the understanding of Jupiter's atmospheric dynamics, and how they will be useful for the determination of water abundance up to 200 bars, which is one of the main objectives of the instrument MWR (MicroWave Radiometer) mounted on the Juno spacecraft. This work will also be useful to prepare the analysis of the JIRAM (Jovian InfraRed Auroral Mapper) 5-microns data aboard Juno.

  18. Microalgae on the arctic ocean section, 1994: species abundance and biomass

    NASA Astrophysics Data System (ADS)

    Booth, Beatrice C.; Horner, Rita A.

    Algal species from the ice, the water directly below the ice (the sub-ice area), and the water column from 21 stations in the Arctic Ocean were examined using epifluorescence and inverted light microscopy. Biomass of autotrophic dinoflagellates and other miscellaneous autotrophic flagellates was determined for the first time in the central Arctic basins. Together these two groups dominated phytoplankton biomass in 74% of samples from the central Arctic, with diatom biomass predominant in the remainder. Picophytoplankton at selected stations in the Canada and Makarov Basins contributed 93% to autotroph cell numbers and 36% to autotroph biomass. Diatom species achieved high biomass in ice and sub-ice samples. The centric diatom Melosira arctica dominated the sub-ice area, while pennate diatoms were major contributors to the ice samples. Despite ample silicate concentrations in the water, diatom frustules were often lightly silicified.

  19. Number of ancestral human species: a molecular perspective.

    PubMed

    Curnoe, D; Thorne, A

    2003-01-01

    Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest

  20. Declining Orangutan Encounter Rates from Wallace to the Present Suggest the Species Was Once More Abundant

    PubMed Central

    Meijaard, Erik; Welsh, Alan; Ancrenaz, Marc; Wich, Serge; Nijman, Vincent; Marshall, Andrew J.

    2010-01-01

    Background Bornean orangutans (Pongo pygmaeus) currently occur at low densities and seeing a wild one is a rare event. Compared to present low encounter rates of orangutans, it is striking how many orangutan each day historic collectors like Alfred Russel Wallace were able to shoot continuously over weeks or even months. Does that indicate that some 150 years ago encounter rates with orangutans, or their densities, were higher than now? Methodology/Principal Findings We test this hypothesis by quantifying encounter rates obtained from hunting accounts, museum collections, and recent field studies, and analysing whether there is a declining trend over time. Logistic regression analyses of our data support such a decline on Borneo between the mid-19th century and the present. Even when controlled for variation in the size of survey and hunting teams and the durations of expeditions, mean daily encounter rates appear to have declined about 6-fold in areas with little or no forest disturbance. Conclusions/Significance This finding has potential consequences for our understanding of orangutans, because it suggests that Bornean orangutans once occurred at higher densities. We explore potential explanations—habitat loss and degradation, hunting, and disease—and conclude that hunting fits the observed patterns best. This suggests that hunting has been underestimated as a key causal factor of orangutan density and distribution, and that species population declines have been more severe than previously estimated based on habitat loss only. Our findings may require us to rethink the biology of orangutans, with much of our ecological understanding possibly being based on field studies of animals living at lower densities than they did historically. Our approach of quantifying species encounter rates from historic data demonstrates that this method can yield valuable information about the ecology and population density of species in the past, providing new insight into

  1. Studies for the Loss of Atomic and Molecular Species from Io

    NASA Technical Reports Server (NTRS)

    Smyth, William H.

    1997-01-01

    The general objective of this project is to advance our theoretical understanding of Io's atmosphere by studying how various atomic and molecular species are lost from this atmosphere and are distributed near the satellite and in the circumplanetary environment of Jupiter. The project is divided into well-defined studies described for the likely dominant atmospheric gases involving species of the SO2 family (SO2, SO, 02, 0, S) and for the trace atmospheric gas atomic sodium. The relative abundance of the members of the S02 family and Na (and its parent Na(x)) at the satellite exobase and their relative spatial densities beyond in the extended corona of lo are not well known but will depend upon a number of factors including the upward transport rate of gases from below, the velocity distribution and corresponding escape rate of gases at the exobase, and the operative magnetospheric/solar-photon driven chemistry for the different gases. This question of relative abundance will be studied in this project.

  2. What is the link of the abundances of volatile species in the coma with the ones in the nucleus ?

    NASA Astrophysics Data System (ADS)

    Marboeuf, U.; Schmitt, B.

    2014-04-01

    The chemical composition of comets is frequently assumed to be directly provided by the observations of the abundances of volatile molecules in the coma. The present work aims to determine the relationship between the chemical composition of the coma, the outgassing profile of volatile molecules and the physicochemical composition of the nucleus. To do this, we have developed a quasi 3D model of a cometary nucleus which takes into account all phase changes and water ice structures and applied this model to the comet 67P/Churyumov-Gerasimenko, the target of the Rosetta mission. We find that the outgassing profile of volatile molecules is a strong indicator of the physical and thermal properties of the solid nucleus. The relative abundance (to H2O) of volatile molecules released from the nucleus interior varies by some orders of magnitude as a function of the distance to the sun, the volatility of species, their abundance and distribution between the 'trapped' and 'condensed' states, the structure of water ice, and the thermal inertia and other physical assumptions (dust mantle, ...) on the nucleus.

  3. From species abundance to opal input: Simple geometrical models of radiolarian skeletons from the Atlantic sector of the Southern Ocean

    NASA Astrophysics Data System (ADS)

    Jacot Des Combes, H.; Abelmann, A.

    2009-05-01

    Radiolarian-based paleoceanographic reconstructions generally use the abundance of selected radiolarian species. However, the recent focus on the opal flux and the development of isotope measurements in biogenic opal and the organic matter embedded in it demands a better knowledge of the origin of the opal. We present here an estimation of the opal content of the skeleton of 63 radiolarian species from two sites in the Southern Ocean. The skeletons are modelled as associations of simple geometrical shapes, and the volume thus obtained is combined with opal density to obtain the amount of opal. These data are, thus, used to determine the most important opal carriers in the radiolarian assemblage in both cores.

  4. Diversity and abundance of mosquito species in relation to their larval habitats in Mizoram, North Eastern Himalayan region.

    PubMed

    Vanlalruia, Khawling; Senthilkumar, Nachimuthu; Gurusubramanian, Guruswami

    2014-09-01

    The abundance, richness and diversity of anopheline and culicid mosquitoes associated with their habitats, season, and physico-chemical quality of water were surveyed along six districts of Mizoram, North Eastern Himalayan region. The productivity of permanent and temporary habitat types was quantified by carrying out weekly larval sampling using a standard dipping method for a period of three years. Diversity was estimated using the Shannon index (H'), Evenness index (Heve), similarity measures cluster analysis and MANOVA. In total, 5 genera and 20 species of mosquitoes were identified: Culex quinquefasciatus, Anopheles barbirostris and Anopheles vagus were the most abundant and widely-distributed species, representing 39.71%, 29.39% and 14.52% of total mosquito individuals sampled, respectively. Anopheles sp. diversity was lowest in Lunglei district (H'=0.48) and highest in Aizawl (H'=2.03), whereas Culex sp. diversity was lowest in Lawngtlai (H'=0.38), and highest in Aizawl (H'=2.99) and Kolasib (H'=2.13). This represents the first update on the diversity and geographic distribution of the mosquitoes of Mizoram. Mosquito larvae were present in both temporary and permanent habitats suitable for breeding with monthly variations dependent on rainfall intensity, temperature, humidity and location. Early instars were more abundant significantly (P<0.0001) than late instars among the habitat types in all study sites. The productivity of mosquito larvae was significantly (P<0.0001) higher in ponds especially in permanent than semi-permanent and temporary. Weekly rainfall intensity led to an increase or decrease in anopheline and culicid larval abundance depending on the location. Mosquito diversity was highest in monsoon season (July-September) and lowest in January-March. A. barbirostris, A. vagus and C. quinquefasciatus appear the most likely habitat generalist as it demonstrates both widespread distribution. Abundance and diversity of culicine and anopheline larvae

  5. Molecular Species Delimitation in the Racomitrium canescens Complex (Grimmiaceae) and Implications for DNA Barcoding of Species Complexes in Mosses

    PubMed Central

    Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

    2013-01-01

    In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses. PMID

  6. Molecular species delimitation in the Racomitrium canescens complex (Grimmiaceae) and implications for DNA barcoding of species complexes in mosses.

    PubMed

    Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

    2013-01-01

    In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses.

  7. Defining Species-Specific Immunodominant B Cell Epitopes for Molecular Serology of Chlamydia Species

    PubMed Central

    Rahman, K. Shamsur; Chowdhury, Erfan U.; Poudel, Anil; Ruettger, Anke; Sachse, Konrad

    2015-01-01

    Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens. PMID:25761461

  8. Defining species-specific immunodominant B cell epitopes for molecular serology of Chlamydia species.

    PubMed

    Rahman, K Shamsur; Chowdhury, Erfan U; Poudel, Anil; Ruettger, Anke; Sachse, Konrad; Kaltenboeck, Bernhard

    2015-05-01

    Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens.

  9. Novel "omics" approach for study of low-abundance, low-molecular-weight components of a complex biological tissue: regional differences between chorionic and basal plates of the human placenta.

    PubMed

    Kedia, Komal; Nichols, Caitlin A; Thulin, Craig D; Graves, Steven W

    2015-11-01

    Tissue proteomics has relied heavily on two-dimensional gel electrophoresis, for protein separation and quantification, then single protein isolation, trypsin digestion, and mass spectrometric protein identification. Such methods are predominantly used for study of high-abundance, full-length proteins. Tissue peptidomics has recently been developed but is still used to study the most highly abundant species, often resulting in observation and identification of dozens of peptides only. Tissue lipidomics is likewise new, and reported studies are limited. We have developed an "omics" approach that enables over 7,000 low-molecular-weight, low-abundance species to be surveyed and have applied this to human placental tissue. Because the placenta is believed to be involved in complications of pregnancy, its proteomic evaluation is of substantial interest. In previous research on the placental proteome, abundant, high-molecular-weight proteins have been studied. Application of large-scale, global proteomics or peptidomics to the placenta have been limited, and would be challenging owing to the anatomic complexity and broad concentration range of proteins in this tissue. In our approach, involving protein depletion, capillary liquid chromatography, and tandem mass spectrometry, we attempted to identify molecular differences between two regions of the same placenta with only slightly different cellular composition. Our analysis revealed 16 species with statistically significant differences between the two regions. Tandem mass spectrometry enabled successful sequencing, or otherwise enabled chemical characterization, of twelve of these. The successful discovery and identification of regional differences between the expression of low-abundance, low-molecular weight biomolecules reveals the potential of our approach.

  10. Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives.

    PubMed

    Matthews, Thomas J; Whittaker, Robert J

    2014-06-01

    Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.

  11. Abundances and implications of volatile-bearing species from evolved gas analysis of the Rocknest aeolian deposit, Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Archer, Paul Douglas; Franz, Heather B.; Sutter, Brad; Arevalo, Ricardo D.; Coll, Patrice; Eigenbrode, Jennifer L.; Glavin, Daniel P.; Jones, John J.; Leshin, Laurie A.; Mahaffy, Paul R.; McAdam, Amy C.; McKay, Christopher P.; Ming, Douglas W.; Morris, Richard V.; Navarro-González, Rafael; Niles, Paul B.; Pavlov, Alex; Squyres, Steven W.; Stern, Jennifer C.; Steele, Andrew; Wray, James J.

    2014-01-01

    The Sample Analysis at Mars (SAM) instrument on the Mars Science Laboratory (MSL) rover Curiosity detected evolved gases during thermal analysis of soil samples from the Rocknest aeolian deposit in Gale Crater. Major species detected (in order of decreasing molar abundance) were H2O, SO2, CO2, and O2, all at the µmol level, with HCl, H2S, NH3, NO, and HCN present at the tens to hundreds of nmol level. We compute weight % numbers for the major gases evolved by assuming a likely source and calculate abundances between 0.5 and 3 wt.%. The evolution of these gases implies the presence of both oxidized (perchlorates) and reduced (sulfides or H-bearing) species as well as minerals formed under alkaline (carbonates) and possibly acidic (sulfates) conditions. Possible source phases in the Rocknest material are hydrated amorphous material, minor clay minerals, and hydrated perchlorate salts (all potential H2O sources), carbonates (CO2), perchlorates (O2 and HCl), and potential N-bearing materials (e.g., Martian nitrates, terrestrial or Martian nitrogenated organics, ammonium salts) that evolve NH3, NO, and/or HCN. We conclude that Rocknest materials are a physical mixture in chemical disequilibrium, consistent with aeolian mixing, and that although weathering is not extensive, it may be ongoing even under current Martian surface conditions.

  12. Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives.

    PubMed

    Matthews, Thomas J; Whittaker, Robert J

    2014-06-01

    Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research. PMID:25360266

  13. Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives

    PubMed Central

    Matthews, Thomas J; Whittaker, Robert J

    2014-01-01

    Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research. PMID:25360266

  14. Diversity and Abundance of House Fly Pupal Parasitoids in Israel, with First Records of Two Spalangia Species.

    PubMed

    Chiel, Elad; Kuslitzky, Wolf

    2016-04-01

    Filth flies (Diptera: Muscidae), particularly the house fly, Musca domestica L., are global pests of livestock production. In this study, we characterized the fauna of house fly pupal parasitoids in Israel and identified factors affecting their diversity and abundance. The study, which included one round of sampling during the fall of 2013 and another round of sampling in the spring of 2014, encompassed 26 locations of common fly-breeding habitats: dairy, egg-laying, and goat farms throughout Israel. Nine parasitoid species were found: Spalangia cameroni Perkins, Spalangia endius Walker, Spalangia drosophilae Ashmead, Spalangia gemina Boucek, Spalangia nigroaenea Curtis, Pachycrepoideus vindemmiae Rondani, Muscidifurax raptor Girault and Sanders, Muscidifurax zaraptor Kogan & Legner (all Hymenoptera: Pteromalidae), and Dirhinus giffardii Silvestri (Hymenoptera: Chalcididae). This is the first record of S. gemina from the Palearctic, as well as the first record of S. drosophilae from the Middle East. The composition and relative abundance of parasitoid species varied markedly among localities, climatic regions (Mediterranean vs. desert), habitat types (dairy vs. egg-laying vs. goat farm), and seasons. Overall, parasitoid richness in egg-laying farms was two- and sevenfold higher than in dairy and goat farms, respectively, and three times higher in Mediterranean than desert climate. The significance and implications of our results for inundative biological control programs of filth flies are discussed. PMID:26637547

  15. Molecular evidence for species-level distinctions in clouded leopards.

    PubMed

    Buckley-Beason, Valerie A; Johnson, Warren E; Nash, Willliam G; Stanyon, Roscoe; Menninger, Joan C; Driscoll, Carlos A; Howard, JoGayle; Bush, Mitch; Page, John E; Roelke, Melody E; Stone, Gary; Martelli, Paolo P; Wen, Ci; Ling, Lin; Duraisingam, Ratna K; Lam, Phan V; O'Brien, Stephen J

    2006-12-01

    Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi).

  16. Molecular evidence for species-level distinctions in clouded leopards.

    PubMed

    Buckley-Beason, Valerie A; Johnson, Warren E; Nash, Willliam G; Stanyon, Roscoe; Menninger, Joan C; Driscoll, Carlos A; Howard, JoGayle; Bush, Mitch; Page, John E; Roelke, Melody E; Stone, Gary; Martelli, Paolo P; Wen, Ci; Ling, Lin; Duraisingam, Ratna K; Lam, Phan V; O'Brien, Stephen J

    2006-12-01

    Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainla