California Department of Conservation

Rapid (3‐5 minutes) generation of maps of instrumental ground‐motion and shaking intensity is accomplished through advances in real‐time seismographic data acquisition combined with newly developed relationships between recorded ground‐motion parameters and expected shaking intensity values. Estimation of shaking over the entire regional extent of southern California is obtained by the spatial interpolation of the measured ground motions with geologically based frequency and amplitude‐dependent site corrections. Production of the maps is automatic, triggered by any significant earthquake in southern California. Maps are now made available within several minutes of the earthquake for public and scientific consumption via the World Wide Web; they will be made available with dedicated communications for emergency response agencies and critical users.

The Landers earthquake, which had a moment magnitude (M(w)) of 7.3, was the largest earthquake to strike the contiguous United States in 40 years. This earthquake resulted from the rupture of five major and many minor right-lateral faults near the southern end of the eastern California shear zone, just north of the San Andreas fault. Its M(w) 6.1 preshock and M(w) 6.2 aftershock had their own aftershocks and foreshocks. Surficial geological observations are consistent with local and far-field seismologic observations of the earthquake. Large surficial offsets (as great as 6 meters) and a relatively short rupture length (85 kilometers) are consistent with seismological calculations of a high stress drop (200 bars), which is in turn consistent with an apparently long recurrence interval for these faults.

Description

We present a review and analysis of the conservation status and International Union for Conservation of Nature (IUCN) threat categories of all 360 currently recognized species of extant and recently extinct turtles and tortoises (Order Testudines). Our analysis is based on the 2018 IUCN Red List status of 251 listed species, augmented by provisional Red List assessments by the IUCN Tortoise and Freshwater Turtle Specialist Group (TFTSG) of 109 currently unlisted species of tortoises and freshwater turtles, as well as re-assessments of several outdated IUCN Red List assessments. Of all recognized species of turtles and tortoises, this combined analysis indicates that 20.0% are Critically Endangered (CR), 35.3% are Critically Endangered or Endangered (CR+EN), and 51.9% are Threatened (CR+EN+Vulnerable). Adjusting for the potential threat levels of Data Deficient (DD) species indicates that 56.3% of all data-sufficient species are Threatened. We calculated percentages of imperiled species and modified Average Threat Levels (ATL; ranging from Least Concern = 1 to Extinct = 8) for various taxonomic and geographic groupings. Proportionally more species in the subfamily Geoemydinae (Asian members of the family Geoemydidae) are imperiled (74.2% CR+EN, 79.0% Threatened, 3.89 ATL) compared to other taxonomic groupings, but the families Podocnemididae, Testudinidae, and Trionychidae and the superfamily Chelonioidea (marine turtles of the families Cheloniidae and Dermochelyidae) also have high percentages of imperiled species and ATLs (42.9-50.0% CR+EN, 73.8-100.0% Threatened, 3.44-4.06 ATL). The subfamily Rhinoclemmydinae (Neotropical turtles of the family Geoemydidae) and the families Kinosternidae and Pelomedusidae have the lowest percentages of imperiled species and ATLs (0%-7.4% CR+EN, 7.4%-13.3% Threatened, 1.65-1.87 ATL). Turtles from Asia have the highest percentages of imperiled species (75.0% CR+EN, 83.0% Threatened, 3.98 ATL), significantly higher than predicted based on the regional species richness, due to much higher levels of exploitation in that geographic region. The family Testudinidae has the highest ATL (4.06) of all Testudines due to the extinction of several species of giant tortoises from Indian and Pacific Ocean islands since 1500 CE. The family Testudinidae also has an ATL higher than all other larger polytypic families (≥ 5 species) of Reptilia or Amphibia. The order Testudines is, on average, more imperiled than all other larger orders (≥ 20 species) of Reptilia, Amphibia, Mammalia, or Aves, but has percentages of CR+EN and Threatened species and an ATL (2.96) similar to those of Primates and Caudata (salamanders).

Prescribed burning has primarily been used as a tool for the control of invasive late-season annual broadleaf and grass species, particularly yellow starthistle, medusahead, barb goatgrass, and several bromes. However, timely burning of a few invasive biennial broadleaves (e.g., sweetclover and garlic mustard), perennial grasses (e.g., bluegrasses and smooth brome), and woody species (e.g., brooms and Chinese tallow tree) also has been successful. In many cases, the effectiveness of prescribed burning can be enhanced when incorporated into an integrated vegetation management program. Although there are some excellent examples of successful use of prescribed burning for the control of invasive species, a limited number of species have been evaluated. In addition, few studies have measured the impact of prescribed burning on the long-term changes in plant communities, impacts to endangered plant species, effects on wildlife and insect populations, and alterations in soil biology, including nutrition, mycorrhizae, and hydrology. In this review, we evaluate the current state of knowledge on prescribed burning as a tool for invasive weed management.

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Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.

Recent analyses have revealed that 38% of municipal sources of drinking water in California have detectable levels of hexavalent chromium. This observation provided new impetus to characterize the carcinogenic risk associated with oral exposure to hexavalent chromium in drinking water. Notwithstanding the well-characterized increases in cancer associated with inhalation exposure to this chemical, the marked reduction of hexavalent chromium to trivalent chromium in the stomach suggests that exposure to hexavalent chromium in drinking water may not pose a carcinogenic risk. A reevaluation of studies that investigated the toxicokinetics, the genotoxicity, and the mechanism of carcinogenicity of hexavalent chromium, as well as the available human and animal cancer studies, was undertaken to determine if there is evidence that exposure to this chemical in drinking water may pose a carcinogenic risk. Mechanistic studies suggest the potential for a carcinogenic response if hexavalent chromium enters cells. Both toxicokinetic and genotoxicity studies indicate that a portion of an orally administered dose of hexavalent chromium is absorbed and gets into cells of several tissues, causing DNA damage. The only lifetime oral study of hexavalent chromium in animals conducted thus far yielded a statistically significant increase in stomach tumors compared to controls. Also, in a limited-term cancer study, co-exposure to hexavalent chromium in drinking water and ultraviolet light produced skin tumors in mice. The only available cancer study of humans exposed to hexavalent chromium in drinking water revealed a statistically significant increase in stomach tumors. Moreover, a meta-analysis of occupational studies also revealed a statistically significant increase in stomach cancers. The increases in stomach tumors in both human and animal studies, along with the toxicokinetic, genotoxic, and mechanistic data, suggest that oral exposure to this agent appears to pose a carcinogenic risk.

Understanding the evolutionary history of diversifying lineages and the delineation of evolutionarily significant units and species remains major challenges for evolutionary biology. Low-cost representational sampling of the genome for single nucleotide polymorphisms shows great potential at the temporal scales that are typically the focus of species delimitation and phylogeography. We apply these markers to a case study of a freshwater turtle, Emydura macquarii, whose systematics has so far defied resolution, to bring to light a dynamic system of substantive allopatric lineages diverging on independent evolutionary trajectories, but held back in the process of speciation by low level and episodic exchange of alleles across drainage divides on various timescales. In the context of low-level episodic gene flow, speciation is often reticulate, rather than a bifurcating process. We argue that species delimitation needs to take into account the pattern of ancestry and descent of diverging lineages in allopatry together with the recent and contemporary processes of dispersal and gene flow that retard and obscure that divergence. Underpinned by a strong focus on lineage diagnosability, this combined approach provides a means for addressing the challenges of incompletely isolated populations with uncommon, but recurrent gene flow in studies of species delimitation, a situation likely to be frequently encountered. Taxonomic decisions in cases of allopatry often require subjective judgements. Our strategy, which adds an additional level of objectivity before that subjectivity is applied, reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation.

The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.

Climate change over the next century is predicted to cause widespread maladaptation in natural systems. This prediction, as well as many sustainable management and conservation practices, assumes that species are adapted to their current climate. However, this assumption is rarely tested. Using a large-scale common garden experiment combined with genome-wide sequencing, we found that valley oak ( Quercus lobata ), a foundational tree species in California ecosystems, showed a signature of adaptational lag to temperature, with fastest growth rates occurring at cooler temperatures than populations are currently experiencing. Future warming under realistic emissions scenarios was predicted to lead to further maladaptation to temperature and reduction in growth rates for valley oak. We then identified genotypes predicted to grow relatively fast under warmer temperatures and demonstrated that selecting seed sources based on their genotype has the potential to mitigate predicted negative consequences of future climate warming on growth rates in valley oak. These results illustrate that the belief of local adaptation underlying many management and conservation practices, such as using local seed sources for restoration, may not hold for some species. If contemporary adaptational lag is commonplace, we will need new approaches to help alleviate predicted negative consequences of climate warming on natural systems. We present one such approach, “genome-informed assisted gene flow,” which optimally matches individuals to future climates based on genotype–phenotype–environment associations.

Abstract Mammoth Mountain is a 50,000- to 200,000-year-old cumulovolcano standing on the southwestern rim of Long Valley in eastern California. On 4 May 1989, two M = 1 earthquakes beneath the south flank of the mountain marked the onset of a swarm that has continued for more than 6 months. In addition to its longevity, noteworthy aspects of this persistent swarm include (1) an exponential-like increase in the rate of activity through the first month; (2) a vertically oriented, planar distribution of hypocenters at depths between 6 and 9 km with a north-northeast strike (roughly perpendicular to the average T-axis orientation for the swarm earthquakes); (3) recurring spasmodic bursts (rapid-fire sequences of similar-sized earthquakes with overlapping coda) and occasional earthquakes with enhanced low-frequency energy; (4) a uniform temporal distribution of the four largest (M ≈ 3) events over the first 4 months of the swarm with a cumulative seismic moment for the entire sequence through 30 September corresponding to a single M ≈ 4 earthquake; (5) a b-value of 1.2; and (6) submicrostrain perturbations on the nearby borehole dilatometer, the first of which led the onset of swarm activity by more than 2 weeks. These aspects of the swarm, together with its location along the southern extension of the youthful Mono-Inyo volcanic chain, which last erupted 500 to 600 years ago, point to a magmatic source for the modest but persistent influx of strain energy into the crust beneath Mammoth Mountain.

The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival and reproduction, and the model predicted stable median population growth and a 15% probability of extinction over 50 years in the absence of inbreeding depression. However, our model also predicted the population will lose 40-57% of its heterozygosity in 50 years. When we reduced demographic parameters proportional to reductions documented in another wild population of mountain lions that experienced inbreeding depression, extinction probability rose to 99.7%. Simulating greater landscape connectivity by increasing immigration to greater than or equal to one migrant per generation appears sufficient to largely maintain genetic diversity and reduce extinction probability. We provide empirical support for the central tenet of the extinction vortex as interactions between genetics and demography greatly increased extinction probability relative to the risk from demographic and environmental stochasticity alone. Our modelling approach realistically integrates demographic and genetic data to provide a comprehensive assessment of factors threatening small populations.

Defining species' niches is central to understanding their distributions and is thus fundamental to basic ecology and climate change projections. Ecological niche models (ENMs) are a key component of making accurate projections and include descriptions of the niche in terms of both response curves and rankings of variable importance. In this study, we evaluate Maxent's ranking of environmental variables based on their importance in delimiting species' range boundaries by asking whether these same variables also govern annual recruitment based on long-term demographic studies. We found that Maxent-based assessments of variable importance in setting range boundaries in the California tiger salamander (Ambystoma californiense; CTS) correlate very well with how important those variables are in governing ongoing recruitment of CTS at the population level. This strong correlation suggests that Maxent's ranking of variable importance captures biologically realistic assessments of factors governing population persistence. However, this result holds only when Maxent models are built using best-practice procedures and variables are ranked based on permutation importance. Our study highlights the need for building high-quality niche models and provides encouraging evidence that when such models are built, they can reflect important aspects of a species' ecology.

Discusses the problem caused by accumulation of forest fuels in the wild-land forests of the western USA under the policy of total fire protection pursued there for many years, and emphasizes the need to find economical and practical ways of reducing fuel hazards in these forests, especially by means of prescribed burning under conditions in which low-intensity fires can be achieved.

A bstract The transient fields from a finite horizontal loop excited by a half sine wave current pulse have been computed numerically for a particular source receiver configuration at a height of 100 meters above a layered ground. The amplitude of the vertical component of the magnetic field has been chosen for the interpretation. Curves of apparent conductivity vs. time, plotted during the off‐time of the signal, show that layering is easily resolved, that resonance effects are present and that polarization effects are detectable for certain types of polarization.

Eight widespread Pleistocene ash layers of east-central and southern California are characterized and correlated on the basis of chemical composition of volcanic glass (determined by neutron activation, electron probe, and energy-dispersive X-ray fluorescence analysis), stratigraphic criteria, and petrographic characteristics. Irt order of increasing age, these are the Lava Creek B ash bed (formerly referred to as the Pearlette type 0 ash bed; about 0.6 m.y.), the Bishop ash bed (0.73 m.y.), the Glass Mountain-D ash bed (estimated to be about 0.8-0.9 m.y.), the Glass Mountain-G ash bed (estimated to be about 1.0-1.1 m.y.), the Bailey ash (1.2 m.y.), the middle white ash of the Manix basin (estimated to be about 1.9 m.y.), the Huckleberry Ridge ash bed (formerly referred to as the Pearlette type B ash bed; about 1.9 m.y.), and the lowermost gray ash of the South Mountain area (Huckleberry Ridge? ash bed; estimated to be about 1.9 m.y.).

Survival of the most variable As more species become highly threatened because of human activity, there has been an increasing push to understand how best to reintroduce or translocate individuals from wild or captive populations. Suggestions have varied from choosing individuals from the most environmentally similar regions to choosing those that might have the best ability to adapt to new environments. Scott et al. used long-term data collected during translocations of Mojave Desert tortoises, including animals formerly kept as pets, to test these questions. Although the overall rates of survival for all tortoises at the site (both reintroduced and native) were extremely low, translocated individuals with the highest heterozygosity survived at much higher rates than those determined to be similar to the target population. Science , this issue p. 1086

Abstract The site response to strong and weak ground motion depends largely on the subsurface conditions at the soil site for the two rock-soil station pairs studied. The first station pair consists of a soft-soil site (Treasure Island) and a sandstone and shale site (Yerba Buena Island). These stations recorded strong ground shaking from the Loma Prieta mainshock and weak ground motion from four aftershocks. The range of peak ground acceleration is from approximately 0.00006 to 0.07 g at the rock site. Compared to the rock site, the strong ground motion at the soft-soil site is amplified by a factor of about 3 over a frequency range from 0.5 to 2.0 Hz. The amplification is much higher for weak motion and suggests a dependence on signal amplitude. For example, near 1 Hz, the site response shows an increasing amplification as magnitude (and the peak velocity at the rock site) decreases. For events of local magnitude 7.0, 4.3, 4.1, 3.5, and 3.3, the maximum soil-site amplifications are 4, 12, 17, 19, and 25, respectively. A second station pair consisting of a stiff-soil site (Gilroy #2) and a sandstone site (Gilroy #1) was also studied with contrasting results. These two stations recorded strong ground shaking from the 1979 Coyote Lake, 1984 Morgan Hill, and 1989 Loma Prieta mainshocks. Weak ground motion was recorded at these stations after the Loma Prieta mainshock. The range of peak ground acceleration is from 0.006 to 0.43 g at the rock site. Unlike the results for the soft-soil study above, the estimated stiff-soil site responses are not significantly different for strong and weak motion from 0.5 to 2.0 Hz. Near 0.7 Hz, the stiff-soil site responses range from 2.5 to 4.5 for strong ground shaking from three mainshocks and from 1.5 to 4.0 for weak ground shaking from thirteen aftershocks.

Site conditions can be classified by the average shear‐wave velocity to 30 meters (Vs30) and used for estimating site effects in seismic hazard calculations. Large scale seismic hazard maps, which include site effects, may be produced, providing Vs30 can be well correlated with geologic units. Vs30 values for several geologic units can be easily classified into soil profile types of the UBC (ICBO 1997). Most geologic units have wide variations in Vs30 and some extensive geologic units, such as older alluvium, the Franciscan Complex or the Puente Formation cannot be easily classified.