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At least 19 recordsLinked to original sources
USGS2010

Computational modeling of bedform evolution in rivers with implications for predictions of flood stage and bed evolution

Uncertainties in flood stage prediction and bed evolution in rivers are frequently associated with the evolution of bedforms over a hydrograph. For the case of flood prediction, the evolution of the bedforms may alter the effective bed roughness, so predictions of stage and velocity based on assuming bedforms retain the same size and shape over a hydrograph will be incorrect. These same effects will produce errors in the prediction of the sediment transport and bed evolution, but in this latter case the errors are typically larger, as even small errors in the prediction of bedform form drag can make very large errors in predicting the rates of sediment motion and the associated erosion and deposition. In situations where flows change slowly, it may be possible to use empirical results that relate bedform morphology to roughness and effective form drag to avoid these errors; but in many cases where the bedforms evolve rapidly and are in disequilibrium with the instantaneous flow, these empirical methods cannot be accurately applied. Over the past few years, computational models for bedform development, migration, and adjustment to varying flows have been developed and tested with a variety of laboratory and field data. These models, which are based on detailed multidimensional flow modeling incorporating large eddy simulation, appear to be capable of predicting bedform dimensions during steady flows as well as their time dependence during discharge variations. In the work presented here, models of this type are used to investigate the impacts of bedform on stage and bed evolution in rivers during flood hydrographs. The method is shown to reproduce hysteresis in rating curves as well as other more subtle effects in the shape of flood waves. Techniques for combining the bedform evolution models with larger-scale models for river reach flow, sediment transport, and bed evolution are described and used to show the importance of including dynamic bedform effects in river modeling. For example calculations for a flood on the Kootenai River, errors of almost 1m in predicted stage and errors of about a factor of two in the predicted maximum depths of erosion can be attributed to bedform evolution. Thus, treating bedforms explicitly in flood and bed evolution models can decrease uncertainty and increase the accuracy of predictions.

Conference Paper↗
USGS2011

Spatiotemporal evolution of dike opening and décollement slip at Kīlauea Volcano, Hawai'i

Rapid changes in ground tilt and GPS positions on Kīlauea Volcano, Hawai'i, are interpreted as resulting from a shallow, two‐segment dike intrusion into the east rift zone that began at 1217 UTC (0217 HST) on 17 June 2007 and lasted almost 3 days. As a result of the intrusion, a very small volume of basalt (about 1500 m 3 ) erupted on 19 June. Northward tilt at a coastal tiltmeter, subsidence of south flank GPS sites, southeastward displacements at southwestern flank GPS sites, and a swarm of flank earthquakes suggest that a slow slip event occurred on the décollement beneath Kīlauea's south flank concurrent with the rift intrusion. We use 4 min GPS positions that include estimates of time‐dependent tropospheric gradients and ground tilt data to study the spatial and temporal relationships between the two inferred shallow, steeply dipping dike segments extending from the surface to about 2 km depth and décollement slip at 8 km depth. We invert for the temporal evolution of distributed dike opening and décollement slip in independent inversions at each time step using a nonnegative least squares algorithm. On the basis of these inversions, the intrusion occurred in two stages that correspond spatially and temporally with concentrated rift zone seismicity. The dike opening began on the western of the two segments before jumping to the eastern segment, where the majority of opening accumulated. Dike opening preceded the start of décollement slip at an 84% confidence level; the latter is indicated by the onset of northward tilt of a coastal tiltmeter. Displacements at southwest flank GPS sites began about 18 h later and are interpreted as resulting from slow slip on the southwestern flank. Additional constraints on the evolution of the intrusion and décollement slip come from inversion of an Envisat interferogram that spans the intrusion until 0822 UTC on 18 June 2007, combined with GPS and tilt data. This inversion shows that up to 0822 UTC on 18 June, décollement slip is only required in a limited region offshore of Ka'ena Point. A similar inversion of the complete event, which includes GPS and tilt data up to 21 June and a second Envisat interferogram spanning the complete intrusion until 21 June, shows décollement slip spread westward across the south flank. This may suggest westward migration of the décollement slip as the event progressed.

Hawaii↗
USGS2009

Magma evolution and ascent at the craters of the moon and neighboring volcanic fields, southern Idaho, USA: Implications for the evolution of polygenetic and monogenetic volcanic fields

The evolution of polygenetic and monogenetic volcanic fields must reflect differences in magma processing during ascent. To assess their evolution we use thermobarometry and geochemistry to evaluate ascent paths for neighboring, nearly coeval volcanic fields in the Snake River Plain, in south-central Idaho, derived from (1) dominantly Holocene polygenetic evolved lavas from the Craters of the Moon lava field (COME) and (2) Quaternary non-evolved, olivine tholeiites (NEOT) from nearby monogenetic volcanic fields. These data show that NEOT have high magmatic temperatures (1205 + or - 27 degrees C) and a narrow temperature range (< 25 degrees C) at any given depth; NEOT parent magmas partially crystallize within the middle crust (14-17 km), but with little time for cooling or assimilation. In contrast, COME magmas partially crystallize at similar depths, but at any given depth exhibit lower temperatures (by ~40 degrees C), and wider temperature ranges (>50 degrees C). Prolonged storage of COME magmas allows them to evolve to higher 87 Sr/ 86 Sr and SiO 2 , and lower MgO and 143 Nd/ 144 Nd. Most importantly, ascent paths control evolution: NEOT often erupt near the axis of the plain where high-flux (Yellowstone-related), pre-Holocene magmatic activity replaces granitic middle crust with basaltic sills, resulting in a net increase in NEOT magma buoyancy. COME flows erupt off-axis, where felsic crustal lithologies sometimes remain intact, providing a barrier to ascent and a source for crustal contamination. A three-stage ascent process explains the entire range of erupted compositions. Stage 1 (40-20 km): picrites are transported to the middle crust, undergoing partial crystallization of olivine + or - clinopyroxene. COME magmas pass through unarmored conduits and assimilate 1% or less of ancient gabbroic crust having high Sr and 87 Sr/ 86 Sr and low SiO 2 . Stage 2 (20-10 km): magmas are stored within the middle crust, and evolve to moderate MgO (10%). NEOT magmas, reaching 10% MgO, are positively buoyant and migrate through the middle crust. COME magmas remain negatively buoyant and so crystallize further and assimilate middle crust. Stage 3 (15-0 km): final ascent and eruption occurs when volatile contents, increased by differentiation, are sufficient (1-2 wt % H 2 O) to provide magma buoyancy through the middle (and upper) crust.

Idaho↗
USGS2017

Evolution, biogeography, and systematics of Puriana: evolution and speciation in Ostracoda, III.

Three types of geographic isolation—land barriers, deep water barriers, and climatic barriers—resulted in three distinct evolutionary responses in Neogene and Quaternary species of the epineritic ostracode genus Puriana . Through systematic, paleobiogeographic, and morphologic study of several hundred fossil and Recent populations from the eastern Pacific, western Atlantic, Gulf of Mexico, and the Caribbean, the phylogeny of the genus and the geography of speciation events were determined. Isolation of large populations by the Isthmus of Panama during the Pliocene did not lead to lineage splitting in species known to have existed before the Isthmus formed. Conversely, the establishment of small isolated populations on Caribbean islands by passive dispersal mechanisms frequently led to the evolution of new species or subspecies. Climatic changes along the southeastern United States during the Pliocene also catalyzed possible parapatric speciation as populations that immigrated to the northeastern periphery of the genus' range split to form new species. The results provide evidence that evolutionary models describing the influence of abiotic events on patterns of evolution and speciation can be tested using properly selected tectonic and climatic events and fossil groups amenable to species-level analysis. Two new species, P. bajaensis and P. paikensis , are described.

Journal of Paleontology↗
USGS2006

Proterozoic evolution of the western margin of the Wyoming craton: Implications for the tectonic and magmatic evolution of the northern Rocky Mountains

Defining the extent and age of basement provinces west of the exposed western margin of the Archean Wyoming craton has been elusive because of thick sedimentary cover and voluminous Cretaceous-Tertiary magmatism. U-Pb zircon geochronological data from small exposures of pre-Belt supergroup basement along the western side of the Wyoming craton, in southwestern Montana, reveal crystallization ages ranging from ???2.4 to ???1.8 Ga. Rock-forming events in the area as young as ???1.6 Ga are also indicated by isotopic (Nd, Pb, Sr) signatures and xenocrystic zircon populations in Cretaceous-Eocene granitoids. Most of this lithosphere is primitive, gives ages ???1.7-1.86 Ga, and occurs in a zone that extends west to the Neoproterozoic rifted margin of Laurentia. These data suggest that the basement west of the exposed Archean Wyoming craton contains accreted juvenile Paleoproterozoic arc-like terranes, along with a possible mafic underplate of similar age. This area is largely under the Mesoproterozoic Belt basin and intruded by the Idaho batholith. We refer to this Paleoproterozoic crust herein as the Selway terrane. The Selway terrane has been more easily reactivated and much more fertile for magma production and mineralization than the thick lithosphere of the Wyoming craton, and is of prime importance for evaluating Neoproterozoic continental reconstructions. ?? 2006 NRC Canada.

Canadian Journal of Earth Sciences↗
USGS2023

Reconstructing the geomorphic evolution and sediment budget history of a dynamic barrier island: Anclote Key, Florida

Decadal to centennial variations in sediment availability are a primary driver of coastal change within barrier systems. Models help explore how barrier morphology relates to past changes in magnitude of sediment availability, but this requires insights and validation from field efforts. In this study, we investigate the progradation of Anclote Key via its morphostratigraphy, a presently dynamic barrier on the Central Florida Gulf Coast. The results of our field efforts, including vibracores, ground-penetrating radar scans, and optically stimulated luminescence dating of sediments, reveal that Anclote Key has gone through at least two phases of sustained island-scale progradation, with an intervening episode of transgression followed by relative stability. We show that these shifts were likely driven by relatively small changes in shoreface sediment availability owing to the island’s limited accommodation and suggest that Anclote Key may have been relatively isolated from the alongshore sediment supply of nearby barriers prior to the late 20 th century.

Florida↗
USGS2011

Projected evolution of California's San Francisco Bay-Delta-River System in a century of continuing climate change

Background Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species. Methodology/Principal Findings We linked a series of models to investigate responses of California's San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010&ndash;2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations. Conclusions/Significance Most of these environmental indicators change substantially over the 21 st century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

California↗
USGS2018

Pore-types and pore-network evolution in Upper Devonian-Lower Mississippian Woodford and Mississippian Barnett mudstones: Insights from laboratory thermal maturation and organic petrology

Pore-evolution models from immature organic-matter (OM) -rich Barnett (0.42%R o ) and Woodford (0.49%R o ) mudstones were compared with models previously developed from low-maturity OM-lean Boquillas (Eagle Ford-equivalent) mudstones to investigate whether (1) different mineralogy (siliceous vs. calcareous) exerts different catalytic and sorption effects and influences OM-pore origin and evolution; and (2) different types of macerals show different OM pore evolution history. Laboratory gold-tube pyrolysis, scanning electron microscopy (SEM) and thin-section petrography, organic petrography, and geochemical characterization were used to investigate the role of bulk mineralogy, maceral type, and thermal maturation on OM-pore evolution. Results suggest that mineralogy has little impact on OM-pore development and evolution. Macerals, identified using both SEM (platy OM, particulate OM, organic–mineral admixtures, Tasmanites ) and organic petrology (vitrinite, inertinite, amorphous organic matter [AOM]/bituminite, telalginite [ Leiosphaeridia , Tasmanites ]), do affect the origin and evolution of OM pores owing to differences in chemical compositions, generation kinetics, and activation-energy distributions between Tasmanites , matrix bituminite, and other types of macerals. Leiosphaeridia and Tasmanites in Woodford mudstone samples exhibit a delay in onset and a shorter period of petroleum generation and pore development compared to the matrix bituminite in the Barnett and Woodford mudstone samples. Pre-oil solid bitumen was observed to have migrated into initial primary mineral pore networks at the bitumen generation stage in both Barnett and Woodford samples. At higher levels of thermal maturation, the volume of primary mineral pores decreases and the pore volume composed of modified mineral pores and OM pores becomes greater. Pore evolution and pore-type heterogeneity in these mudstones is a function of the initial mineral pore network, types of kerogen and macerals, and generation kinetics of individual macerals upon thermal maturation.

Oklahoma↗
USGS2003

Evolution of CAM and C 4 carbon-concentrating mechanisms

Mechanisms for concentrating carbon around the Rubisco enzyme, which drives the carbon-reducing steps in photosynthesis, are widespread in plants; in vascular plants they are known as crassulacean acid metabolism (CAM) and C 4 photosynthesis. CAM is common in desert succulents, tropical epiphytes, and aquatic plants and is characterized by nighttime fixation of CO2. The proximal selective factor driving the evolution of this CO2-concentrating pathway is low daytime CO2, which results from the unusual reverse stomatal behavior of terrestrial CAM species or from patterns of ambient CO2 availability for aquatic CAM species. In terrestrials the ultimate selective factor is water stress that has selected for increased water use efficiency. In aquatics the ultimate selective factor is diel fluctuations in CO2 availability for palustrine species and extreme oligotrophic conditions for lacustrine species. C4 photosynthesis is based on similar biochemistry but carboxylation steps are spatially separated in the leaf rather than temporally as in CAM. This biochemical pathway is most commonly associated with a specialized leaf anatomy known as Kranz anatomy; however, there are exceptions. The ultimate selective factor driving the evolution of this pathway is excessively high photorespiration that inhibits normal C3 photosynthesis under high light and high temperature in both terrestrial and aquatic habitats. CAM is an ancient pathway that likely has been present since the Paleozoic era in aquatic species from shallow-water palustrine habitats. While atmospheric CO2 levels have undoubtedly affected the evolution of terrestrial plant carbon-concentrating mechanisms, there is reason to believe that past atmospheric changes have not played as important a selective role in the aquatic milieu since palustrine habitats today are not generally carbon sinks, and the selective factors driving aquatic CAM are autogenic. Terrestrial CAM, in contrast, is of increasing selective value under extreme water deficits, and undoubtedly, high Mesozoic CO2 levels reduced the amount of landscape perceived by plants as water limited. Late Tertiary and Quaternary reductions in atmospheric CO2, coupled with increasing seasonality, were probably times of substantial species radiation and ecological expansion for CAM plants. C4 photosynthesis occurs in only about half as many families as CAM, and three-fourths of C4 species are either grasses or sedges. Molecular phylogenies indicate C4 is a more recent innovation than CAM and that it originated in the mid-Tertiary, 20–30 Ma, although some data support an earlier origin. While the timing of the origin of C4 remains controversial, the nearly explosive increase in C4 species is clearly documented in the late Miocene, 4–7 Ma. Increasing seasonality has been widely suggested as an important climatic stimulus for this C4 expansion. Alternatively, based on models of photosynthetic quantum yield at different temperatures and CO2 concentration, it has been hypothesized that the late Miocene C4 expansion resulted from declining atmospheric CO2 levels. This model is most appropriate for explaining the transition from C3 grasslands to C4 grasslands but by itself may not be sufficient to explain the more likely scenario of a late Miocene transition from C3 woodland/ savanna to C4 grasslands. A largely unexplored hypothesis is that climatic changes in late Miocene altered disturbance regimes, in particular the incidence of fires, which today are often associated with maintenance of C4 grasslands. Oceanic charcoal sediments that appear to represent Aeolian deposits from continental wildfires follow a strikingly similar pattern of explosive increase in late Miocene. Climate, CO2, and disturbance are not mutually exclusive explanations and probably all acted in concert to promote the expansion of C4 grasslands. More recently, late Quaternary changes in CO2 may have been responsible for driving major changes in the landscape distribution of C4 species. The theory is sound; however, many of the studies cited in support of this model are open to alternative interpretations, and none has eliminated climatic factors as important selective agents. CAM and C4 evolution required coupling of biochemical pathways with structural changes in photosynthetic tissues, succulence in CAM and Kranz in C4. This was apparently accomplished by piecemeal evolution beginning with mechanisms for recapturing respiratory CO2, although this need not have been so in aquatic CAM species. It has been proposed that the extreme rarity of both pathways in the same plant results from biochemical and structural incompatibilities (Sage 2002). Equally important is the fact that the selective environments are quite different, with CAM evolution thriving on stressful sites inhospitable to C3 species whereas C4 evolution has selected for rapid growth capable of outcompeting associated C3 plants.

International Journal of Plant Sciences↗
USGS2026

Dynamics and evolution of the Kı̄lauea lower East Rift Zone 2018 fissure 8 lava flow and implications for multiphase magma properties

The 2018 Kı̄lauea lower East Rift Zone (KLERZ) eruption was one of the most voluminous eruptions on the Island of Hawai’i in the past 200 years, leading to major disruption and destroying over 700 homes and structures. The majority of the erupted magma was emitted as a lava flow from Ahu’ailā’au (fissure 8), which was active from late May to early August. To better understand the evolution of long-lived channelized lava flows, we examined the evolution of velocity, texture, and inferred rheology of the fissure 8 lava in space and time. We quantified lava flow surface velocities using particle image velocimetry in more than 200 aerial videos that span the lava flow duration and length. Velocity measurements were analyzed together with vesicularity and crystallinity measurements from 9 co-located post-eruptive field samples to understand the textural evolution of this flow and its impact on lava rheology and flow velocity. The fissure 8 flow was highly vesicular, with 79%–88% vesicularity at the vent, decreasing to 16%–26% vesicularity 12.5 km from the vent. The volume fraction occupied by crystals 50 in size increased from 6% at the vent to about 18% at 12.5 km downstream. We find that the effective flow viscosity increased at a quadratic rate with distance. Using experimentally determined liquid viscosity and applying established models to account for the effect of crystals and bubbles, we attribute this increase primarily to textural evolution driven initially by the near-vent loss of deformable bubbles and later by cooling and crystal growth. We demonstrate the importance of accounting for the evolution of vesicularity and the role of vesicles by showing that utilizing this capability in the open-source thermo-rheological lava flow propagation model PyFLOWGO allows for more accurate predictions of the observed flow velocities. Our modeling results suggest that small bubbles behaving rigidly are required to simulate the observed flow length, speed, and viscosities. Flow velocities of the fissure 8 lava also varied with time, driven by near-daily collapse events of the summit caldera. Temporal velocity changes were characterized by a period of steep acceleration, with the volumetric flux peaking around 4 h after a caldera collapse, followed by a period of gradual deceleration lasting up to 40 h or until the next collapse event. We use this temporal behavior to estimate the compressibility of the magma inside the plumbing system between the summit reservoir and the lower East Rift Zone. Overall, quantifying the spatial and temporal evolution of the KLERZ eruption provides information about magma and lava properties that can inform predictive modeling and hazard assessment during an eruption.

Hawaii↗
USGS2016

Evolution of viral virulence: empirical studies

The concept of virulence as a pathogen trait that can evolve in response to selection has led to a large body of virulence evolution theory developed in the 1980-1990s. Various aspects of this theory predict increased or decreased virulence in response to a complex array of selection pressures including mode of transmission, changes in host, mixed infection, vector-borne transmission, environmental changes, host vaccination, host resistance, and co-evolution of virus and host. A fundamental concept is prediction of trade-offs between the costs and benefits associated with higher virulence, leading to selection of optimal virulence levels. Through a combination of observational and experimental studies, including experimental evolution of viruses during serial passage, many of these predictions have now been explored in systems ranging from bacteriophage to viruses of plants, invertebrates, and vertebrate hosts. This chapter summarizes empirical studies of viral virulence evolution in numerous diverse systems, including the classic models myxomavirus in rabbits, Marek's disease virus in chickens, and HIV in humans. Collectively these studies support some aspects of virulence evolution theory, suggest modifications for other aspects, and show that predictions may apply in some virus:host interactions but not in others. Finally, we consider how virulence evolution theory applies to disease management in the field.

Book chapter↗
USGS2017

Population genetics and demography unite ecology and evolution

The interplay of ecology and evolution has been a rich area of research for decades. A surge of interest in this area was catalyzed by the observation that evolution by natural selection can operate at the same contemporary timescales as ecological dynamics. Specifically, recent eco-evolutionary research focuses on how rapid adaptation influences ecology, and vice versa. Evolution by non-adaptive forces also occurs quickly, with ecological consequences, but understanding the full scope of ecology–evolution (eco–evo) interactions requires explicitly addressing population-level processes – genetic and demographic. We show the strong ecological effects of non-adaptive evolutionary forces and, more broadly, the value of population-level research for gaining a mechanistic understanding of eco–evo interactions. The breadth of eco-evolutionary research should expand to incorporate the breadth of evolution itself.

Trends in Ecology and Evolution↗
USGS2006

Speculations on continental crustal evolution

The evolution of the continental crust is a topic that has challenged Earth scientists since the earliest hypotheses of crustal evolution were put forth by such luminaries as Hutton, the 18th century Scottish scientist, and later by Stille (Germany), Argand (France), and Dana (United States). Recent geophysical observations provide important constraints on hypotheses of crustal evolution, and the most important of these observations are reviewed in a companion paper [ Mooney and Meissner , 1991], henceforth referred to as Paper 1. In this article we briefly speculate on crustal evolution using both geological and geophysical data as guidelines. For the past 25 years, the basic framework for models of the evolution of the Earth's crust and lithosphere has been plate tectonics. This framework has been particularly successful in explaining the processes that form and modify the oceanic crust but has had somewhat more limited success in its application to the continental crust. Some of the basic tenets of plate tectonics, as applied to the continental crust, are listed below. Continental masses coalesce and disperse as ocean basins open and close in the Wilson cycle.

Eos, Earth and Space Science News↗
USGS2017

A genetic signature of the evolution of loss of flight in the Galapagos cormorant

INTRODUCTION Changes in the size and proportion of limbs and other structures have played a key role in the evolution of species. One common class of limb modification is recurrent wing reduction and loss of flight in birds. Indeed, Darwin used the occurrence of flightless birds as an argument in favor of his theory of natural selection. Loss of flight has evolved repeatedly and is found among 26 families of birds in 17 different orders. Despite the frequency of these modifications, we have a limited understanding of their underpinnings at the genetic and molecular levels. RATIONALE To better understand the evolution of changes in limb size, we studied a classic case of recent loss of flight in the Galapagos cormorant ( Phalacrocorax harrisi ). Cormorants are large water birds that live in coastal areas or near lakes, and P. harrisi is the only flightless cormorant among approximately 40 extant species. The entire population is distributed along the coastlines of Isabela and Fernandina islands in the Galapagos archipelago. P. harrisi has a pair of short wings, which are smaller than those of any other cormorant. The extreme reduction of the wings and pectoral skeleton observed in P. harrisi is an attractive model for studying the evolution of loss of flight because it occurred very recently; phylogenetic evidence suggests that P. harrisi diverged from its flighted relatives within the past 2 million years. We developed a comparative and predictive genomics approach that uses the genome sequences of P. harrisi and its flighted relatives to find candidate genetic variants that likely contributed to the evolution of loss of flight. RESULTS We sequenced and de novo assembled the whole genomes of P. harrisi and three closely related flighted cormorant species. We identified thousands of coding variants exclusive to P. harrisi and classified them according to their probability of altering protein function based on conservation. Variants most likely to alter protein function were significantly enriched in genes mutated in human skeletal ciliopathies, including Ofd1 , Evc , Wdr34 , and Ift122 . We carried out experiments in Caenorhabditis elegans to confirm that a missense variant present in the Galapagos cormorant IFT122 protein is sufficient to affect ciliary function. The primary cilium is essential for Hedgehog (Hh) signaling in vertebrates, and individuals affected by ciliopathies have small limbs and ribcages, mirroring the phenotype of P. harrisi . We also identified a 4–amino acid deletion in the regulatory domain of Cux1 , a highly conserved transcription factor that has been experimentally shown to regulate limb growth in chicken. The four missing amino acids are perfectly conserved in all birds and mammals sequenced to date. We tested the consequences of this deletion in a chondrogenic cell line and showed that it impairs the ability of CUX1 to transcriptionally up-regulate cilia-related genes (some of which contain function-altering variants in P. harrisi ) and to promote chondrogenic differentiation. Finally, we show that positive selection may have played a role in the fixation of the variants associated with loss of flight in P. harrisi . CONCLUSION Our results indicate that the combined effect of variants in genes necessary for the correct transcriptional regulation and function of the primary cilium likely contributed to the evolution of highly reduced wings and other skeletal adaptations associated with loss of flight in P. harrisi . Our approach may be generally useful for identification of variants underlying evolutionary novelty from genomes of closely related species.

Science↗
USGS2000

Stable isotope evolution and paleolimnology of ancient Lake Creede

The lacustrine carbonate and travertine (tufa) deposits of ancient Lake Creede preserve a remarkable record of the isotopic evolution of the lake. That record indicates that the δ18O of the lake water, and by analogy its salinity, evolved through evaporation. Limited and less reliable data on hydrous minerals and fluid inclusions in early diagenetic carbonates indicate that the δD of the lake waters also evolved through evaporation. The isotope data place restrictions on models of the physical limnology of the lake and its evolution. The closed-basin Lake Creede formed shortly after collapse of the 26.9 Ma Creede caldera. Throughout most of its history it occupied the northern three quarters of the moat between the resurgent dome and wall of the caldera. The Creede Formation was deposited in the basin, dominantly as lacustrine sediments. Travertine mounds interfinger with Creede Formation sediments along the inner and outer margins of the lake basin. An estimated one-half of the original thickness of the Creede Formation has been lost mainly to erosion although scattered remnants of the upper portion remain on the caldera walls. Two diamond core holes (CCM-1 and CCM-2) sampled the uneroded portion of the Creede Formation as part of the U.S. Continental Drilling Program. Volcaniclastic material, including tuff units deposited directly into the lake and ash washed in from the watershed, compose the main lithologies of the Creede Formation. These volcaniclastic strata were produced by episodic ring-fracture volcanism. Lacustrine carbonates make up about 15% of the section sampled by drill core. They occur as 1 mm to 2 cm low-Mg calcite laminae alternating with siliciclastic laminae in scattered intervals throughout the preserved section. The carbonate laminae are accumulations of 5–20 µm crystallites (microsparites) and brine shrimp fecal pellets (peloids) composed mainly of microsparite particles. Low-Mg calcite also occurs as an early diagenetic replacement of gypsum or ikaite (CaCO3 ·6H2O) crystals grown displacively in the muds and silts near the water-sediment interface (rice grains). Other studies indicate that aragonite was the original CaCO3 precipitate forming the microsparite and peloidal laminae and that it converted to calcite during burial diagenesis. Samples from CCM-2 and nearby outcrop do not appear to have undergone significant isotope exchange during recrystallization. Samples from CCM-1 and nearby outcrop, however, appear to have undergone extensive oxygen isotope exchange with meteoric water-dominated fluids possibly during a local 17.6 Ma hydrothermal event. The δ18O-δ13C data set produced by microsampling of individual carbonate lamellae and rice grains is exceptional in several aspects and provides important clues concerning the evolution of limnologic structure of the lake and its chemical and isotopic composition. Travertine and ikaite pseudomorphs in travertine deposits extend the record an additional 330 m above the collar of CCM-2. The δ18O values on CCM-2 samples range from 10.4‰ to 37.3‰ and δ13C values range from –10.8‰ to 9.6‰. The data fall into two distinct groups, a covariant group and an invariant group. The covariant group shows a strong negative covariance and a large range of δ18O and δ13C values. The negative covariance is opposite that normally reported for lacustrine carbonates. The large range of δ18O and δ13C values requires that the carbonates precipitated from waters have a large range of temperature and carbon and oxygen isotopic composition. The invariant group has a narrow range of large δ18O values (35‰ ± 2‰) and a wide range of δ13C values (–10.8‰ to 9.6‰), indicating precipitation from waters with a narrow range of temperature and δ18O but a wide range in δ13C of aqueous carbon. The ranges of isotope values for microsparite and peloid samples are virtually identical; two-thirds are in the covariant group. By contrast, the values for almost all rice grain samples are in the invariant group. The range in δ18O for all samples reflects precipitation from waters having varying proportions of deep, cold evaporated lake water and shallow, warmer meteoric water. The range for δ13C reflects varying proportions of organic carbon and carbon of volcanic or atmospheric origin, probably dominantly volcanic, in the aqueous carbon. Changes in the detailed carbon-oxygen isotope systematics with stratigraphic position define three periods of isotopic evolution of Lake Creede. Period I is represented by the lowest ~200 m of Creede Formation core in CCM-2. Analyses of individual microsparite and peloidal carbonate laminae within single thin sections of samples from that interval are tightly grouped. The data set as a whole shows a negative covariance. Rice grains are not found in this interval. Period II is represented by the succeeding 120 m of core in CCM-2. In that interval, δ13C-δ18O values for individual microsparite and peloidal carbonate laminae within single thin sections show strong negative covariance, and the set of values for the entire interval also shows strong negative covariance. Rice grains occur near the top of the interval. Period III is represented by the upper 225 m of CCM-2 core. In this interval, rice grains are abundant and δ13C-δ18O values for microsparite and peloidal laminae as well as rice grains fall in the invariant group. During Period I the lake was well mixed and the oxygen isotopic composition of the lake in the productive zone was only slightly influenced by short-term (e.g., annual) variations in the water budget of the lake. In Period II the lake was stratified, possibly with annual overturn. The productive zone included the mixolimnion and the isotopic composition of the microsparites and peloids reflected mixtures of shallow surface (meteoric) water containing volcanic or atmospheric CO2 (epilimnion) and cold underlying waters, the oxygen isotopic compositions of which had evolved through evaporation and were dominated by CO2 produced by the oxidation of organic matter (hypolimnion). During Period III the lake remained stratified. The productive zone was in the hypolimnion, probably due to a thinning of the epilimnion resulting from an increase in the surface area of the lake or a decrease in input waters reflecting a climate change. An upsection increase in values of δ18O for the heaviest samples during Periods I and II indicates evaporative concentration of 18O and, by analogy, salinity in the hypolimnion. The δD-δ18O evolution of the lake is inferred on theoretical evaporation trends, comparison to Mono Lake, and measurement of the δD in fluid inclusions in a calcite pseudomorph after ikaite. The δD-δ18O composition of the lake water followed a curved path that eventually hooked over at a nearly constant δ18O value for the lake of 2‰ ± 2‰ Travertine (tufa) mounds formed along the inner and outer margins of the lake in a zone of mixing of warm, volcanic CO2-bearing, meteoric waters and lake water. Ikaite crystals formed on the mounds from unmixed saline lake water, probably below the thermocline. As the position of the thermocline deepened, likely following the spring runoff, the ikaite was replaced by calcite and the resulting “pearls” were covered with travertine deposited from mixed meteoric and lake waters. The upsection increase in δ18O values of the carbonates, the long period of invariance of large δ18OH2O values, the presence of brine shrimp fecal pellets, and the inferred hooked δD-δ18O path are consistent with evidence from other studies that Lake Creede obtained significant salinity rather early in its history and certainly by the time the lake became permanently stratified.

Colorado↗
USGS2020

Probabilistic application of an integrated catchment-estuary-coastal system model to assess the evolution of inlet-interrupted coasts over the 21st century

Inlet-interrupted sandy coasts are dynamic and complex coastal systems with continuously evolving geomorphological behaviors under the influences of both climate change and human activities. These coastal systems are of great importance to society (e.g., providing habitats, navigation, and recreational activities) and are affected by both oceanic and terrestrial processes. Therefore, the evolution of these inlet-interrupted coasts is better assessed by considering the entirety of the Catchment-Estuary-Coastal (CEC) systems, under plausible future scenarios for climate change and increasing pressures due to population growth and human activities. Such a holistic assessment of the long-term evolution of CEC systems can be achieved via reduced-complexity modeling techniques, which are also ably quantifying the uncertainties associated with the projections due to their lower simulation times. Here, we develop a novel probabilistic modeling framework to quantify the input-driven uncertainties associated with the evolution of CEC systems over the 21 st century. In this new approach, probabilistic assessment of the evolution of inlet-interrupted coasts is achieved by (1) probabilistically computing the exchange sediment volume between the inlet-estuary system and its adjacent coast, and (2) distributing the computed sediment volumes along the inlet-interrupted coast. The model is applied at three case study sites: Alsea estuary (United States), Dyfi estuary (United Kingdom), and Kalutara inlet (Sri Lanka). Model results indicate that there are significant uncertainties in projected volume exchange at all the CEC systems (min-max range of 2.0 million cubic meters in 2100 for RCP 8.5), and the uncertainties in these projected volumes illustrate the need for probabilistic modeling approaches to evaluate the long-term evolution of CEC systems. A comparison of 50 th percentile probabilistic projections with deterministic estimates shows that the deterministic approach overestimates the sediment volume exchange in 2100 by 15–30% at Alsea and Kalutara estuary systems. Projections of coastline change obtained for the case study sites show that accounting for all key processes governing coastline change along inlet-interrupted coasts in computing coastline change results in projections that are between 20 and 134% greater than the projections that would be obtained if only the Bruun effect were taken into account, underlining the inaccuracies associated with using the Bruun rule at inlet-interrupted coasts.

Frontiers in Applied Mathematics and Statistics↗
USGS2022

Undeveloped and developed phases in the centennial evolution of a barrier-marsh-lagoon system: The case of Long Beach Island, New Jersey

Barrier islands and their associated backbarrier environments protect mainland population centers and infrastructure from storm impacts, support biodiversity, and provide long-term carbon storage, among other ecosystem services. Despite their socio-economic and ecological importance, the response of coupled barrier-marsh-lagoon environments to sea-level rise is poorly understood. Undeveloped barrier-marsh-lagoon systems typically respond to sea-level rise through the process of landward migration, driven by storm overwash and landward mainland marsh expansion. Such response, however, can be affected by human development and engineering activities such as lagoon dredging and shoreline stabilization. To better understand the difference in the response between developed and undeveloped barrier-marsh-lagoon environments to sea-level rise, we perform a local morphologic analysis that describes the evolution of Long Beach Island (LBI), New Jersey, over the last 182 years. We find that between 1840 and 1934 the LBI system experienced landward migration of all five boundaries, including 171 meters of shoreline retreat. Between the 1920s and 1950s, however, there was a significant shift in system behavior that coincided with the onset of groin construction, which was enhanced by beach nourishment and lagoon dredging practices. From 1934 to 2022 the LBI system experienced ~22 meters of shoreline progradation and a rapid decline in marsh platform extent. Additionally, we extend a morphodynamic model to describe the evolution of the system in terms of five geomorphic boundaries: the ocean shoreline and backbarrier-marsh interface, the seaward and landward lagoon-marsh boundaries, and the landward limit of the inland marsh. We couple this numerical modeling effort with the map analysis during the undeveloped phase of LBI evolution, between 1840 and 1934. Despite its simplicity, the modeling framework can describe the average cross-shore evolution of the barrier-marsh-lagoon system during this period without accounting for human landscape modifications, supporting the premise that natural processes were the key drivers of morphological change. Overall, these results suggest that anthropogenic effects have played a major role in the evolution of LBI over the past century by altering overwash fluxes and marsh-lagoon geometry; this is likely the case for other barrier-marsh-lagoon environments around the world.

New Jersey↗