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DNA methylation–based age prediction and sex-specific epigenetic aging in a lizard with female-biased longevity
Sex differences in life span are widespread across animal taxa, but their causes remain unresolved. Alterations to the epigenome are hypothesized to contribute to vertebrate aging, and DNA methylation–based aging clocks allow for quantitative estimation of biological aging trajectories. Here, we investigate the influence of age, sex, and their interaction on genome-wide DNA methylation patterns in the brown anole (Anolis sagrei), a lizard with pronounced female-biased survival and longevity. We develop a series of age predictor models and find that, contrary to our predictions, rates of epigenetic aging were not slower in female lizards. However, methylation states at loci acquiring age-associated changes appear to be more “youthful” in young females, suggesting that female DNA methylomes are preemptively fortified in early life in opposition to the direction of age-related drift. Collectively, our findings provide insights into epigenetic aging in reptiles and suggest that early-life epigenetic profiles may be more informative than rates of change for predicting sex biases in longevity.
A Lizard-inspired Tube Inspector (LTI) Robot
This final report summarizes the research findings of the current project. This project is a collaboration between New Mexico State University (NMSU) as a lead (Recipient) and Arizona State University (ASU) as a Co-Recipient. Tubular structures are common components of boilers and heat exchangers in power plants. Over time, these components may suffer corrosion, cracks, and stress-corrosion cracks in either the body or the welded connections. A single tube leakage can cause an outage of several weeks. Regular inspection is a key safety factor when ensuring that power plants are maintained in reliable, operational condition. This inspection, however, is challenging, time-consuming, and in many cases impossible due to accessibility issues and safety concerns. Recent developments in robotic-based inspection can offer a great solution. Hard-to-reach places can be inspected without overhauling the unit, saving time and cost. Although several robots have been designed and implemented successfully for inspecting power plant components, in particular tubular structures, their mobility and flexibility are limited. Most of these robots use wheels for mobility which reduces their maneuverability of these robots. Moreover, they usually use magnets to attach to tubes which will not work on tubes with non-ferromagnetic materials. These robots usually carry measurement tools for a particular non-destructive testing (NDT) method such as ultrasound testing (UT) that requires a couplant to perform a point-by-point (scanning) inspection of the tubular structure. In this project, we developed a versatile lizard-inspired tube inspector (LTI) robot with embedded inspection sensing components for tube inspection which removes the need for point-by-point scanning of tube surface for crack and corrosion detection. Inspired by a “lizard”, the novelty of the current project is the integration of couplant-free ultrasound sensing and transmission, advanced data-driven defect detection and imaging, and friction-based mechanical mobility components in a single robot to eliminate a need for smooth surfaces and simple geometry for mobility and scanning. The LTI robot could replace the wheel-based approach with friction-based mobility to significantly increase the flexibility and maneuverability of the robot. The LTI robot can get into a power plant unit, such as a boiler, from a small area allowing it to access a component of interest for inspection (e.g., move on OD, curved and flat surfaces, non-ferromagnetic or ferromagnetic materials, and tubes with rough surfaces and complex geometries). Additionally, an advanced data-driven method using ultrasound data was pioneered to allow the robot to detect defects in the entire area between the robot’s multi-functional mobility system (grippers). Integrating a couplant-free ultrasound sensing in the robot’s grippers as well as using advanced data-driven methods allowed the LTI to detect defects in the entire cross-section of a tube using its grippers when stationary and when mobile.
Viability, behavior, and color expression in the offspring of matings between common wall lizard Podarcis muralis color morphs
Abstract Color polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including color and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilization success, embryonic viability, newborn quality, antipredator, and foraging behavior, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where color morphs are frequently assumed to reflect alternative phenotypic optima (e.g., alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expressions depended on recessive homozygosity at 2 separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behavior. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete color morphs in P. muralis from the Pyrenees.
Evolutionary and demographic correlates of Pleistocene coastline changes in the Sicilian wall lizard Podarcis wagleriana
Abstract Aim Emergence of coastal lowlands during Pleistocene ice ages might have provided conditions for glacial expansions (demographic and spatial), rather than contraction, of coastal populations of temperate species. Here, we tested these predictions in the insular endemic Sicilian wall lizard Podarcis wagleriana . Location Sicily and neighbouring islands. Methods We sampled 179 individuals from 45 localities across the whole range of P. wagleriana . We investigated demographic and spatial variations through time using Bayesian coalescent models (Bayesian phylogeographic reconstruction, Extended Bayesian Skyline plots, Isolation‐with‐migration models) based on multilocus DNA sequence data. We used species distribution modelling to reconstruct present and past habitat suitability. Results We found two main lineages distributed in the east and west portions of the current species range and a third lineage restricted to a small area in the north of Sicily. Multiple lines of evidence from palaeogeographic (shorelines), palaeoclimatic (species distribution models), and multilocus genetic data (demographic and spatial Bayesian reconstructions) indicate that these lineages originated in distinct refugia, located in the north‐western and south‐eastern coastal lowlands, during Middle Pleistocene interglacial phases, and came into secondary contact following demographic and spatial expansions during the last glacial phase. Main conclusions This scenario of interglacial contraction and glacial expansion is in sharp contrast with patterns commonly observed in temperate species on the continent but parallels recent findings on other Mediterranean island endemics. Such a reverse expansion–contraction ( EC ) dynamic has been likely associated with glacial increases of climatically suitable coastal lowlands, suggesting this might be a general pattern in Mediterranean island species and also in other coastal regions strongly affected by glacial marine regressions during glacial episodes. This study provides explicit predictions and some methodological recommendations for testing the reverse EC model in other region and taxa.
The role of metabolism in understanding the altitudinal segregation pattern of two potentially interacting lizards
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Herpetological Survey for the Lawrence Livermore National Laboratory Site 300
Pursuant to Subcontract Number B644180 between ECORP Consulting, Inc. (ECORP) and Lawrence Livermore National Security, LLC. (LLNS) at Lawrence Livermore National Laboratory (LLNL), ECORP conducted focused herpetological surveys at LLNL’s Experimental Test Site (Site 300) during the spring of 2021. The results of these surveys will provide supporting information for a Site-wide Environmental Impact Statement (SWEIS). The herpetological surveys targeted three special-status reptile species including Blainville’s (coast) Horned Lizard (Phrynosoma blainvillii), Northern California Legless Lizard (Anniella pulchra), and San Joaquin Coachwhip (Masticophis flagellum ruddocki) on the approximately 6,800-acre Site 300 in Alameda and San Joaquin counties. Special-status amphibian species were not targets of this survey effort.
Scavenging along an ecological interface: utilization of amphibian and reptile carcasses around isolated wetlands
Abstract Scavenging is an influential ecosystem process, providing many weak, but stabilizing food web links. Amphibians and reptiles (i.e., herpetofauna) utilize land/water interfaces and can have large biomasses concentrated here, making them important vectors of nutrients between aquatic and terrestrial systems and a valuable resource to scavengers. There are limited data on the fate of herpetofauna carrion, and thus, it is unknown how such carcasses are incorporated into food webs or how habitat and carcass characteristics influence which scavengers acquire these resources. We used camera traps to determine the proportion of experimental amphibian and reptile carcasses (lizards, salamanders, frogs, and toads) scavenged by vertebrates and invertebrates in two different habitats (wetland and upland) during the spring in the southeastern USA . Vertebrates removed 19.8% of all herpetofauna carcasses in both habitats, with the remaining carcasses removed by invertebrates (80.2%). We used log‐linear models to evaluate the impact of habitat and carcass type on scavenging. We determined that habitat, but not carcass type, was influential in determining whether a vertebrate or invertebrate scavenged a carcass, with vertebrates able to scavenge more carcasses in wetland than in upland areas. In less than two days, 86.2% of all carcasses in both habitat types were completely scavenged, and carcasses in wetlands were removed more quickly, suggesting intense competition between vertebrates and invertebrates. Additionally, we observed low vertebrate scavenger richness, which we attribute to high invertebrate activity in the spring and the small size of the herpetofauna carcasses (<100 g). We identified the scavenging pathways along which herpetofauna are incorporated into the food web and the factors that influence those pathways, suggesting the large extent and spatial scale of this resource's influence on food web connections and consequently food web and ecosystem stability.
Identification and characterization of a class of MALAT1 -like genomic loci
The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript ( MALAT1 ) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis . Structural and computational analyses revealed a co-occurrence of components of the 3' end module. MALAT1 -like genes in Anolis carolinensis are highly expressed in adult testis, thus we named them testis-abundant long noncoding RNAs (tancRNAs). MALAT1 -like loci also produce multiple small RNA species, including PIWI-interacting RNAs (piRNAs), from the antisense strand. The 3' ends of tancRNAs serve as potential targets for the PIWI-piRNA complex. Furthermore, we have identified an evolutionarily conserved class of long noncoding RNAs (lncRNAs) with similar structural constraints, post-transcriptional processing, and subcellular localization and a distinct function in spermatocytes.
Summary of the Snowmastodon Project Special Volume A high-elevation, multi-proxy biotic and environmental record of MIS 6–4 from the Ziegler Reservoir fossil site, Snowmass Village, Colorado, USA
Abstract In North America, terrestrial records of biodiversity and climate change that span Marine Oxygen Isotope Stage (MIS) 5 are rare. Where found, they provide insight into how the coupling of the ocean–atmosphere system is manifested in biotic and environmental records and how the biosphere responds to climate change. In 2010–2011, construction at Ziegler Reservoir near Snowmass Village, Colorado (USA) revealed a nearly continuous, lacustrine/wetland sedimentary sequence that preserved evidence of past plant communities between ~140 and 55 ka, including all of MIS 5. At an elevation of 2705 m, the Ziegler Reservoir fossil site also contained thousands of well-preserved bones of late Pleistocene megafauna, including mastodons, mammoths, ground sloths, horses, camels, deer, bison, black bear, coyotes, and bighorn sheep. In addition, the site contained more than 26,000 bones from at least 30 species of small animals including salamanders, otters, muskrats, minks, rabbits, beavers, frogs, lizards, snakes, fish, and birds. The combination of macro- and micro-vertebrates, invertebrates, terrestrial and aquatic plant macrofossils, a detailed pollen record, and a robust, directly dated stratigraphic framework shows that high-elevation ecosystems in the Rocky Mountains of Colorado are climatically sensitive and varied dramatically throughout MIS 5.
Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates
Abstract Pleistocene climatic cycles altered species distributions in the Eastern Nearctic of North America, yet the degree of congruent demographic response to the Pleistocene among codistributed taxa remains unknown. We use a hierarchical approximate Bayesian computational approach to test if population sizes across lineages of snakes, lizards, turtles, mammals, birds, salamanders and frogs in this region expanded synchronously to Late Pleistocene climate changes. Expansion occurred in 75% of 74 lineages, and of these, population size trajectories across the community were partially synchronous, with coexpansion found in at least 50% of lineages in each taxonomic group. For those taxa expanding outside of these synchronous pulses, factors related to when they entered the community, ecological thresholds or biotic interactions likely condition their timing of response to Pleistocene climate change. Unified timing of population size change across communities in response to Pleistocene climate cycles is likely rare in North America.
Seaborgite, LiNa6K2(UO2)(SO4)5(SO3OH)(H2O), the First Uranyl Mineral Containing Lithium
Abstract Seaborgite (IMA2019-087), LiNa6K2(UO2)(SO4)5(SO3OH)(H2O), is a new mineral species from the Blue Lizard mine, Red Canyon, San Juan County, Utah, U.S.A. It is a secondary phase found on gypsum in association with copiapite, ferrinatrite, ivsite, metavoltine, and römerite. Seaborgite occurs in sprays of light-yellow, long flattened prisms or blades, up to about 0.2 mm in length. Crystals are elongated on [100], flattened on {010}, and exhibit the forms {100}, {010}, {001}, and {101}. The mineral is transparent with vitreous luster and very pale-yellow streak. It exhibits bright lime-green fluorescence under a 405 nm laser. The Mohs hardness is ~2½. The mineral has brittle tenacity, curved or conchoidal fracture, and one good cleavage on {100}. The measured density is 2.97(2) g/cm3. The mineral is immediately soluble in H2O at room temperature. The mineral is optically biaxial (–), α = 1.505(2), β = 1.522(2), γ = 1.536(2) (white light); 2Vmeas = 85(1)°; moderate r < ν dispersion; orientation X ^ a ≈ 10°; pleochroic X colorless, Y and Z light green-yellow; X < Y ≈ Z. EPMA and LA-ICP-MS analyses of seaborgite undermeasured its Li, K, and Na. The empirical formula using Li, Na, and K based on the structure refinement is Li1.00Na5.81K2.19(UO2)(SO4)5(SO3OH)(H2O). Seaborgite is triclinic, P1, a = 5.4511(4), b = 14.4870(12), c = 15.8735(15) Å, α = 76.295(5), β = 81.439(6), γ = 85.511(6)°, V = 1203.07(18) Å3, and Z = 2. The structure (R1 = 0.0377 for 1935 I = 2σI) contains [(UO2)2(SO4)8]4– uranyl-sulfate clusters that are linked into a band by bridging LiO4 tetrahedra. The bands are linked through peripheral SO4 tetrahedra forming a thick heteropolyhedral layer. Channels within the layers contain a K site, while an additional K site, six Na sites, and an SO3OH group occupy the space between the heteropolyhedral layers.
Ecological Monitoring and Compliance Program 2014 Report
The Ecological Monitoring and Compliance Program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO, formerly Nevada Site Office), monitors the ecosystem of the Nevada National Security Site (NNSS) and ensures compliance with laws and regulations pertaining to NNSS biota. This report summarizes the program’s activities conducted by National Security Technologies, LLC (NSTec), during calendar year 2014. Program activities included (a) biological surveys at proposed activity sites, (b) desert tortoise compliance, (c) ecosystem monitoring, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, and (f) habitat restoration monitoring. During 2014, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives. Sensitive and protected/regulated species of the NNSS include 42 plants, 1 mollusk, 2 reptiles, 236 birds, and 27 mammals. These species are protected, regulated, or considered sensitive according to state or federal regulations and natural resource agencies and organizations. The desert tortoise (Gopherus agassizii) and the western yellow-billed cuckoo (Coccyzus americanus) are the only species on the NNSS protected under the Endangered Species Act, both listed as threatened. However, only one record of the cuckoo has ever been documented on the NNSS, and there is no good habitat for this species on the NNSS. It is considered a rare migrant. Biological surveys for the presence of sensitive and protected/regulated species and important biological resources on which they depend were conducted for 18 projects. A total of 199.18 hectares (ha) was surveyed for these projects. Sensitive and protected/regulated species and important biological resources found during these surveys included a predator burrow, one sidewinder rattlesnake (Crotalus cerastes), two mating speckled rattlesnakes (Crotalus mitchellii), and several species of cacti. NSTec provided to project managers a written summary report of all survey findings and mitigation recommendations, where applicable. Of the 18 projects on the NNSS, 15 occurred within the range of the threatened desert tortoise. Approximately 2.19 ha of desert tortoise habitat were disturbed. No desert tortoises were accidentally injured or killed by project activities, and no tortoises were killed by vehicles. On 13 occasions, tortoises were moved off the road and out of harm’s way. Six tortoises were found and transmitters attached as part of an approved study to assess impacts of vehicles on tortoises on the NNSS. NSTec biologists continued to monitor 37 juvenile desert tortoises as part of a collaborative effort to study survival and temperament of translocated animals. From 1978 until 2013, there has been an average of 11.2 wildland fires per year on the NNSS with an average of about 83.7 ha burned per fire. There were no wildland fires documented on the NNSS during 2014. Results from the wildland fuel surveys showed a very low risk of wildland fire due to reduced fuel loads caused by limited natural precipitation. Limited reptile trapping and reptile roadkill surveys were conducted to better define species distribution on the NNSS. Sixteen reptiles were trapped representing five species. Combined with data from 2013, 183 road kills were detected, representing 11 snake and 8 lizard species. Selected natural water sources were monitored to assess trends in physical and biological parameters, and one new water source was found. Wildlife use at five water troughs and four radiologically contaminated sumps was documented using motion-activated cameras. As part of the statewide effort to disseminate information throughout the botanical community, NSTec prepared a shape file with site-specific data for all 17 sensitive plants on the NNSS and provided it to the Nevada Natural Heritage Program for inclusion in their statewide database. No field surveys were conducted this year for sensitive plants on the NNSS due to poor growing conditions. Surveys of sensitive and protected/regulated animals during 2014 focused on winter raptors, bats, wild horses (Equus caballus), mule deer (Odocoileus hemionus), desert bighorn sheep (Ovis Canadensis nelsoni), and mountain lions (Puma concolor). Two permanent, long-term winter raptor survey routes were established and sampled in January and February. A total of 27 raptors representing 4 species were observed. The wild horse population increased from 30 to 41, with several yearlings recruiting into the population, possibly due to the death of a mountain lion known to prey on horse foals. Mule deer abundance and density measured with standardized deer surveys was similar to 2013 and appears to be stable. Desert bighorn sheep, including rams, ewes, and lambs, were detected using motion-activated cameras at four water sources. There are plans to conduct helicopter surveys to census the population during September 2015 and then capture and radio-collar up to 20 sheep during November 2015. Over 150 sheep scat samples have been collected for genetic analysis to try to determine how sheep on the NNSS are related to surrounding sheep populations. Information is presented about bird mortalities, Migratory Bird Treaty Act compliance, and a summary of nuisance animals and their control on the NNSS. A total of 93 mountain lion images (i.e., photographs or video clips) were taken during 220,379 camera hours at 16 of 32 sites sampled and another 11,946 images of at least 29 species other than mountain lions were taken as well. A mountain lion telemetry study continued in 2014. NNSS7 was tracked from January 1 to November 15 using a global positioning system satellite transmitter. He consumed 21 mule deer, 17 desert bighorn sheep, 1 juvenile bobcat, and 3 coyotes. Mule deer were primarily taken in the summer and fall. No new mountain lions were captured. A minimum of four adult lions (two males, two females), a subadult male, and three kittens were known to inhabit the NNSS during 2014. Two previously revegetated sites on the NNSS and one on the Tonopah Test Range (TTR) were monitored in 2014. The cover cap on the U-3ax/bl disposal unit, revegetated in 2000, and the 92-Acre Site at the Area 5 Radioactive Waste Management Complex, revegetated in 2011, were the restoration sites monitored on the NNSS. The Corrective Action Unit 407 Rollercoaster RADSAFE site, revegetated in 2000, was the restoration site monitored on the TTR. Plant cover and density were recorded at all sites except U-3ax/bl (qualitative monitoring), and reclamation success standards were evaluated, where applicable.
Arroyo Mocho Habitat Suitability Assessment for Sensitive Reptiles, Amphibians, and Fish
Sequoia Ecological Consulting, Inc. (Sequoia) has prepared this habitat suitability assessment for the purpose of assessing current habitat suitability and evaluating the potential presence of special-status species at and near the Arroyo Mocho Pumping Station (Arroyo Mocho). The Study Area is located 7.5 miles southeast of the City of Livermore in Alameda County, California. Our analysis provides a description of presence and habitat suitability for special-status reptiles, amphibians, and fish within the Study Area and identifies potential conservation measures. Special-status animals are designated by the US Fish and Wildlife Service (USFWS) and the California Department of Fish and Wildlife (CDFW). This analysis focuses on California tiger salamander (Ambystoma californiense), California red-legged frog (Rana draytonii), foothill yellow-legged frog (Rana boylii), western pond turtle (Emys marmorata), Alameda whipsnake (Masticophis lateralis euryxanthus), Coast horned lizard (Phrynosoma blainvilli), and central California coast distinct population segment (DPS) steelhead (Oncorhynchus mykiss), per the request of Lawrence Livermore National Laboratory.
Integrating Electromagnetic Acoustic Transducers in a Modular Robotic Gripper for Inspecting Tubular Components
Tubular structures are critical components in infrastructure such as power plants. Throughout their life, they are subjected to extreme conditions or suffer from defects such as corrosion and cracks. Although regular inspection of these components is necessary, such inspection is limited by safety-related risks and limited access for human inspection. Robots can provide a solution for automatic inspection. The main challenge, however, lies in integrating sensors for nondestructive evaluation with robotic platforms. As part of developing a versatile lizard-inspired tube inspector robot, in this study the authors propose to integrate electromagnetic acoustic transducers into a modular robotic gripper for use in automated ultrasonic inspection. In particular, spiral coils with cylindrical magnets are integrated into a novel friction-based gripper to excite Lamb waves in thin cylindrical structures. To evaluate the performance of the integrated sensors, the gripper was attached to a robotic arm manipulator and tested on pipes of different outer diameters. Two sets of tests were carried out on both defect-free pipes and pipes with simulated defects, including surface partial cracking and corrosion. The inspection results indicated that transmitted and received signals could be acquired with an acceptable signal-to-noise ratio in the time domain. Moreover, the simulated defects could be successfully detected using the integrated robotic sensing system.
Western Red-tailed Skink ( Plestiodon Gilberti Rubricaudatus ) Distribution and Habitat Use in Southern Nevada, USA
Western Red-tailed Skinks ( Plestiodon Gilberti Rubricaudatus ) are a Species of Conservation Priority in Nevada and a Species of Greatest Conservation Need in Arizona. Information about this species is lacking, especially for Nevada. We conducted a study from 2006–2011 to determine distribution, abundance, and habitat use of the Western Red-tailed Skink on the Nevada National Security Site (NNSS) in southern Nevada, USA. We used stand-alone funnel traps set in rocky habitats as our primary trapping method. We detected skinks at 28 of the 154 trapping sites and documented 38 individual skinks during 31,119 trap days. Occupied sites occurred in 10 vegetation associations and 12 geological formations at an average elevation of 1,727 m ± 197 m (range, 1,310–2,095 m). Using an occupancy modeling framework, we found that skinks were most likely to occur at mid-elevation sites with south-facing slopes. The model also weakly suggested that Sagebrush-dominated sites and wet or mesic sites were more likely to harbor skinks. Other measurable sources of variation among sampled sites (e.g., vegetation and substrate classifications) had little apparent effect on skink occurrence. Genetic analysis of 33 skinks from the NNSS indicated all belong to a mitochondrial clade that is restricted to central-eastern California and southwestern Nevada (Inyo clade).