Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard.

A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.

Seizing the moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy.

Conservation science and environmental regulation are sibling constructs of the latter half of the 20th century, part of a more general awakening to humanity's effect on the natural world in the wake of 2 world wars. Efforts to understand the evolution of biodiversity using the models of population genetics and the data derived from DNA sequencing, paired with legal and political mandates to protect biodiversity through novel laws, regulations, and conventions arose concurrently. The extremely rapid rate of development of new molecular tools to document and compare genetic identities, and the global goal of prioritizing species and habitats for protection are separate enterprises that have benefited from each other, ultimately leading to improved outcomes for each. In this article, we explore how the California Conservation Genomics Project has, and should, contribute to ongoing and future conservation implementation, and how it serves as a model for other geopolitical regions and taxon-oriented conservation efforts. One of our primary conclusions is that conservation genomics can now be applied, at scale, to inform decision-makers and identify regions and their contained species that are most resilient, and most in need of conservation interventions.

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern.

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.

Mass Transfer in Boronate Ester 2D COF Single Crystals.

Unlike graphene and similar structures, 2D covalent organic frameworks (2D COFs) exhibit intrinsic porosity with a high areal density of well-defined and uniform openings. Given the pore size adjustability, 2D COFs are likely to outperform artificially perforated inorganic layers with respect to their prospects in membrane separation. Yet, exploring the mass transport in 2D COFs is hidden by the lack of laterally extended free-standing membranes. This work reports on direct molecular permeation measurements with single crystals of an interfacially synthesized boronate ester 2D COF. In accordance with the material topography, the atmospheric and noble gases readily pass the suspended nanosheets while their areal porosity is quantified to be almost 40% exceeding that in any 2D membranes known. However, bulkier aromatic hydrocarbons are found to deviate substantially from Graham's law of diffusion. Counterintuitively, the permeation rate is demonstrated to rise from benzene to toluene and further to xylene despite the increase in the molecular mass and dimensions. The results are interpreted in terms of adsorption-mediated flow that appears to be an important transport mechanism for microporous planar nanomaterials.

Protein Nanopore Membranes Prepared by a Simple Langmuir-Schaefer Approach.

Filtration through membranes with nanopores is typically associated with high transmembrane pressures and high energy consumption. This problem can be addressed by reducing the respective membrane thickness. Here, a simple procedure is described to prepare ultrathin membranes based on protein nanopores, which exhibit excellent water permeance, two orders of magnitude superior to comparable, industrially applied membranes. Furthermore, incorporation of either closed or open protein nanopores allows tailoring the membrane's ion permeability. To form such membranes, the transmembrane protein ferric hydroxamate uptake protein component A (FhuA) or its open-pore variant are assembled at the air-water interface of a Langmuir trough, compressed to a dense film, crosslinked by glutaraldehyde, and transferred to various support materials. This approach allows to prepare monolayer or multilayer membranes with a very high density of protein nanopores. Freestanding membranes covering holes up to 5 µm in diameter are visualized by atomic force microscopy (AFM), helium ion microscopy, and transmission electron microscopy. AFM PeakForce quantitative nanomechanical property mapping (PeakForce QNM)  demonstrates remarkable mechanical stability and elastic properties of freestanding monolayer membranes with a thickness of only 5 nm. The new protein membrane can pave the way to energy-efficient nanofiltration.

Carbon Nanomembranes from Aromatic Carboxylate Precursors.

Self-assembled monolayers (SAMs) serve as convenient platform for fabricating carbon nanomembranes (CNMs) of extended lateral dimensions. Highly porous CNMs are emerging as interesting materials for membrane technologies as they exhibit selectivity for water permeation and, owing to their reduced dimensionality, promise increased energy efficiency compared to established systems. In the present study terphenylcarboxylate SAMs, prepared on silver underpotential deposited on Au and irradiated by 100 eV electrons, were successfully converted into free-standing CNMs. Infrared and X-ray photoelectron spectroscopy reveal pronounced chemical changes both of the anchoring carboxylate moiety and the aromatic backbone upon electron irradiation. Permeation studies showed high specificity for water as demonstrated by the separation from tetrahydrofuran. Compared to thiols on gold, the standard CNM precursor system, the carboxylic acid based SAM exhibits equivalent characteristics. This suggests that electron-induced carbonization is insensitive to the particular choice of the anchor moiety and, therefore, the choice of precursor molecules can be extended to the versatile class of aromatic carboxylic acids.

In the surf zone: Reproductive strategy of the calico surfperch (Amphistichus koelzi) in a comparative context.

We examined the reproductive life history of calico surfperch (Amphistichus koelzi), including mating season, pregnancy, gestation and multiple paternity utilizing restriction site-associated DNA sequencing. Furthermore, we compared the mating season of calico with barred (Amphistichus argenteus), walleye (Hyperprosopon argenteum) and silver (Hyperprosopon ellipticum) surfperches to determine if the timing of reproduction is divergent within and between the genera. In calico surfperch, the mating season occurs from October to November, and females gestate from December to May. All broods exhibit multiple paternity with a range of four to seven sires per brood. The mating season of calico overlaps completely with barred surfperch; however, barred surfperches have a protracted mating season which extends until the beginning of December, which may be due to differences in reproductive strategy such as size at first reproduction. In the genus, the Hyperprosopon mating season begins earlier than Amphistichus, with divergence in the onset of mating between Hyperprosopon congeners of approximately 1 month.

Use of stochastic patch occupancy models in the California red-legged frog for Bayesian inference regarding past events and future persistence.

Assessing causes of population decline is critically important to management of threatened species. Stochastic patch occupancy models (SPOMs) are popular tools for examining spatial and temporal dynamics of populations when presence-absence data in multiple habitat patches are available. We developed a Bayesian Markov chain method that extends existing SPOMs by focusing on past environmental changes that may have altered occupancy patterns prior to the beginning of data collection. Using occupancy data from 3 creeks, we applied the method to assess 2 hypothesized causes of population decline-in situ die-off and residual impact of past source population loss-in the California red-legged frog. Despite having no data for the 20-30 years between the hypothetical event leading to population decline and the first data collected, we were able to discriminate among hypotheses, finding evidence that in situ die-off increased in 2 of the creeks. Although the creeks had comparable numbers of occupied segments, owing to different extinction-colonization dynamics, our model predicted an 8-fold difference in persistence probabilities of their populations to 2030. Adding a source population led to a greater predicted persistence probability than did decreasing the in situ die-off, emphasizing that reversing the deleterious impacts of a disturbance may not be the most efficient management strategy. We expect our method will be useful for studying dynamics and evaluating management strategies of many species.

Uso de Modelos Estocásticos de Ocupación de Fragmentos de la Rana Californiana de Patas Rojas para la Inferencia Bayesiana con Respecto a Eventos Pasados y su Persistencia en el Futuro Resumen La evaluación de las causas de la declinación poblacional es de importancia crítica para el manejo de especies amenazadas. Los modelos estocásticos de ocupación de parches (SPOMs, en inglés) son herramientas populares para examinar las dinámicas espaciales y temporales de las poblaciones cuando están disponibles los datos de presencia-ausencia para múltiples parches de hábitat. Desarrollamos un método bayesiano de cadena de Markov que extiende a los SPOMs existentes al enfocarse en los cambios ambientales pasados que podrían haber alterado los patrones de ocupación previos al inicio de la recolección de datos. Con los datos de ocupación de tres arroyos, aplicamos este método para evaluar dos causas hipotéticas de la declinación poblacional - muerte in situ e impacto residual de causas anteriores de pérdida de una poblacion fuente - de la rana californiana de patas rojas. A pesar de no tener datos para 20 - 30 años entre el evento hipotético que derivó en la declinación poblacional y los primeros datos recolectados, pudimos discriminar entre las hipótesis, encontrando evidencia de que la muerte in situ incrementó en dos de los arroyos. Aunque los arroyos tuvieron un número comparable de segmentos ocupados, debido a diferentes dinámicas de colonización - extinción, nuestro modelo predijo una diferencia ocho veces mayor en las probabilidades de persistencia de las poblaciones hasta el 2030. La suma de una población fuente resultó en una mayor probabilidad de persistencia pronosticada que con la reducción de la muerte in situ, enfatizando que la reversión de los impactos dañinos de una perturbación puede no ser la mejor estrategia de manejo. Esperamos que nuestro método sea útil para el estudio de las dinámicas y para la evaluación de las estrategias de manejo de muchas especies.

Historical Population Size Change and Differentiation of Relict Populations of the Endangered Giant Kangaroo Rat.

From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species' range, including 1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and 2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This keystone species underwent a ~97% range reduction over the past century, resulting in a current range that is highly fragmented, with 2 dominant northern and southern populations occurring 150 km apart. We sequenced >800 bp of mitochondrial DNA and genotyped 17 nuclear microsatellites in >275 D. ingens to assess the evolutionary relationship of these populations as well as the genetic structure within the northern metapopulation. A Bayesian Skyline Plot indicated that the species experienced a demographic expansion toward the end of the Pleistocene, with a recent population decline. Northern and southern D. ingens split 1857-13 443 years ago, prior to the massive conversion of the San Joaquin Valley to irrigated agriculture. We recommend that the northern and southern populations of D. ingens be re-classified as distinct population segments under the United States Endangered Species Act. We also observed population structure and asymmetrical migration within northern D. ingens where the Tumey Hills acted as a source contributing gene flow to all peripheral populations. This emphasized the importance of this location in the conservation of the metapopulation as a whole.

The effect of consumer pressure and abiotic stress on positive plant interactions are mediated by extreme climatic events.

Environmental extremes resulting from a changing climate can have profound implications for plant interactions in desert communities. Positive interactions can buffer plant communities from abiotic stress and consumer pressure caused by climatic extremes, but limited research has explored this empirically. We tested the hypothesis that the mechanism of shrub facilitation on an annual plant community can change with precipitation extremes in deserts. During years of extreme drought and above-average rainfall in a desert, we measured plant interactions and biomass while manipulating a soil moisture gradient and reducing consumer pressure. Shrubs facilitated the annual plant community at all levels of soil moisture through reductions in microclimatic stress in both years and herbivore protection in the wet year only. Shrub facilitation and the high rainfall year contributed to the dominance of a competitive annual species in the plant community. Precipitation patterns in deserts determine the magnitude and type of facilitation mechanisms. Moreover, shrub facilitation mediates the interspecific competition within the associated annual community between years with different rainfall amounts. Examining multiple drivers during extreme climate events is a challenging area of research, but it is a necessary consideration given forecasts predicting that these events will increase in frequency and magnitude.

Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert.

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes.

Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae).

We use mitochondrial and multi-locus nuclear DNA sequence data to infer both species boundaries and species relationships within California nemesiid spiders. Higher-level phylogenetic data show that the California radiation is monophyletic and distantly related to European members of the genus Brachythele. As such, we consider all California nemesiid taxa to belong to the genus Calisoga Chamberlin, 1937. Rather than find support for one or two taxa as previously hypothesized, genetic data reveal Calisoga to be a species-rich radiation of spiders, including perhaps dozens of species. This conclusion is supported by multiple mitochondrial barcoding analyses, and also independent analyses of nuclear data that reveal general genealogical congruence. We discovered three instances of sympatry, and genetic data indicate reproductive isolation when in sympatry. An examination of female reproductive morphology does not reveal species-specific characters, and observed male morphological differences for a subset of putative species are subtle. Our coalescent species tree analysis of putative species lays the groundwork for future research on the taxonomy and biogeographic history of this remarkable endemic radiation.

Defect-Healed Carbon Nanomembranes for Enhanced Salt Separation: Scalable Synthesis and Performance.

Carbon nanomembranes (CNMs), with a high density of subnanometer channels, enable superior salt separation performance compared to conventional membranes. However, defects that occur during the synthesis and transfer processes impede their technical realization on a macroscopic scale. Here, we introduce a practical and scalable interfacial polymerization method to effectively heal defects while preserving the subnanometer pores within CNMs. The defect-healed freestanding CNMs show an exceptional performance in forward osmosis (FO), achieving a water flux of 105 L m-2 h-1 and a specific reverse salt flux of 0.1 g L-1 when measured with 1 M NaCl as draw solution. This water flux is 10 times higher than that of commercially available FO membranes, and the reverse salt flux is 70% lower. Through successful implementation of the defect-healing method and support optimization, we demonstrate the synthesis of fully functional, centimeter-scale CNM-based composite membranes showing high water permeance and a high salt rejection. Our defect-healing method presents a promising pathway to overcome limitations in CNM synthesis, advancing their potential for practical salt separation applications.

Sub-Nanometer Depth Profiling of Native Metal Oxide Layers Within Single Fixed-Angle X-Ray Photoelectron Spectra.

Many metals form nanometer-thin self-passivating oxide layers upon exposure to the atmosphere, which affects a wide range of interfacial properties and shapes the way how metals interact with their environment. Such native oxide layers are commonly analyzed by X-ray photoelectron spectroscopy (XPS), which provides a depth-resolved chemical state and compositional analysis either by ion etching or modeling of the electron escape depths. The latter is commonly used to calculate the average thickness of a native oxide layer. However, the measurement of concentration profiles at the oxide-metal interface remains challenging. Here, a simple and accessible approach for the depth profiling of ultrathin oxide layers within single fixed-angle XPS spectra is proposed. Instead of using only one peak in the spectrum, as is usually the case, all peaks within the energy range of a standard lab device are utilized, thus resembling energy-resolved XPS without the need for a synchrotron. New models that allow the calculation of depth-resolved concentration profiles at the oxide-metal interface are derived and tested, which are also valid for angular- and energy-resolved XPS. The proposed method not only improves the accuracy of earlier approaches but also paves the way for a more holistic understanding of the XPS spectrum.

Hydric physiology and ecology of a federally endangered desert lizard.

Animals can respond to extreme climates by behaviourally avoiding it or by physiologically coping with it. We understand behavioural and physiological thermoregulation, but water balance has largely been neglected. Climate change includes both global warming and changes in precipitation regimes, so improving our understanding of organismal water balance is increasingly urgent. We assessed the hydric physiology of US federally endangered blunt-nosed leopard lizards (Gambelia sila) by measuring cutaneous evaporative water loss (CEWL), plasma osmolality and body condition. Measurements were taken throughout their active season, the short period of year when these lizards can be found aboveground. Compared to a more mesic species, G. sila had low CEWL which is potentially desert-adaptive, and high plasma osmolality that could be indicative of dehydration. We hypothesized that throughout the G. sila active season, as their habitat got hotter and drier, G. sila would become more dehydrated and watertight. Instead, CEWL and plasma osmolality showed minimal change for females and non-linear change for males, which we hypothesize is connected to sex-specific reproductive behaviours and changes in food availability. We also measured thermoregulation and microhabitat use, expecting that more dehydrated lizards would have lower body temperature, poorer thermoregulatory accuracy and spend less time aboveground. However, we found no effect of CEWL, plasma osmolality or body condition on these thermal and behavioural metrics. Finally, G. sila spends considerable time belowground in burrows, and burrows may serve not only as essential thermal refugia but also hydric refugia.

Scalable Synthesis of Carbon Nanomembranes from Amorphous Molecular Layers.

Nanoporous carbon nanomembranes (CNMs) created by self-assembled monolayers ideally combine a high water flux and precise ion selectivity for molecular separation and water desalination. However, their practical implementation is often challenged by the availability of large epitaxial substrates, limiting the membrane up-scaling. Here, we report a scalable synthesis of CNMs from poly(4-vinylbiphenyl) (PVBP) spin-coated on SiO2/Si wafers. Electron irradiation of the amorphous PVBP molecular layers induces the formation of a continuous membrane with a thickness of 15 nm and a high density of subnanometer pores, providing a water permeance as high as 530 L m-2 h-1 bar-1, while repelling ions and molecules larger than 1 nm in size. A further introduction of a reinforced porous block copolymer layer enables the fabrication of centimeter-scale CNM composites that efficiently separate organic dyes from water. These results suggest a feasible route for large-scale nanomembrane fabrication.

Shrub density effects on the presence of an endangered lizard of the Carrizo Plain National Monument, California.

Positive associations between animals and foundational shrub species are frequent in desert ecosystems for shelter, resources, refuge, and other key ecological processes. Herein, we tested the impact of the density of the shrub species Ephedra californica on the presence and habitat use of the federally endangered lizard species, Gambelia sila. To do this, we used a 3-year radio telemetry dataset and satellite-based counts of shrub density across sites at the Carrizo Plain National Monument in San Luis Obispo County, CA. The effect of shrub density on lizard presence was contrasted with previous shrub cover analyses to determine whether measures of shrub density were superior to shrub cover in predicting lizard presence. Increasing shrub density increased lizard presence. As shrub density increased, lizards were located more frequently "above ground" versus "below ground" in burrows. Male lizards had significantly larger home ranges than females, but both sexes were similarly associated with increasing shrub densities. Shrub density and shrub cover models did not significantly differ in their prediction of lizard presence. These findings suggest that both habitat measures are effective analogs and that ecologically, both cover and the density of foundation shrub species are key factors for some desert lizards.

Nanofibers are a matter of perspective: effects of methodology and subjectivity on diameter measurements.

Nanofibers are currently among the most researched nanomaterials in materials science. Various high-resolution microscopy techniques are used for morphological investigations, with the diameter as primary characteristic. Since methodological factors influencing the diameter distribution are usually ignored, numerical values can hardly be compared across different or even within single studies. Here, we investigate influencing factors such as microscopy technique, degree of magnification, eventual coatings, and the analysts' bias in the image selection and evaluation. We imaged a single nanofiber sample using scanning electron microscopy (SEM), helium ion microscopy (HIM), atomic force microscopy (AFM), and transmission electron microscopy (TEM). These techniques yield significant methodological variations between the diameter distributions. We further observed a strong influence of analysts' subjectivity, with a consistent average deviation between 4 different analysts of up to 31%. The average deviation between micrographs within each category was 14%, revealing a considerable influence of micrograph selection and strong potential for cherry picking. The mean values were mostly comparable with the results using automated image analysis software, which was more reproducible, much faster, and more accurate for images with lower magnification. The results demonstrate that one of the most frequently measured characteristics of nanofibers is subject to strong systematic fluctuations that are rarely if ever addressed.

Hard carbon microspheres with bimodal size distribution and hierarchical porosity via hydrothermal carbonization of trehalose.

Hydrothermal carbonization (HTC) is an efficient thermochemical method for the conversion of organic feedstock to carbonaceous solids. HTC of different saccharides is known to produce microspheres (MS) with mostly Gaussian size distribution, which are utilized as functional materials in various applications, both as pristine MS and as a precursor for hard carbon MS. Although the average size of the MS can be influenced by adjusting the process parameters, there is no reliable mechanism to affect their size distribution. Our results demonstrate that HTC of trehalose, in contrast to other saccharides, results in a distinctly bimodal sphere diameter distribution consisting of small spheres with diameters of (2.1 ± 0.2) µm and of large spheres with diameters of (10.4 ± 2.6) µm. Remarkably, after pyrolytic post-carbonization at 1000 °C the MS develop a multimodal pore size distribution with abundant macropores > 100 nm, mesopores > 10 nm and micropores < 2 nm, which were examined by small-angle X-ray scattering and visualized by charge-compensated helium ion microscopy. The bimodal size distribution and hierarchical porosity provide an extraordinary set of properties and potential variables for the tailored synthesis of hierarchical porous carbons, making trehalose-derived hard carbon MS a highly promising material for applications in catalysis, filtration, and energy storage devices.

Thickness-Varied Carbon Nanomembranes from Polycyclic Aromatic Hydrocarbons.

Despite the prospects of intrinsically porous planar nanomaterials in separation applications, their synthesis on a large scale remains challenging. In particular, preparing water-selective carbon nanomembranes (CNMs) from self-assembled monolayers (SAMs) is limited by the cost of epitaxial metal substrates and molecular precursors with specific chemical functionalities. In this work, we present a facile fabrication of CNMs from polycyclic aromatic hydrocarbons (PAHs) that are drop-cast onto arbitrary supports, including foils and metalized films. The electron-induced carbonization is shown to result in continuous membranes of variable thickness, and the material is characterized with a number of spectroscopic and microscopic techniques. Permeation measurements with freestanding membranes reveal a high degree of porosity, but the selectivity is found to strongly depend on the thickness. While the permeance of helium remains almost the same for 6.5 and 3.0 nm thick CNMs, water permeance increases by 2 orders of magnitude. We rationalize the membrane performance with the help of kinetic modeling and vapor adsorption experiments.