Hidden Markov Models for Extended Batch Data

Batch marking provides an important and efficient way to estimate the survival probabilities and population sizes of wild animals. It is particularly useful when dealing with animals that are difficult to mark individually. For the first time, we provide the likelihood for extended batch-marking experiments. It is often the case that samples contain individuals that remain unmarked, due to time and other constraints, and this information has not previously been analyzed. We provide ways of modeling such information, including an open N-mixture approach. We demonstrate that models for both marked and unmarked individuals are hidden Markov models; this provides a unified approach, and is the key to developing methods for fast likelihood computation and maximization. Likelihoods for marked and unmarked individuals can easily be combined using integrated population modeling. This allows the simultaneous estimation of population size and immigration, in addition to survival, as well as efficient estimation of standard errors and methods of model selection and evaluation, using standard likelihood techniques. Alternative methods for estimating population size are presented and compared. An illustration is provided by a weather-loach data set, previously analyzed by means of a complex procedure of constructing a pseudo likelihood, the formation of estimating equations, the use of sandwich estimates of variance, and piecemeal estimation of population size. Simulation provides general validation of the hidden Markov model methods developed and demonstrates their excellent performance and efficiency. This is especially notable due to the large numbers of hidden states that may be typically require

Survey of Antibiotic-producing Bacteria Associated with the Epidermal Mucus Layers of Rays and Skates

Elasmobranchs represent a distinct group of cartilaginous fishes that harbor a remarkable ability to heal wounds rapidly and without infection. To date very little work has addressed this phenomenon although it is suggested that antibiotic capabilities associated with epidermal surfaces may be a factor. The study of benefits derived from mutualistic interactions between unicellular and multicellular organisms is a rapidly growing area of research. Here we survey and identify bacterial associates of three ray and one skate species in order to assess the potential for antibiotic production from elasmobranch associated bacteria as a novel source for new antibiotics

An Accurate Distance to High-Velocity Cloud Complex C

We report an accurate distance of d = 10+/-2.5kpc to the high-velocity cloud Complex C. Using high signal-to-noise Keck/HIRES spectra of two horizontal-branch stars, we have detected CaII K absorption lines from the cloud. Significant non-detections toward a further 3 stars yield robust lower distance limits. The resulting HI mass of Complex C is 4.9^{+2.8}_{-2.2} x 10^6 Msun; a total mass of 8.2^{+4.6}_{-2.6} x 10^6 Msun is implied, after corrections for helium and ionization. At 10kpc, Complex C has physical dimensions 3x15 kpc, and if it is as thick as it is wide, then the average density is log ~ -2.5. We estimate the contribution of Complex C to the mass influx may be as high as ~0.14 Msun/yr.Comment: Resubmitted to ApJ. 8 figure

Range-Wide Declines of Northern Spotted Owl Populations in the Pacific Northwest: A Meta-Analysis

The northern spotted owl (Strix occidentalis caurina) inhabits older coniferous forests in the Pacific Northwest and has been at the center of forest management issues in this region. The immediate threats to this federally listed species include habitat loss and competition with barred owls (Strix varia), which invaded from eastern North America. We conducted a prospective meta-analysis to assess population trends and factors affecting those trends in northern spotted owls using 26 years of survey and capture-recapture data from 11 study areas across the owls\u27 geographic range to analyze demographic traits, rates of population change, and occupancy parameters for spotted owl territories. We found that northern spotted owl populations experienced significant declines of 6–9% annually on 6 study areas and 2–5% annually on 5 other study areas. Annual declines translated to ≤35% of the populations remaining on 7 study areas since 1995. Barred owl presence on spotted owl territories was the primary factor negatively affecting apparent survival, recruitment, and ultimately, rates of population change. Analysis of spotted and barred owl detections in an occupancy framework corroborated the capture-recapture analyses with barred owl presence increasing territorial extinction and decreasing territorial colonization of spotted owls. While landscape habitat components reduced the effect of barred owls on these rates of decline, they did not reverse the negative trend. Our analyses indicated that northern spotted owl populations potentially face extirpation if the negative effects of barred owls are not ameliorated while maintaining northern spotted owl habitat across their range

An analysis of monthly home range size in the critically endangered California Condor Gymnogyps californianus

Condors and vultures comprise the only group of terrestrial vertebrates in the world that are obligate scavengers, and these species move widely to locate ephemeral, unpredictable, and patchily-distributed food resources. In this study, we used high-resolution GPS location data to quantify monthly home range size of the critically endangered California Condor Gymnogyps californianus throughout the annual cycle in California. We assessed whether individual-level characteristics (age, sex and breeding status) and factors related to endangered species recovery program efforts (rearing method, release site) were linked to variation in monthly home range size. We found that monthly home range size varied across the annual cycle, with the largest monthly home ranges observed during late summer and early fall (July-October), a pattern that may be linked to seasonal changes in thermals that facilitate movement. Monthly home ranges of adults were significantly larger than those of immatures, but males and females used monthly home ranges of similar size throughout the year and breeding adults did not differ from non-breeding adults in their average monthly home range size. Individuals from each of three release sites differed significantly in the size of their monthly home ranges, and no differences in monthly home range size were detected between condors reared under captive conditions relative to those reared in the wild. Our study provides an important foundation for understanding the movement ecology of the California Condor and it highlights the importance of seasonal variation in space use for effective conservation planning for this critically endangered species

Resource Selection by the California Condor (Gymnogyps californianus) Relative to Terrestrial-Based Habitats and Meteorological Conditions

Condors and vultures are distinct from most other terrestrial birds because they use extensive soaring flight for their daily movements. Therefore, assessing resource selection by these avian scavengers requires quantifying the availability of terrestrial-based habitats, as well as meteorological variables that influence atmospheric conditions necessary for soaring. In this study, we undertook the first quantitative assessment of habitat- and meteorological-based resource selection in the endangered California condor (Gymnogyps californianus) within its California range and across the annual cycle. We found that condor use of terrestrial areas did not change markedly within the annual cycle, and that condor use was greatest for habitats where food resources and potential predators could be detected and where terrain was amenable for taking off from the ground in flight (e.g., sparse habitats, coastal areas). Condors originating from different release sites differed in their use of habitat, but this was likely due in part to variation in habitats surrounding release sites. Meteorological conditions were linked to condor use of ecological subregions, with thermal height, thermal velocity, and wind speed having both positive (selection) and negative (avoidance) effects on condor use in different areas. We found little evidence of systematic effects between individual characteristics (i.e., sex, age, breeding status) or components of the species management program (i.e., release site, rearing method) relative to meteorological conditions. Our findings indicate that habitat type and meteorological conditions can interact in complex ways to influence condor resource selection across landscapes, which is noteworthy given the extent of anthropogenic stressors that may impact condor populations (e.g., lead poisoning, wind energy development). Additional studies will be valuable to assess small-scale condor movements in light of these stressors to help minimize their risk to this critically endangered species

Demographic response of northern spotted owls to barred owl removal

Federally listed as threatened in 1990 primarily because of habitat loss, the northern spotted owl (Strix occidentalis caurina) has continued to decline despite conservation efforts resulting in forested habitat being reserved throughout its range. Recently, there is growing evidence the congeneric invasive barred owl (Strix varia) may be responsible for the continued decline primarily by excluding spotted owls from their preferred habitat. We used a long-term demographic study for spotted owls in coastal northern California as the basis for a pilot barred owl removal experiment. Our demography study used capture–recapture, reproductive output, and territory occupancy data collected from 1990 to 2013 to evaluate trends in vital rates and populations. We used a classic before-after-control-impact (BACI) experimental design to investigate the demographic response of northern spotted owls to the lethal removal of barred owls. According to the best 2-species dynamic occupancy model, there was no evidence of differences in barred or northern spotted owl occupancy prior to the initiation of the treatment (barred owl removal). After treatment, barred owl occupancy was lower in the treated relative to the untreated areas and spotted owl occupancy was higher relative to the untreated areas. Barred owl removal decreased spotted owl territory extinction rates but did not affect territory colonization rates. As a result, spotted owl occupancy increased in the treated area and continued to decline in the untreated areas. Prior to and after barred owl removal, there was no evidence that average fecundity differed on the 2 study areas. However, the greater number of occupied spotted owl sites on the treated areas resulted in greater productivity in the treated areas based on empirical counts of fledged young. Prior to removal, survival was declining at a rate of approximately 0.2% per year for treated and untreated areas. Following treatment, estimated survival was 0.859 for the treated areas and 0.822 for the untreated areas. Derived estimates of population change on both study areas showed the same general decline before removal with an estimated slope of –0.0036 per year. Following removal, the rate of population change on the treated areas increased to an average of 1.029 but decreased to an average of 0.870 on the untreated areas. The results from this first experiment demonstrated that lethal removal of barred owls allowed the recovery of northern spotted owl populations in the treated portions of our study area. If additional federally funded barred owl removal experiments provide similar results, this could be the foundation for development of a long-term conservation strategy for northern spotted owls.This is the publisher’s final pdf. The article is copyrighted by the Wildlife Society and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291937-2817Keywords: barred owl, removal experiment, northern spotted owl, demography, competitio

Three Warm Jupiters around Solar-analog Stars Detected with TESS*

We report the discovery and characterization of three giant exoplanets orbiting solar-analog stars, detected by the TESS space mission and confirmed through ground-based photometry and radial velocity measurements taken at La Silla observatory with FEROS. TOI-2373 b is a warm Jupiter orbiting its host star every ∼13.3 days, and is one of the most massive known exoplanet with a precisely determined mass and radius around a star similar to the Sun, with an estimated mass of m _p = ${9.3}_{-0.2}^{+0.2}\,{M}_{\mathrm{jup}}$ and a radius of r _p = ${0.93}_{-0.2}^{+0.2}\,{R}_{\mathrm{jup}}$ . With a mean density of $\rho ={14.4}_{-1.0}^{+0.9}\,{\rm{g}}\,{\mathrm{cm}}^{-3}$ , TOI-2373 b is among the densest planets discovered so far. TOI-2416 b orbits its host star on a moderately eccentric orbit with a period of ∼8.3 days and an eccentricity of e = ${0.32}_{-0.02}^{+0.02}$ . TOI-2416 b is more massive than Jupiter with m _p = ${3.0}_{-0.09}^{+0.10}\,{M}_{\mathrm{jup}}$ , however is significantly smaller with a radius of r _p = ${0.88}_{-0.02}^{+0.02},{R}_{\mathrm{jup}}$ , leading to a high mean density of $\rho ={5.4}_{-0.3}^{+0.3}\,{\rm{g}}\,{\mathrm{cm}}^{-3}$ . TOI-2524 b is a warm Jupiter near the hot Jupiter transition region, orbiting its star every ∼7.2 days on a circular orbit. It is less massive than Jupiter with a mass of m _p = ${0.64}_{-0.04}^{+0.04}\,{M}_{\mathrm{jup}}$ , and is consistent with an inflated radius of r _p = ${1.00}_{-0.03}^{+0.02}\,{R}_{\mathrm{jup}}$ , leading to a low mean density of $\rho ={0.79}_{-0.08}^{+0.08}\,{\rm{g}}\,{\mathrm{cm}}^{-3}$ . The newly discovered exoplanets TOI-2373 b, TOI-2416 b, and TOI-2524 b have estimated equilibrium temperatures of ${860}_{-10}^{+10}$ K, ${1080}_{-10}^{+10}$ K, and ${1100}_{-20}^{+20}$ K, respectively, placing them in the sparsely populated transition zone between hot and warm Jupiters

Range-wide sources of variation in reproductive rates of northern spotted owls

We conducted a range-wide investigation of the dynamics of site-level reproductive rate of northern spotted owls using survey data from 11 study areas across the subspecies geographic range collected during 1993–2018. Our analytical approach accounted for imperfect detection of owl pairs and misclassification of successful reproduction (i.e., at least one young fledged) and contributed further insights into northern spotted owl population ecology and dynamics. Both nondetection and state misclassification were important, especially because factors affecting these sources of error also affected focal ecological parameters. Annual probabilities of site occupancy were greatest at sites with successful reproduction in the previous year and lowest for sites not occupied by a pair in the previous year. Site-specific occupancy transition probabilities declined over time and were negatively affected by barred owl presence. Overall, the site-specific probability of successful reproduction showed substantial year-to-year fluctuations and was similar for occupied sites that did or did not experience successful reproduction the previous year. Site-specific probabilities for successful reproduction were very small for sites that were unoccupied the previous year. Barred owl presence negatively affected the probability of successful reproduction by northern spotted owls in Washington and California, as predicted, but the effect in Oregon was mixed. The proportions of sites occupied by northern spotted owl pairs showed steep, near-monotonic declines over the study period, with all study areas showing the lowest observed levels of occupancy to date. If trends continue it is likely that northern spotted owls will become extirpated throughout large portions of their range in the coming decades

TESS Hunt for Young and Maturing Exoplanets (THYME). X. A Two-planet System in the 210 Myr MELANGE-5 Association

Young (<500 Myr) planets are critical to studying how planets form and evolve. Among these young planetary systems, multiplanet configurations are particularly useful, as they provide a means to control for variables within a system. Here, we report the discovery and characterization of a young planetary system, TOI-1224. We show that the planet host resides within a young population we denote as MELANGE-5. By employing a range of age-dating methods—isochrone fitting, lithium abundance analysis, gyrochronology, and Gaia excess variability—we estimate the age of MELANGE-5 to be 210 ± 27 Myr. MELANGE-5 is situated in close proximity to previously identified younger (80–110 Myr) associations, Crius 221 and Theia 424/Volans-Carina, motivating further work to map out the group boundaries. In addition to a planet candidate detected by the TESS pipeline and alerted as a TESS object of interest, TOI-1224 b, we identify a second planet, TOI-1224 c, using custom search tools optimized for young stars (Notch and LOCoR). We find that the planets are 2.10 ± 0.09 R⊕ and 2.88 ± 0.10 R⊕ and orbit their host star every 4.18 and 17.95 days, respectively. With their bright (K = 9.1 mag), small (R* = 0.44 R⊙), and cool (Teff = 3326 K) host star, these planets represent excellent candidates for atmospheric characterization with JWST