Modelling patterns of coexistence of three congeneric headwater fishes

1. Mechanisms driving patterns of occurrence and co-occurrence among North American freshwater fishes are poorly understood. In particular, the influence of biotic interactions on coexistence among stream reaches and their effects on regional species distribution patterns is not well understood for congeneric headwater fishes.
2. Occupancy models provide a useful framework for examining patterns of co-occurrence while also accounting for imperfect detection. Occupancy models may be extended to test for evidence that a dominant species influences the occurrence of a subordinate species and thus evaluate support for the hypothesis that species interactions drive patterns of coexistence.
3. We examined patterns of occurrence and co-occurrence at the stream-reach scale among three species of darters (Percidae: Etheostomatinae) that occupy headwater streams within a Gulf Coastal Plain drainage in the south-eastern U.S.A. We assessed species occurrences at 97 sites in first- to third-order streams on one occasion each and used data from four sub-reaches sampled with equal effort at each site to estimate species-specific detection probabilities. Following sampling, a suite of habitat variables was collected at three equidistant points along each of the three transects established within a sub-reach. Coarse (stream-segment, catchment, network) scale variables were also incorporated using geospatial data. Single-species and two-species occupancy models were used to examine patterns of occupancy and coexistence.
4. The occupancy of each species was influenced by distinct habitat variables. Goldstripe darters (Etheostoma parvipinne) were constrained by a stream size gradient, groundwater input appeared to influence the occurrence of Yazoo darters (Etheostoma raneyi), and local habitat heterogeneity (e.g. variation in depth and current velocity) appeared to influence the occupancy of redspot darters (Etheostoma artesiae).
5. We found no evidence that the presence of one species influenced the occurrence of another within a stream-reach based on two-species occupancy models. Rather, species co-occurrences were best explained as independent occurrences within a stream-reach according to species-specific habitat associations.
6. Occupancy modelling may provide a suitable framework for evaluating the influence of biotic interactions among congeneric stream fishes along species-specific habitat gradients at the stream reach scale. Our study offers insight into how habitat variation can influence coexistence of potential competitors across a large river system.

     

Metabolomic profiling of wild‐type and mutant soybean root nodules using laser‐ablation electrospray ionization mass spectrometry reveals altered metabolism

The establishment of the nitrogen‐fixing symbiosis between soybean and Bradyrhizobium japonicum is a complex process. To document the changes in plant metabolism as a result of symbiosis, we utilized laser ablation electrospray ionization‐mass spectrometry (LAESI‐MS) for in situ metabolic profiling of wild‐type nodules, nodules infected with a B. japonicum nifH mutant unable to fix nitrogen, nodules doubly infected by both strains, and nodules formed on plants mutated in the stearoyl‐acyl carrier protein desaturase (sacpd‐c) gene, which were previously shown to have an altered nodule ultrastructure. The results showed that the relative abundance of fatty acids, purines, and lipids was significantly changed in response to the symbiosis. The nifH mutant nodules had elevated levels of jasmonic acid, correlating with signs of nitrogen deprivation. Nodules resulting from the mixed inoculant displayed similar, overlapping metabolic distributions within the sectors of effective (fix⁺) and ineffective (nifH mutant, fix^?) endosymbionts. These data are inconsistent with the notion that plant sanctioning is cell autonomous. Nodules lacking sacpd‐c displayed an elevation of soyasaponins and organic acids in the central necrotic regions. The present study demonstrates the utility of LAESI‐MS for high‐throughput screening of plant phenotypes. Overall, nodules disrupted in the symbiosis were elevated in metabolites related to plant defense.     

POST-FIRE REGENERATION OF SOUTHERN CALIFORNIA CHAPARRAL

Succession of chaparral shrubs was studied for the first 4 years after fire on the four major slope faces at three elevations in southern California. Although total cover fluctuated from year to year, shrub cover increased annually through the third year. There was little or no increase in shrub cover between the third and fourth years. Four years after fire the shrubs covered 55% ground surface at the highest elevation site but only 28% at the lowest elevation site. Shrub cover was similar between slope faces with one exception; at the lowest elevation site shrub cover was twice as great on the north and east-facing slopes as on the south and west-facing slopes. Post-fire recovery of shrubs was by seedlings and/or resprouts. Yucca whipplei was an exception in that it did not resprout once the aboveground parts were killed nor did seedlings establish after fire, however the aboveground parts of many Y. whipplei survived the fire. Species which reproduced entirely by seed did so in the first post-fire year from soil-stored seed with the exception of Ceanothus greggii at the highest elevation site. This species was entirely absent the first year after fire but abundant in the second year. Species producing both resprouts and seedlings varied from site to site in the proportion of resprouts:seedlings. Between 83–100% of the post-fire populations of Cercocarpus betuloides, Arctostaphylos glandulosa, and Xylococcus bicolor were resprouts whereas 12–13% of Ceanothus tomentosus were resprouts. For Adenostoma fasciculatum, resprouts constituted 27–54% of the population at the lowest elevation and 65–94% at the highest elevation; whereas, the Quercus dumosa population was 100% resprouts at the lowest elevation and 31–67% resprouts at the highest elevation. Data are presented on the height of resprouts and seedlings for all species at the end of the first post-fire year.     

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate that the method provides a significant improvement in sensitivity compared to previous cloning methods while maintaining reproducible identification of diverse small RNA species. This method should have widespread applications in a variety of contexts, including biomarker discovery from scarce samples of human tissue or body fluids.     

Mutagenicity tests of diflubenzuron in the micronucleus test in mice, the L5178Y mouse lymphoma forward mutation assay, and the Ames Salmonella reverse mutation test.

Diflubenzuron, one of a new class of pesticides believed to act via inhibition of chitin synthesis in the developing insect cuticle, was tested for possible mutagenic activity using the micronucleus test in mice, the L5178Y mouse lymphoma forward mutation test at the thymidine kinase locus, and the Ames Salmonella/microsome reverse mutation test. No mutagenic effect was found.     

The role of breast milk in protecting urban Peruvian children against cryptosporidiosis.

To test the hypothesis that breast milk of nursing mothers may afford children protection against cryptosporidiosis, a prospective cohort study was carried out in the young peoples' community of San Juan de Miraflores near Lima, Peru. Mothers and newborn children were sorted into cohort groups based on the mothers' breast milk antibody response to Cryptosporidium sporozoites using an antibody-capture enzyme-linked immunosorbent assay to detect parasite-specific immunoglobulin A. Children were monitored for Cryptosporidium infection using an indirect immunofluorescence assay. Of 211 mothers enrolled in the study, 39 (18.5%) had high breast milk antibody titers, 107 (50.7%) had medium titers, and 65 (30.8%) had low titers. Sixty-one episodes of Cryptosporidium infection were detected in 50 children of these mothers. Eleven (22%) had mothers in the high antibody titer group, 20 (40%) had mothers in the medium titer group, and 19 (38%) had mothers in the low titer group. The prevalence of infection within children of each group was 0.17, 0.19 and 0.38 respectively. There was no significant difference in the prevalence or duration of infection among children of the different groups. The data does not support the notion that there is protection from Cryptosporidium infection afforded children whose mothers have demonstrable breast milk antibodies against the parasite.