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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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Lizard reflectivity change and its effect on light transmission through body wall.
Light transmission through body wall of living color-labile desert iguanas measured by spectrophotometry, discussing skin pigment effects
Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree‐alignment and similarity‐alignment
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Diversification with gene flow and niche divergence in a lizard species along the South American “diagonal of open formations”
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Molecular evidence for a terrestrial origin of snakes
Biologists have debated the origin of snakes since the nineteenth century. One hypothesis suggests that snakes are most closely related to terrestrial lizards, and reduced their limbs on land. An alternative hypothesis proposes that snakes are most closely related to Cretaceous marine lizards, such as mosasaurs, and reduced their limbs in water. A presumed close relationship between living monitor lizards, believed to be close relatives of the extinct mosasaurs, and snakes has bolstered the marine origin hypothesis. Here, we show that DNA sequence evidence does not support a close relationship between snakes and monitor lizards, and thus supports a terrestrial origin of snakes.
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.