Explore the vast range of titles available.

The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species–population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units‐Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio‐Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. FST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater‐fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes. The tips in the tree of life serve as foci for conservation and management, yet clear conservation unit delimitations are masked by inherent variance at the species‐population interface, and modern genomic applications can be difficult to parse for this purpose. Here, we present a study that provides a framework for parsing these data using speckled dace (Cyprinidae: Rhinichthys osculus), an endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem (DVE). Our study offers three salient conclusions: a blueprint for a multi‐faceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered DVE fishes.

The Amargosa vole is a highly endangered rodent endemic to a small stretch of the Amargosa River basin in Inyo County, California. It specializes on a single, nutritionally marginal food source in nature. As part of a conservation effort to preserve the species, a captive breeding population was established to serve as an insurance colony and a source of individuals to release into the wild as restored habitat becomes available. The colony has successfully been maintained on commercial diets for multiple generations, but there are concerns that colony animals could lose gut microbes necessary to digest a wild diet. We analyzed feces from colony-reared and recently captured wild-born voles on various diets, and foregut contents from colony and wild voles. Unexpectedly, fecal microbial composition did not greatly differ despite drastically different diets and differences observed were mostly in low-abundance microbes. In contrast, colony vole foregut microbiomes were dominated by Allobaculum sp. while wild foreguts were dominated by Lactobacillus sp. If these bacterial community differences result in beneficial functional differences in digestion, then captive-reared Amargosa voles should be prepared prior to release into the wild to minimize or eliminate those differences to maximize their chance of success.

Causes of morbidity and mortality and a survey of infectious disease agents were collated from wild and colony-raised endangered Amargosa voles (Microtus californicus scirpensis). Six voles from the wild and 295 voles in the captive-breeding colony were included in the study upon identification of an infectious agent during screening, identification of clinical signs of disease, or finding a pathological condition or infectious agent on necropsy. Findings included 28 significant or incidental pathological conditions of seven organ systems and 19 parasitic, viral, bacterial, or fungal agents. Several voles captured in the wild had fungal osteomyelitis of the tail that disseminated systemically in a vole brought from the wild to the colony and may have been caused by a Penicillium sp. Three voles reintroduced from the colony to the wild experienced inanition and subsequent severe hepatic and moderate renal tubular lipidosis. The most common significant pathological conditions in colony-reared voles were chronic interstitial nephritis with proteinosis; cardiomyopathy; trichobezoars that, in intestines or cecocolic junctions, sometimes induced local rupture or infarction with peritonitis; multifocal gastrointestinal ulceration and colibacillosis; acute renal tubular necrosis or nephritis; sepsis; hepatic and renal lipidosis; molar apical elongation sometimes progressing to invasion of the calvarium; and mammary tumors. Uncommon diagnoses included intervertebral disc disease; microvascular dysplasia; and multifocal bacterial abscessation. Common or clinically important infectious agents included Demodex sp. mites in hair follicles, Demodex sp. in esophageal mucosa, and an outbreak of tropical rat mites thought to have been introduced via the straw bedding; gastrointestinal Helicobacter sp.; attaching and effacing Escherichia coli; and Citrobacter braakii, a possible zoonotic bacterium. This survey of species-specific diseases and pathogens was possible because the established health surveillance program that is part of the species recovery plan allowed for monitoring of voles throughout the duration of their natural life spans in captivity.

Staff at a university laboratory responsible for management of a captive insurance colony of endangered Amargosa voles (Microtus californicus scirpensis) discovered an outbreak of tropical rat mites (Ornithonyssus bacoti) infesting 106 voles. This bloodsucking mesostigmatid mite typically occurs in laboratory settings and can cause weight loss, wounds, or other negative impacts on health. The source of the infestation was likely feral rodents, and the route was suspected to be straw bedding. Twenty-nine of the 106 (27.4%) infested voles developed ulcerated dorsal skin lesions that resolved when treated with topical selamectin. A triad approach was implemented to eradicate the mites, consisting of environmental management, individual animal treatment, and training. Voles were moved individually into a clean room containing only autoclaved materials (including straw), cages were treated with permethrin-impregnated cotton, treatment order was instituted to avoid transferring mites, and voles coming from outside were quarantined. All animals in an infested room were treated with topical selamectin, and personnel were trained on risks and new procedures. No adverse effects from the use of selamectin were identified, and this efficient protocol does not require the long-term use of acaricides. This report documents infestation of an endangered rodent with an exotic parasite, safe use of permethrin and selamectin in this species, and comprehensive management to manage a large infestation.

Estimation of groundwater flowpaths and effective recharge was performed in the vicinity of Amargosa Desert, Nevada, USA, using multivariate statistical methods (MSMs) and a simple elevation-dependent chloride mass-balance method modified by estimating a minimum effective recharge elevation (MERE). MSMs were applied to major ion data to explain the relationships among different groundwater chemical species, define hydrochemical facies needed to determine groundwater flowpaths and evolution, and identify the influence of surface and geologic features on groundwater. For each defined watershed, an average groundwater chloride concentration is used and the chloride deposition rate is assessed in the subject watersheds over all land elevations above the estimated MERE by assuming two constant spatial and temporal concentrations of chloride in precipitation which is a function of elevation. The MERE for the Amargosa Desert was appraised as 1200 m above mean sea level (m-amsl), based upon the elevation of the orifice of Cane Spring (1237 m-amsl), one of the lowest elevation, permanent springs, on the Nevada National Security Site. This minimum elevation is the cutoff altitude for our calculations at which precipitation is considered to make a significant contribution to recharge. Elevation-dependent precipitation was evaluated relating elevation data from the online mapping software ACME Labs Mapper 2.1 and precipitation data from the PRISM Climate Group’s PRISM. These analyses provide further insight into the hydrology of the region and demonstrate the strong impact surface and geologic features can have on surface water infiltration and groundwater in arid regions. Specifically, evidence is presented of past focused recharge around the ephemeral Fortymile Wash and interaction between geologic faults and groundwater infiltration and flowpaths. In addition, groundwater flow, based upon water chemistry, appears to be segmented by major faults. Groundwater recharge in the vicinity of the Amargosa Desert has been estimated around 15,280 acre-ft/year.

Rare plants are often associated with distinctive soil types, and understanding why endemic species occur in unique environments is fundamental for their management. At Ash Meadows National Wildlife Refuge in southern Nevada, USA, we evaluated whether the limited distribution of endangered Amargosa niterwort (Nitrophila mohavensis) is explained by this species' tolerance of saline soils on salt-encrusted mud flats compared with the broadly distributed desert saltgrass (Distichlis spicata var. stricta). We simultaneously explored whether niterwort distribution is restricted from expanding due to interspecific competition with saltgrass. Surface soils collected throughout niterwort's range were unexpectedly less saline with lower extractable Na, seasonal electroconductivity, and Na absorption ratio, and higher soil moisture than in adjacent saltgrass or mixed shrub habitats. Comparison of niterwort and saltgrass growth along an experimental salinity gradient in a greenhouse demonstrated lower growth of niterwort at all but the highest NaCl concentrations. Although growth of niterwort ramets was similar when transplanted into both habitats at the refuge below Crystal Reservoir, niterwort reproductive effort was considerably higher in saltgrass compared to its own habitat, implying reallocation of resources to sexual reproduction to maximize fitness when the probability of ramet mortality increases with greater salinity stress. Saltgrass was not a demonstrated direct competitor of niterwort; however, this species is known to increase soil salinity by exuding salt ions and through litterfall. Niterwort conservation will benefit from protecting hydrological processes that reduce salinity stress and preventing saltgrass colonization into niterwort habitat.

Recent population expansion throughout the Southwest United States has created an unprecedented demand for already limited water resources, which may have severe consequences on the persistence of some species. Two such species are the federally protected Nitrophila mohavensis (Chenopodiaceae) and Grindelia fraxino-pratensis (Asteraceae) found in Amargosa Valley, one valley east of Death Valley, California. Because both species are federally protected, no plant material could be harvested for analysis. We therefore used a chamber system to collect transpired water for isotopic analysis. After a correction for isotopic enrichment during transpiration, δ¹⁸O values of plant xylem water were significantly different between N. mohavensis and G. fraxino-pratensis throughout the study. Using a multisource mixing model, we found that both N. mohavensis and G. fraxino-pratensis used soil moisture near the soil surface in early spring when surface water was present. However, during the dry summer months, G. fraxino-pratensis tracked soil moisture to deeper depths, whereas N. mohavensis continued to use soil moisture near the soil surface. These results indicate that pumping groundwater and subsequently lowering the water table may directly prevent G. fraxino-pratensis from accessing water, whereas these same conditions may indirectly affect N. mohavensis by reducing surface soil moisture and thus its ability to access water.

Microtus californicus scirpensis is an endangered, isolated subspecies of California vole. It requires water pools and riparian bulrush (Schoenoplectus americanus) and occupies some of the rarest habitat of any North American mammal. The minimally vegetated, extremely arid desert surrounding the pools is essentially uninhabitable for Ixodes species ticks. We describe an enzootic cycle of Borrelia carolinensis in Ixodes minor ticks at a site 3500 km distant from the region in which I. minor is known to occur in Tecopa Host Springs, Inyo County, eastern Mojave Desert, California. Voles were live‐trapped, and ticks and blood samples queried by PCR and DNA sequencing for identification and determination of the presence of Borrelia spp. Between 2011–2013, we found 21 Ixodes minor ticks (prevalence 4–8%) on Amargosa voles and Reithrodontomys megalotis. DNA sequencing of 16S rRNA from ticks yielded 99% identity to I. minor. There was 92% identity with I. minor in the calreticulin gene fragment. Three ticks (23.1%), 15 (24%) voles, three (27%) house mice, and one (7%) harvest mice were PCR positive for Borrelia spp. Sequencing of the 5S‐23S intergenic spacer region and flagellin gene assigned Amargosa vole Borrelia strains to B. carolinensis. Ixodes minor, first described in 1902 from a single Guatemalan record, reportedly occurs only in the southeast American on small mammals and birds. The source of this tick in the Mojave Desert and time scale for introduction is not known but likely via migratory birds. Borrelia strains in the Amargosa ecosystem most closely resemble B. carolinensis. B. carolinensis occurs in a rodent‐I. minor enzootic cycle in the southeast U.S. although its epidemiological significance for people or rodents is unknown. The presence of a tick and Borrelia spp. only known from southeast U.S. in this extremely isolated habitat on the other side of the continent is of serious concern because it suggests that the animals in the ecosystem could be vulnerable to further incursions of pathogens and parasites. The Amargosa vole is an endangered, extremely isolated rodent found only in small marsh patches in the Amargosa River drainage in the Mojave Desert. We describe an enzootic cycle of the bacterium Borrelia carolinensis in Ixodes minor ticks at a site 3500 km distant from the American southeast where I. minor is known to occur. Photo by Judy Palmer.

Nitrophila mohavensis , commonly known as Amargosa niterwort, is a perennial forb classified in the family Chenopodiaceae. The species is restricted to moist alkaline soils of the Ash Meadows National Wildlife Refuge and nearby localities within the Amargosa River basin and is currently listed as endangered. We isolated several polymorphic microsatellite loci and characterized genotypes from individuals spanning the range of the species as a means of inferring reproductive mode and population structure for the species. Out of 178 plants sampled from 35 different sample sites, there were 78 different multilocus genotypes. Most individuals had unique genotypes; however, there were many genotypes that were found in more than one individual and the most common genotype was sampled from 13 individuals. In addition, three genotypes were sampled from individuals across the range of the species, a maximum distance of more than 50 km. The results suggest that N. mohavensis reproduces clonally and by outcrossing. The relative frequency of the two reproductive strategies appears to vary among localities. There is not strong genetic differentiation among geographically separated clusters of plants. While the species is locally abundant and does not appear to suffer from inbreeding due to a small number of genets, continued local groundwater extraction coupled with forecasts of increasing regional desiccation due to accelerated climate change may combine to cause future population declines of N. mohavensis across its range.

The procedures used for bauxite resource estimation are summarised using examples from Australia, Africa, South America and Asia. In the all studied cases the bauxite resources were estimated by drilling and sampling drill holes at 0.25–0.5 m intervals. Short sampling intervals are necessary for accurate estimation of the mineralisation contacts. Samples of the non-consolidated bauxites usually beneficiated by sieving and removing the barren fine grained material prior to chemical assays. Consolidated bauxites are not beneficiated and processed in a conventional manner. Bauxites density is preferably measured using the sand replacement method which is a formally certified technique for measuring bauxite density at the Australian deposits. Bauxites grade is estimated using conventional geostatistical techniques, which are commonly applied after geometry of the bauxite seam is flattened using ‘equal thickness unfolding’ method, or, in some cases, using ‘top flattening’ approach. Conversion resources to the ore reserves requires the following mining and processing conditions to be taken into considerations:Haulage distance;A vertical mining selectivity of 0.25–0.5 m;Pre-production infill drilling is usually used for grade control purposes;Grindability of the bauxites and quantification of the Bond Work Index;Optimal mesh size for bauxite beneficiation;Detailed chemical and mineralogical characterisation of the crude bauxite, including deleterious components, in particular iron and silica;Characterisation of the pre-desilication behaviour of the bauxite;Characterisation of the alumina extraction;The refinery parameters, including recovered alumina, refinery caustic consumption and red mud loading; Presence of the organic carbon, oxalate formation rate and carbonate formation rate;The mud settling rate, mud compaction and overflow clarity.