Influences of in-stream habitat and upstream land-use on site occupancy of the Kanawha darter (Etheostoma kanawhae): A narrowly distributed species from the New River (Upper Kanawha Basin)

1. Freshwater communities are threatened by the conversion of natural landscapes for urban and agricultural purposes. Changes to land use may disrupt stream nutrient and geomorphological processes and reduce water quality, increase sedimentation, and decrease habitat heterogeneity eventually leading to species loss and decreases in ecosystem productivity. Endemic species are frequently at greater risk of habitat-mediated fragmentation and extirpation due to their constrained distributions.
2. The Kanawha darter (Etheostoma kanawhae) is an understudied fish endemic to the New River Drainage in North Carolina and Virginia, USA. To investigate the potential effect(s) of land-use change on Kanawha darters, naïve occupancy was modelled using instream habitat characteristics and upstream forest cover.
3. Generalized linear models revealed that instream habitat and forest cover are reliable predictors of Kanawha darter site occupancy. Specifically, models demonstrated that occupancy increased in reaches with reduced stream width, velocity, and bedrock substrate but higher concentrations of coarse woody material. Kanawha darter occupancy was also positively associated with the extent of forest cover in upstream catchments.
4. Although Kanawha darters are not currently considered imperilled, most populations occurred in isolated reaches separated by large sections of unoccupied habitat. Continuing ex-urban development in riparian zones is likely to be the primary threat to Kanawha darters and other endemic species in this catchment. Resource managers and stakeholders should preserve forest cover in headwaters and occupied tributaries and protect or restore riparian zones along the main-stem South and North Forks of the New River to preserve high-quality habitat and enhance connectivity among isolated Kanawha darter populations.
5. As human populations in montane regions continue to grow, there is a need to understand how land-use change affects endemic freshwater species. This study further supports the importance of retaining forest cover as an effective strategy for protecting and restoring populations of endemic fishes in high-gradient streams.

     

Multi-scale Modeling of Animal Movement and General Behavior Data Using Hidden Markov Models with Hierarchical Structures

Hidden Markov models (HMMs) are commonly used to model animal movement data and infer aspects of animal behavior. An HMM assumes that each data point from a time series of observations stems from one of N possible states. The states are loosely connected to behavioral modes that manifest themselves at the temporal resolution at which observations are made. Due to advances in tag technology and tracking with digital video recordings, data can be collected at increasingly fine temporal resolutions. Yet, inferences at time scales cruder than those at which data are collected and, which correspond to larger-scale behavioral processes, are not yet answered via HMMs. We include additional hierarchical structures to the basic HMM framework, incorporating multiple Markov chains at various time scales. The hierarchically structured HMMs allow for behavioral inferences at multiple time scales and can also serve as a means to avoid coarsening data. Our proposed framework is one of the first that models animal behavior simultaneously at multiple time scales, opening new possibilities in the area of animal movement and behavior modeling. We illustrate the application of hierarchically structured HMMs in two real-data examples: (i) vertical movements of harbor porpoises observed in the field, and (ii) garter snake movement data collected as part of an experimental design. Supplementary materials accompanying this paper appear online.     

The molecular basis for recognition of bacterial ligands at equine TLR2, TLR1 and TLR6

TLR2 recognises bacterial lipopeptides and lipoteichoic acid, and forms heterodimers with TLR1 or TLR6. TLR2 is relatively well characterised in mice and humans, with published crystal structures of human TLR2/1/Pam3CSK4 and murine TLR2/6/Pam2CSK4. Equine TLR4 is activated by a different panel of ligands to human and murine TLR4, but less is known about species differences at TLR2. We therefore cloned equine TLR2, TLR1 and TLR6, which showed over 80% sequence identity with these receptors from other mammals, and performed a structure-function analysis. TLR2/1 and TLR2/6 from both horses and humans dose-dependently responded to lipoteichoic acid from Staphylococcus aureus, with no significant species difference in EC50 at either receptor pair. The EC50 of Pam2CSK4 was the same for equine and human TLR2/6, indicating amino acid differences between the two species’ TLRs do not significantly affect ligand recognition. Species differences were seen between the responses to Pam2CSK4 and Pam3CSK4 at TLR2/1. Human TLR2/1, as expected, responded to Pam3CSK4 with greater potency and efficacy than Pam2CSK4. At equine TLR2/1, however, Pam3CSK4 was less potent than Pam2CSK4, with both ligands having similar efficacies. Molecular modelling indicates that the majority of non-conserved ligand-interacting residues are at the periphery of the TLR2 binding pocket and in the ligand peptide-interacting regions, which may cause subtle effects on ligand positioning. These results suggest that there are potentially important species differences in recognition of lipopeptides by TLR2/1, which may affect how the horse deals with bacterial infections.     

Changes to freshwater mussel assemblages after 25 years of impoundment and river habitat fragmentation

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Effects of small dam condition and drainage on stream fish community structure

Low‐head dams are ubiquitous in eastern North America, and small dam removal projects seek to improve habitat conditions for resident and migratory fishes. Effects of small dams of varying status on local fish communities are poorly documented, and recent work suggests benefits of maintaining fragmentation. We sampled fish at 25 dams (9 breached, 7 relict, 9 intact) in three river basins in North Carolina, USA. Fishes were sampled at three reaches/dam from 2010 to 2011. Study reaches were located upstream (free‐flowing reaches), downstream (tailrace) and >500 m downstream of dams (n = 75 reaches). Analyses revealed significantly elevated fish CPUE, taxa richness and percentage intolerant taxa in intact dam tailraces suggesting small dams may improve conditions for resident taxa. Breached dam tailrace reaches exhibited lower fish CPUE, taxa richness and percentage intolerant taxa relative to upstream reference reaches. Relict dams exhibited no between‐reach differences in fish community metrics. Nonmetric multidimensional scaling revealed drainage‐specific stream fish responses across study drainages. Tar and Roanoke drainage streams with intact and relict dams supported fish assemblages indicative of natural communities, whereas Neuse Drainage streams with intact and breached dams contained disturbed habitats and communities. These data demonstrate fish community responses to dam condition are drainage specific but communities in streams with intact and relict dams are largely similar. Additionally, breached dams may warrant higher removal priorities than intact dams because they negatively influence fish communities. The variability in response to some dams indicates managers, regardless of region or country, should consider holistic approaches to dam removals on a case‐by‐case basis.     

Impact of Fly Ash Amendment and Incorporation Method on Hydraulic Properties of a Sandy Soil

Coal fly ash has physical and chemical characteristics that makeit useful as a soil amendment, one of the more important beingthe potential to permanently improve the soil water relations ofsandy, drought-prone soils. We axemined changes in theinfiltration rate and water holding capacity of a sandy soilafter application of high rates (up to 950 Mg ha^-1) of aClass F fly ash. Fly ash was applied to large field plots byeither conventional tillage (CT; moldboard plow-disk) orintensive tillage (IT; chisel plow-rotovate-disk), and tomicroplots using a rototiller. Infiltration rate (i) wasmeasured in both studies with a disk permeameter on threeoccasions over a 12-month period. Ash effects on gravimetric water content (θ_g) at the 0–40 cm soil depth were measuredduring a 168 hr period following a 2.5 cm rainfall event andwater release curves (33 to 500 kPa) were constructed in thelaboratory using soils from the large plots. In both studiesi was decreased by ～80% one year after additionof fly ash and θ_gin ash-amended soil was higher than unamended soil throughoutthe 168 hr monitoring period. Soil water distribution variedwith tillage; the IT treatment had the highest θ_g increasesin the 0–20 cm depth while the CT treatment had θ_gincreases throughout the 0–40 cm depth. Soil water content anddistribution in ash-amended microplots were similar to ITtreatments. Fly ash amendment not only increased water holdingcapacity but also increased plant available water by 7–13% inthe 100–300 kPa range. These results suggest fly ash amendmentmay have the potential to improve crop production in excessivelydrained soils by decreasing i and increasing the amountof plant available water in the root zone.     

Isotopic trophic guild structure of a diverse subtropical South American fish community

Characterization of food web structure may provide key insights into ecological function, community or population dynamics and evolutionary forces in aquatic ecosystems. We measured stable isotope ratios of 23 fish species from the Rio Cuareim, a fifth‐order tributary of the Rio Uruguay basin, a major drainage of subtropical South America. Our goals were to (i) describe the food web structure, (ii) compare trophic segregation at trophic guild and taxonomic scales and (iii) estimate the relative importance of basal resources supporting fish biomass. Although community‐level isotopic overlap was high, trophic guilds and taxonomic groups can be clearly differentiated using stable isotope ratios. Omnivore and herbivore guilds display a broader δ¹³C range than insectivore or piscivore guilds. The food chain consists of approximately three trophic levels, and most fishes are supported by algal carbon. Understanding food web structure may be important for future conservation programs in subtropical river systems by identifying top predators, taxa that may occupy unique trophic roles and taxa that directly engage basal resources.