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The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California's coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae., (Published by Oxford University Press on behalf of The American Genetic Association 2022.)

Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.)

Most Americans receive their drinking water from publicly supplied sources, a large portion of it from groundwater. Mapping these populations consistently and at a high resolution is important for understanding where the resource is used and needs to be protected. The results show that 269 million people are supplied by public supply, 107 million are supplied by groundwater and 162 million are supplied by surface water. The population using public supply drinking water was mapped in two ways: the census enhanced method (CEM) evenly distributes the population across populated census blocks, and the urban land-use enhanced method (ULUEM) distributes the population only to certain urban land use designations. In addition, a two-dimensional polygon dataset was created for the conterminous U.S. that identifies 177 unique Hydrogeologic Mapping Units (HMUs) with similar hydrogeologic characteristics. The HMUs do not overlap, but they can delineate areas where stacked hydrogeologic regions (HRs) contribute drinking water from below the surface. HRs are waterbearing geologic regions identified as either a principal aquifers (PA) or secondary hydrogeologic regions (SHR). Within each HMU, the wells were used to determine the proportion of each HR that is providing groundwater to the HMU. In 63% of the HMUs, a single HR is providing water to the public supply wells located within it, while the rest of the HMUs show that the wells are tapping up to a maximum of four stacked HRs. In total, groundwater from 108 HRs provide drinking water for public supply, six of which provide more than 50% of the groundwater used for public supply drinking water. The aquifer serving the largest number of equivalent people (>17 million) is the glacial aquifer. The HR providing the greatest number of people per km 2 is the Biscayne aquifer in Florida at nearly 453 people per km 2 ., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier B.V.)

Domestic wells provide drinking water supply for approximately 40 million people in the United States. Knowing the location of these wells, and the populations they serve, is important for identifying heavily used aquifers, locations susceptible to contamination, and populations potentially impacted by poor-quality groundwater. The 1990 census was the last nationally consistent survey of a home's source of water, and has not been surveyed since. This paper presents a method for projecting the population dependent on domestic wells for years after 1990, using information from the 1990 census along with population data from subsequent censuses. The method is based on the "domestic ratio" at the census block-group level, defined here as the number of households dependent on domestic wells divided by the total population. Analysis of 1990 data (>220,000 block-groups) indicates that the domestic ratio is a function of the household density. As household density increases, the domestic ratio decreases, once a household density threshold is met. The 1990 data were used to develop a relationship between household density and the domestic ratio. The fitted model, along with household density data from 2000 and 2010, was used to estimate domestic ratios for each decadal year. In turn, the number of households dependent on domestic wells was estimated at the block-group level for 2000 and 2010. High-resolution census-block population data were used to refine the spatial distribution of domestic-well usage and to convert the data into population numbers. The results are presented in two downloadable raster datasets for each decadal year. It is estimated that the total population using domestic-well water in the contiguous U.S. increased 1.5% from 1990 to 2000 to a total of 37.25 million people and increased slightly from 2000 to 2010 to 37.29 million people., (Published by Elsevier B.V.)

The U.S. Geological Survey (USGS) previously identified and mapped 62 Principal Aquifers (PAs) in the U.S., with 57 located in the conterminous states. Areas outside of PAs, which account for about 40% of the conterminous U.S., were collectively identified as "other rocks." This paper, for the first time, subdivides this large area into internally-consistent features, defined here as Secondary Hydrogeologic Regions (SHRs). SHRs are areas of other rock within which the rocks or deposits are of comparable age, lithology, geologic or physiographic setting, and relationship to the presence or absence of underling PAs or overlying glacial deposits. A total of 69 SHRs were identified. The number and size of SHRs identified in this paper are comparable to the number and size of PAs previously identified by the USGS. From a two-dimensional perspective, SHRs are complementary to PAs, mapped only where the PAs were not identified on the USGS PA map and not mapped where the PAs were identified. SHRs generally consist of low permeability rocks or deposits, but can include locally productive aquifers. The two maps, taken together, provide a comprehensive, national-scale hydrogeologic framework for assessing and understanding groundwater systems., (Published 2018. This article is a U.S. Government work and is in the public domain in the USA. Groundwater published by Wiley Periodicals, Inc. on behalf ofNational Ground Water Association.)

Argon-39 can be used as a tracer for age-dating glaciers, oceans, and more recently, groundwater. With a half-life of 269 years, 39 Ar fills an intermediate age range gap (50-1,000 years) not currently covered by other common groundwater tracers. Therefore, adding this tracer to the data suite for groundwater studies provides an important tool for improving our understanding of groundwater systems. We present the methods employed for arriving at an age-date for a given sample of argon degassed from groundwater., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of the Uma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence/single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM>1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata×cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by-product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size-divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype-environment associations that further support the case for ecological speciation in these lizards.

Geochemical evaluation of the sources and movement of saline groundwater in coastal aquifers can aid in the initial mapping of the subsurface when geological information is unavailable. Chloride concentrations of groundwater in a coastal aquifer near San Diego, California, range from about 57 to 39,400 mg/L. On the basis of relative proportions of major-ions, the chemical composition is classified as Na-Ca-Cl-SO4, Na-Cl, or Na-Ca-Cl type water. δ(2)H and δ(18)O values range from -47.7‰ to -12.8‰ and from -7.0‰ to -1.2‰, respectively. The isotopically depleted groundwater occurs in the deeper part of the coastal aquifer, and the isotopically enriched groundwater occurs in zones of sea water intrusion. (87)Sr/(86)Sr ratios range from about 0.7050 to 0.7090, and differ between shallower and deeper flow paths in the coastal aquifer. (3)H and (14)C analyses indicate that most of the groundwater was recharged many thousands of years ago. The analysis of multiple chemical and isotopic tracers indicates that the sources and movement of saline groundwater in the San Diego coastal aquifer are dominated by: (1) recharge of local precipitation in relatively shallow parts of the flow system; (2) regional flow of recharge of higher-elevation precipitation along deep flow paths that freshen a previously saline aquifer; and (3) intrusion of sea water that entered the aquifer primarily during premodern times. Two northwest-to-southeast trending sections show the spatial distribution of the different geochemical groups and suggest the subsurface in the coastal aquifer can be separated into two predominant hydrostratigraphic layers., (© 2013, National Ground Water Association.)

Hi-Desert Water District (HDWD), the primary water-management agency in the Warren Groundwater Basin, California, plans to construct a waste water treatment plant to reduce future septic-tank effluent from reaching the groundwater system. The treated waste water will be reclaimed by recharging the groundwater basin via recharge ponds as part of a larger conjunctive-use strategy. HDWD wishes to identify the least-cost conjunctive-use strategies for managing imported surface water, reclaimed water, and local groundwater. As formulated, the mixed-integer nonlinear programming (MINLP) groundwater-management problem seeks to minimize water-delivery costs subject to constraints including potential locations of the new pumping wells, California State regulations, groundwater-level constraints, water-supply demand, available imported water, and pump/recharge capacities. In this study, a hybrid-optimization algorithm, which couples a genetic algorithm and successive-linear programming, is developed to solve the MINLP problem. The algorithm was tested by comparing results to the enumerative solution for a simplified version of the HDWD groundwater-management problem. The results indicate that the hybrid-optimization algorithm can identify the global optimum. The hybrid-optimization algorithm is then applied to solve a complex groundwater-management problem. Sensitivity analyses were also performed to assess the impact of varying the new recharge pond orientation, varying the mixing ratio of reclaimed water and pumped water, and varying the amount of imported water available. The developed conjunctive management model can provide HDWD water managers with information that will improve their ability to manage their surface water, reclaimed water, and groundwater resources., (Ground Water © 2011, National Ground Water Association. This article is a U.S. Government work and is in the public domain in the USA.)

The extension of MODFLOW onto the landscape with the Farm Process (MF-FMP) facilitates fully coupled simulation of the use and movement of water from precipitation, streamflow and runoff, groundwater flow, and consumption by natural and agricultural vegetation throughout the hydrologic system at all times. This allows for more complete analysis of conjunctive use water-resource systems than previously possible with MODFLOW by combining relevant aspects of the landscape with the groundwater and surface water components. This analysis is accomplished using distributed cell-by-cell supply-constrained and demand-driven components across the landscape within "water-balance subregions" comprised of one or more model cells that can represent a single farm, a group of farms, or other hydrologic or geopolitical entities. Simulation of micro-agriculture in the Pajaro Valley and macro-agriculture in the Central Valley are used to demonstrate the utility of MF-FMP. For Pajaro Valley, the simulation of an aquifer storage and recovery system and related coastal water distribution system to supplant coastal pumpage was analyzed subject to climate variations and additional supplemental sources such as local runoff. For the Central Valley, analysis of conjunctive use from different hydrologic settings of northern and southern subregions shows how and when precipitation, surface water, and groundwater are important to conjunctive use. The examples show that through MF-FMP's ability to simulate natural and anthropogenic components of the hydrologic cycle, the distribution and dynamics of supply and demand can be analyzed, understood, and managed. This analysis of conjunctive use would be difficult without embedding them in the simulation and are difficult to estimate a priori.

Recently, there have been several suggestions that Goldmann applanation tonometry can be performed without fluorescein. In order to determine the clinical efficacy of performing Goldmann applanation tonometry without fluorescein, 100 consecutive patients had applanation tonometry performed without fluorescein (Ophthetic only) and with fluorescein (Fluress), according to a predetermined randomization schedule. It was found that the average difference between readings with fluorescein and without fluorescein was 7.01 mm Hg. Tonometry readings without fluorescein were lower than readings with fluorescein. In addition, regression analysis indicated that the differences between the readings with and without fluorescein increased as intraocular pressure increased. By not utilizing fluorescein in Goldmann applanation tonometry, the clinician will record lower readings. In addition, greater errors in measurement occur with increasing intraocular pressures. Because eyes with higher intraocular pressures are at a greater risk to develop glaucomatous optic atrophy and loss of visual field, the merits of Goldmann applanation tonometry without fluorescein are speculative.