Kin grouping is insufficient to explain the inclusive fitness gains of conspecific brood parasitism in the common eider.

Conspecific brood parasitism allows females to exploit other females' nests and enhance their reproductive output. Here, we test a recent theoretical model of how host females gain inclusive fitness from brood parasitism. High levels of relatedness between host and parasitizer can be maintained either by: (a) kin recognizing and parasitizing each other as a form of cooperative breeding or (b) natal philopatry and nest site fidelity facilitating the formation of kin groups, thereby increasing the probability of parasitism between relatives nesting in close proximity. To address these two hypotheses we genotyped feathers and hatch membranes of common eiders (Somateria mollissima) from western Hudson Bay, Canada, using a noninvasive sampling methodology. We found that most instances of brood parasitism do result in inclusive fitness gains. Furthermore, females with failed nests moved an average of 492 m from their previous year's nest site, while successful females only moved an average of 13 m. Therefore, we observed host-parasite relatedness can occur at levels higher than would be expected by chance even in the absence of kin grouping, suggesting that closely related females nesting near one another is not essential to maintain high host-parasitizer relatedness. In addition, kin grouping is only a transient phenomenon that cannot occur every year due to the propensity for females of failed nests to nest farther away from their nest site in subsequent years than females with successful nests, which provides support for kin recognition as a more likely mechanism to maintain high host-parasitizer relatedness over time.

A comparison of drone imagery and ground-based methods for estimating the extent of habitat destruction by lesser snow geese (Anser caerulescens caerulescens) in La Pérouse Bay.

Lesser snow goose (Anser caerulescens caerulescens) populations have dramatically altered vegetation communities through increased foraging pressure. In remote regions, regular habitat assessments are logistically challenging and time consuming. Drones are increasingly being used by ecologists to conduct habitat assessments, but reliance on georeferenced data as ground truth may not always be feasible. We estimated goose habitat degradation using photointerpretation of drone imagery and compared estimates to those made with ground-based linear transects. In July 2016, we surveyed five study plots in La Pérouse Bay, Manitoba, to evaluate the effectiveness of a fixed-wing drone with simple Red Green Blue (RGB) imagery for evaluating habitat degradation by snow geese. Ground-based land cover data was collected and grouped into barren, shrub, or non-shrub categories. We compared estimates between ground-based transects and those made from unsupervised classification of drone imagery collected at altitudes of 75, 100, and 120 m above ground level (ground sampling distances of 2.4, 3.2, and 3.8 cm respectively). We found large time savings during the data collection step of drone surveys, but these savings were ultimately lost during imagery processing. Based on photointerpretation, overall accuracy of drone imagery was generally high (88.8% to 92.0%) and Kappa coefficients were similar to previously published habitat assessments from drone imagery. Mixed model estimates indicated 75m drone imagery overestimated barren (F2,182 = 100.03, P < 0.0001) and shrub classes (F2,182 = 160.16, P < 0.0001) compared to ground estimates. Inconspicuous graminoid and forb species (non-shrubs) were difficult to detect from drone imagery and were underestimated compared to ground-based transects (F2,182 = 843.77, P < 0.0001). Our findings corroborate previous findings, and that simple RGB imagery is useful for evaluating broad scale goose damage, and may play an important role in measuring habitat destruction by geese and other agents of environmental change.

Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing.

High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.

A Stenotrophomonas maltophilia Strain Evades a Major Caenorhabditis elegans Defense Pathway.

Stenotrophomonas maltophilia is a ubiquitous bacterium and an emerging nosocomial pathogen. This bacterium is resistant to many antibiotics, associated with a number of infections, and a significant health risk, especially for immunocompromised patients. Given that Caenorhabditis elegans shares many conserved genetic pathways and pathway components with higher organisms, the study of its interaction with bacterial pathogens has biomedical implications. S. maltophilia has been isolated in association with nematodes from grassland soils, and it is likely that C. elegans encounters this bacterium in nature. We found that a local S. maltophilia isolate, JCMS, is more virulent than the other S. maltophilia isolates (R551-3 and K279a) tested. JCMS virulence correlates with intestinal distension and bacterial accumulation and requires the bacteria to be alive. Many of the conserved innate immune pathways that serve to protect C. elegans from various pathogenic bacteria also play a role in combating S. maltophilia JCMS. However, S. maltophilia JCMS is virulent to normally pathogen-resistant DAF-2/16 insulin-like signaling pathway mutants. Furthermore, several insulin-like signaling effector genes were not significantly differentially expressed between S. maltophilia JCMS and avirulent bacteria (Escherichia coli OP50). Taken together, these findings suggest that S. maltophilia JCMS evades the pathogen resistance conferred by the loss of DAF-2/16 pathway components. In summary, we have discovered a novel host-pathogen interaction between C. elegans and S. maltophilia and established a new animal model with which to study the mode of action of this emerging nosocomial pathogen.

Invertebrates associated with a horizontal-flow, subsurface constructed wetland in a northern climate.

Wetlands function as buffers between terrestrial and aquatic ecosystems, filtering pollutants generated by human activity. Constructed wetlands were developed to mimic the physical and biological filtering functions of natural systems for the treatment of human and animal waste under controlled conditions. Previous studies on the effect of constructed wetlands on native invertebrate populations have concentrated almost exclusively on mosquitoes. Here, we present the first study investigating the relationship between vegetation cover and aeration regime, and the diversity and abundance of nematodes and springtails (Collembola) in a constructed wetland designed to treat dairy farm wastewater in northwestern Vermont. We investigated four treatment cells differing in aeration regime and vegetation cover, but equally overlaid by a layer of compost to provide insulation. Analysis showed that nematodes were most abundant in the nonplanted and nonaerated cells, and that bacterivorous nematodes dominated the community in all cells. Springtails were found to be most numerous in the planted and nonaerated cells. We hypothesize that the vegetation provided differing environmental niches that supported a more diverse system of bacteria and fungi, as well as offering protection from predators and inclement weather. Nematodes were likely imported with the original compost material, while springtails migrated into the cells either via air, water, or direct locomotion.

Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations.

Next-generation sequencing (NGS) technologies provide a rapid means to generate genomic resources for species exhibiting interesting ecological and evolutionary variation but for which such resources are scant or nonexistent. In the current report, we utilize 454 pyrosequencing to obtain transcriptome information for multiple individuals and tissue types from geographically disparate and ecologically differentiated populations of the perennial sunflower species Helianthus maximiliani. A total of 850 275 raw reads were obtained averaging 355 bp in length. Reads were assembled, postprocessing, into 16 681 unique contigs with an N50 of 898 bp and a total length of 13.6 Mb. A majority (67%) of these contigs were annotated based on comparison with the Arabidopsis thaliana genome (TAIR10). Contigs were identified that exhibit high similarity to genes associated with natural variation in flowering time and freezing tolerance in other plant species and will facilitate future studies aimed at elucidating the molecular basis of clinal life history variation and adaptive differentiation in H. maximiliani. Large numbers of gene-associated simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs) also were identified that can be deployed in mapping and population genomic analyses.

Effect of prey richness on a consumer's intrinsic growth rate.

The intrinsic growth rate of non-selective microbivores increases asymptotically with increasing prey biomass, but we do not know how intrinsic growth rate is affected by prey richness. The objective of this experiment was to determine the effect of prey richness on the growth kinetics of nematode predators while grazing on mixed bacterial lawns. We found that the intrinsic growth rate of Caenorhabditis elegans in laboratory culture increased asymptotically with prey richness. The mechanism of this pattern was primarily due to the best available prey species in the mixture: the intrinsic growth rate of the consumer feeding on a mixture of prey was approximately equal to the intrinsic growth rate of the predator when feeding on the single best prey in monoculture. This was analogous to the selection effect observed in biodiversity-ecosystem functioning relationships. Generation time, and not reproductive output, was the life history trait component that was most consistent with the pattern of intrinsic growth rate. Our results suggest that in order to link invertebrate consumers' growth rates to their microbial species composition in the field, it will be necessary to determine the ability of microbivorous invertebrates to selectively forage in natural environments and to better understand the micro-scale distribution of microbial communities in their natural environments.

Several Grassland Soil Nematode Species Are Insensitive to RNA-Mediated Interference.

Phenotypic analysis of defects caused by RNA mediated interference (RNAi) in Caenorhabditis elegans has proven to be a powerful tool for determining gene function. In this study we investigated the effectiveness of RNAi in four non-model grassland soil nematodes, Oscheius sp FVV-2., Rhabditis sp, Mesorhabditis sp., and Acrobeloides sp. In contrast to reference experiments performed using C. elegans and Caenorhabditis briggsae, feeding bacteria expressing dsRNA and injecting dsRNA into the gonad did not produce the expected RNAi knockdown phenotypes in any of the grassland nematodes. Quantitative reverse-transcribed PCR (qRT-PCR) assays did not detect a statistically significant reduction in the mRNA levels of endogenous genes targeted by RNAi in Oscheius sp., and Mesorhabditis sp. From these studies we conclude that due to low effectiveness and inconsistent reproducibility, RNAi knockdown phenotypes in non-Caenorhabditis nematodes should be interpreted cautiously.

Normalization and centering of array-based heterologous genome hybridization based on divergent control probes.

BACKGROUND: Hybridization of heterologous (non-specific) nucleic acids onto arrays designed for model-organisms has been proposed as a viable genomic resource for estimating sequence variation and gene expression in non-model organisms. However, conventional methods of normalization that assume equivalent distributions (such as quantile normalization) are inappropriate when applied to non-specific (heterologous) hybridization. We propose an algorithm for normalizing and centering intensity data from heterologous hybridization that makes no prior assumptions of distribution, reduces the false appearance of homology, and provides a way for researchers to confirm whether heterologous hybridization is suitable. RESULTS: Data are normalized by adjusting for Gibbs free energy binding, and centered by adjusting for the median of a common set of control probes assumed to be equivalently dissimilar for all species. This procedure was compared to existing approaches and found to be as successful as Loess normalization at detecting sequence variations (deletions) and even more successful than quantile normalization at reducing the accumulation of false positive probe matches between two related nematode species, Caenorhabditis elegans and C. briggsae. Despite the improvements, we still found that probe fluorescence intensity was too poorly correlated with sequence similarity to result in reliable detection of matching probe sequence. CONCLUSIONS: Cross-species hybridizations can be a way to adapt genome-enabled tools for closely related non-model organisms, but data must be appropriately normalized and centered in a way that accommodates hybridization of nucleic acids with diverged sequence. For short, 25-mer probes, hybridization intensity alone may be insufficiently correlated with sequence similarity to allow reliable inference of homology at the probe level.

Effects of altered temperature and precipitation on desert protozoa associated with biological soil crusts.

Biological soil crusts are diverse assemblages of bacteria, cyanobacteria, algae, fungi, lichens, and mosses that cover much of arid land soils. The objective of this study was to quantify protozoa associated with biological soil crusts and test the response of protozoa to increased temperature and precipitation as is predicted by some global climate models. Protozoa were more abundant when associated with cyanobacteria/lichen crusts than with cyanobacteria crusts alone. Amoebae, flagellates, and ciliates originating from the Colorado Plateau desert (cool desert, primarily winter precipitation) declined 50-, 10-, and 100-fold, respectively, when moved in field mesocosms to the Chihuahuan Desert (hot desert, primarily summer rain). However, this was not observed in protozoa collected from the Chihuahuan Desert and moved to the Sonoran desert (hot desert, also summer rain, but warmer than Chihuahuan Desert). Protozoa in culture began to encyst at 37 degrees C. Cysts survived the upper end of daily temperatures (37-55 degrees C), and could be stimulated to excyst if temperatures were reduced to 15 degrees C or lower. Results from this study suggest that cool desert protozoa are influenced negatively by increased summer precipitation during excessive summer temperatures, and that desert protozoa may be adapted to a specific desert's temperature and precipitation regime.

Observed differences in life history characteristics of nematodes Aphelenchus and Acrobeloides upon exposure to copper and benzo(a)pyrene.

Maturity index values reflect life history characteristics often inferred by morphology. We tested the hypothesis that Acrobeloides and Aphelenchus are sensitive to chemical pollutants, opposite of what their colonizer-persister (CP) value of 2 suggests. Acrobeloides and Aphelenchus were reared at 19 degrees C and provided diets of Escherichia coli and Rhizoctonia solani, respectively. LC50 values for Aphelenchus exposed to copper or benzo(a)pyrene (BaP) are greater than Acrobeloides. Copper impedes growth of Acrobeloides at 10 microg/g, and results in 100% mortality at 20 microg/g. In contrast, Aphelenchus is more resilient, with no visible impact at 20 microg/g. Acrobeloides and Aphelenchus were sensitive to much lower concentrations of BaP than copper, i.e., 0.5 microg/g inhibited development of Acrobeloides and 2 microg/g for Aphelenchus. Egg size and hatch were unaffected at 15 microg/g copper. In contrast, 0.5 microg/g BaP reduced both egg size and hatch for Aphelenchus but not Acrobeloides. Survival of Acrobeloides and reproduction of Aphelenchus responded differently to copper and BaP, implying the relationship between this classification and their sensitivity to short-term effects may be less straightforward than presumed. Refinement of index values based on empirical evidence can be used to improve sensitivity and interpretation of nematode community indices for environmental monitoring.