Probability Of Colonization Research Articles

Molecular analysis of cutaneous yeast isolates in the mycobiota of children with atopic dermatitis.

The skin of patients with atopic dermatitis (AD) has a greater diversity of mycobiota. An observational, prospective, cross-sectional, analytical, and comparative study was conducted involving 80 patients with AD Group (ADG) and 50 individuals without AD (wADG) in a tertiary hospital in Brazil. Skin scale samples were collected from the frontal, cervical, fossae cubital, and popliteal regions and identified using molecular biology techniques. The results showed that 47.5% of ADG had identified yeasts compared to 0% of wADG (P<.001). The yeasts Rhodotorula mucilaginosa and Candida parapsilosis were the most abundant. The probability of colonization increased with age, showing values of 40% at 60 months and 80% at 220 months (P=.09). The cervical region (12.5%) was colonized to the greatest extent. Our findings revealed that positive mycology was not more probable when the scoring of atopic dermatitis or eczema area and severity index value increased (P=.23 and .53, respectively). The results showed that the sex, age, and different population types directly affected the composition of the mycobiota in the population analyzed. A higher frequency of colonization and greater diversity of yeast species were detected in the cutaneous mycobiota of children with AD.

Dynamic occupancy modelling of Asian elephants (Elephas maximus) reveals increasing landscape use in Nepal

Large mammals with general habitat needs can persist throughout mixed used landscapes, however, human-wildlife conflict frequently leads to their restriction to protected areas. Conservation efforts, especially for reducing conflicts with humans, can enhance tolerance of humans towards species like Asian elephants (Elephas maximus) in human-dominated landscapes. Here, we examine how elephant use in the Chure Terai Madhesh Landscape (CTML) covering the entire elephant range of Nepal changed between 2012 and 2020 in relationship to protection status and environmental conditions. We systematically surveyed ~ 42,000 km2 of potential habitat, by dividing the study area into 159 grid cells of 15 × 15 km2 and recorded elephant signs during the cool, dry season in three years (2012, 2018 and 2020). We analyzed the survey data in a single-species, multi-season (dynamic) occupancy modeling framework to test hypotheses regarding the influence of environmental conditions and protected area status on landscape use by elephants over time. The best-supported model included protected area effects on initial use, colonization, and detection probability as well as temporal variation in colonization and detection probability. Initial use and colonization rates were higher in protected areas, however elephants increasingly used cells located both inside and outside the protected areas, and the difference in use between protected areas and outside declined as elephants use became prevalent across most of the landscape. While elephant use was patchily distributed in the first year of surveys consistent with past descriptions of four sub-populations, elephant use consolidated into a western and eastern region in subsequent years with a gap in their distribution occurring between Chitwan and Bardiya National Parks. Our manuscript highlights the increasing landscape use by elephants in both protected areas and areas outside protected areas and suggests that management interventions that focus on reducing conflicts can promote greater use of both protected areas and areas outside of protected areas.

Is Klerksdorp die oudste dorp in Transvaal?

This article refutes the claim that Klerksdorp (and not Potchefstroom) is the Transvaal's oldest town, mainly because the assumption that Klerksdorp was founded in 1837 rests upon memory and tradition. It argues moreover that the history of the Great Trek rules out the probability of White settlement in the Western Transvaal before mid-1838. It concludes by indicating that no archival sources or evidence could be traced to prove that a settlement existed at Schoonspruit before March 1840. The settlement which took place there afterwards was basically not a town but a farm. The word erf was not used until the end of the 1840s and indeed referred to arable land or cultivated fields. Although by 1850 the Schoonspruit-settlement did resemble a town and was called Klerksdorp it bore no resemblance to any early Voortrekker dorp. The founding in 1888 of Nuwe Dorp was therefore not merely an extension of Ou Dorp but in fact the establishment of a separate town to provide for the needs of the new gold-diggings at Klerksdorp.

Using irregular ranger patrols to quantify elephant occupancy in non‐protected and community‐modified landscapes

AbstractWhile wildlife management efforts have primarily focused on protected areas, unprotected areas – including community‐owned lands – are becoming increasingly important as habitat linkages and dispersal areas between multiple protected areas for species and processes that sustain them. However, these unprotected areas and community lands often lack structured protection measures and face numerous threats to both species and habitats. Involvement of local communities in the management of these areas through community‐led strategies can enhance safety for both people and wildlife, thereby promoting coexistence. To examine the effectiveness of community‐led strategies for managing wildlife outside protected areas, we fit multi‐season occupancy models on African elephant (Loxodonta africana) sightings data collected by volunteer Village Game Scouts (VGS) while on irregular and demand‐driven patrols within Mwanga district in Northern Tanzania. Patrol data were processed using the Spatial Monitoring And Reporting Tool (SMART). We estimated elephant probability of occupancy, detection, colonization and extinction, identifying key elephant dispersal areas in the community‐modified areas within the district. Our results indicate that proximity to Tsavo West National Park and the availability of seasonal water sources positively influenced the probability of elephant colonization. In contrast, the proportion of built‐up and farmed areas, and distance to permanent water sources, negatively influenced the probability of colonization. The number of scout patrols did not significantly influence the probability of elephant colonization or extinction, and elephant occupancy remained relatively stable during the study period. Our study highlights the complementary role of non‐protected areas in maintaining populations of endangered species such as elephants. We demonstrate that structured, volunteer community‐led strategies coupled with effective communication with authorities, can be used to monitor wildlife spatial distribution and identify factors influencing their distribution in non‐protected areas. We recommend community‐led protection measures for corridors and dispersal areas, as well as transboundary collaboration to maintain landscape connectivity for endangered species such as elephants.

MDRO Colonization Among Nursing Homes Patients: A Risk Classification Tool for Early Identification

Background: Nursing homes (NHs) have high prevalence of multi-drug resistant organisms (MDROs) with rates exceeding those in hospitals. This study proposes quantifying patients’ risk of MDRO colonization and creating a risk profile for the NH patient populations to assist in reducing MDRO burden in health care facilities. Methods: We assessed a risk classification model using data from a prospective cohort study (2018 Pathways study). Patient sample included 783 newly admitted patients followed for up to 180 days and 9,587 samples collected from patients during 2,089 visits. Individual risk factors of MDRO colonization were assessed using unadjusted logistic regression, and patients were risk classified based on number of risk factors. Multivariate regression was performed to obtain odds of MDRO colonization for patient risk groups adjusting for patient age, sex, race, and length of NH stay (LOS). The risk classification tool developed using Pathways data was also tested among a sample of NH residents from Veterans Administration (N=190). Results: The patient sample (Pathways data) was 43.2% male, 37.2% Black with a mean age 74 years. 69.3% were colonized with a MDRO during the study. In unadjusted regression, recent antibiotic use (p&lt;.001), open wounds (p&lt;.05), use of urinary catheter or feeding tube (p&lt;.001), functional disability (p&lt;.001), diabetes (p&lt;.01), and preadmission hospital stay over 14 days (p&lt;.001) were associated with colonization, while Charlson comorbidity score, age, sex, and race were not. In adjusted analysis (c-statistic=0.75), a patient’s colonization risk increased with the number of risk factors (Figure 1), with 47.2% expected colonization among patients with none of the risk factors and 86.7% expected colonization among patients with four or more risk factors. The risk classification model had similar performance among male and female patients, and among Black and White patients (Figure 2). Secondary analysis using data obtained from separate, Veterans Administration facilities provided preliminary validation of the risk scoring tool. The model had acceptable fit (c-statistic=0.71). Veterans with four or more risk factors had 87.8% expected probability of MDRO colonization compared with 39.6% colonization among those without any risk factors. Veterans with less than four risk factors also had higher colonization, but these differences were not statistically significant. Conclusions. Despite system-wide efforts to reduce MDRO burden, prevalence of MDRO colonization remains high in NHs. The risk classification tool can assist in early identification of most vulnerable NH patients to direct targeted interventions such as education, enhanced environmental cleaning, and active surveillance.Disclosure: Lona Mody: NIH, VA, CDC, Kahn Foundation; Honoraria: UpToDate; Contracted Research: Nano-Vibronix

Recent progress in hukou reform and labor market integration in China: 1996–2022

To investigate the household registration system (hukou) reform in China, it is important to quantify the thresholds of obtaining hukou in urban areas at the city level. We build a new index to measure the likelihood of obtaining urban hukou for migrants in each destination city, termed the “settlement probability”, based on individual information of floating population from the population census and hukou policies of 332 cities from 1996 to 2022. We find that the average settlement probability has been steadily increasing since 1999, reaching 91% in 2022, and 15 provinces have achieved low thresholds. We further build a simple general spatial equilibrium model with the factor of settlement probability to investigate the impacts of hukou reform. The empirical analysis shows there is a mismatch between settlement probability and settlement intentions. Moreover, we find that higher settlement probability is significantly correlated with more migrants' inflow, lower migrants' wages and higher urban housing prices, especially in more developed cities. Therefore, hukou reform is crucial for enhancing the integration of China's labor market.

Invasibility framework to predict the early colonization of alien Sonneratia in mangrove: Implications for coastal area management

Invasibility, or an ecosystem's susceptibility to invasion, plays a critical role in managing biological invasions but is challenging to quantify due to its dependence on specific ecosystem variables. This limitation restricts the practical application of this concept in the control of alien species. This study aims to simplify invasibility into measurable components and develop an applicable framework to predict early colonization of alien plants within the coastal mangrove ecosystem. We used the unchanneled path length (UPL), a widely applied hydrological connectivity-related indicator, to assess the accessibility of the mangrove. The enhanced vegetation index (EVI), positively correlated with above-ground biomass, was used to evaluate the potential competitive intensity. Firstly, building on existing studies, we developed a four-quadrant concept model integrating the effects of EVI and UPL on the early colonization of the alien species Sonneratia apetala. Our results revealed significant differences in EVI and UPL values between colonized and uncolonized areas, with colonized regions displaying markedly lower values (P < 0.001). Additionally, logistic regression showed a significant negative association between the probability of successful colonization by S. apetala and both indicators (P < 0.001). These results validate the effectiveness of our conceptual model. Furtherly, we identified four key niche opportunities for exotic species in mangrove: mudflats outside the mangrove forest, tidal creeks, canopy gaps, and unmanaged abandoned aquaculture ponds. Overall, this study provides important insight into the ecological processes of alien S. apetala colonization and practical information for management of coastal areas susceptible to invasion. Additionally, it presents a case study on the practical application of the concept of invasibility in the management of alien species.

Predicting lung cancer's metastats' locations using bioclinical model

BackgroundLung cancer is a global leading cause of cancer-related deaths, and metastasis profoundly influences treatment outcomes. The limitations of conventional imaging in detecting small metastases highlight the crucial need for advanced diagnostic approaches.MethodsThis study developed a bioclinical model using three-dimensional CT scans to predict the spatial spread of lung cancer metastasis. Utilizing a three-layer biological model, we identified regions with a high probability of metastasis colonization and validated the model on real-world data from 10 patients.FindingsThe validated bioclinical model demonstrated a promising 74% accuracy in predicting metastasis locations, showcasing the potential of integrating biophysical and machine learning models. These findings underscore the significance of a more comprehensive approach to lung cancer diagnosis and treatment.InterpretationThis study's integration of biophysical and machine learning models contributes to advancing lung cancer diagnosis and treatment, providing nuanced insights for informed decision-making.

Building pondscapes for amphibian metapopulations.

The success of ponds constructed to restore ecological infrastructure for pond-breeding amphibians and benefit aquatic biodiversity depends on where and how they are built. We studied effects of pond and landscape characteristics, including connectivity, on metapopulation dynamics of 12 amphibian species in Switzerland. To understand the determinants of long-term occupancy (here summarized as incidence), environmental effects on both colonization and persistence should be considered. We fitted dynamic occupancy models to 20years of monitoring data on a pond construction program to quantify effects of pond and landscape characteristics and different connectivity metrics on colonization and persistence probabilities in constructed ponds. Connectivity to existing populations explained dynamics better than structural connectivity metrics, and simple metrics (distance to the nearest neighbor population, population density) were useful surrogates for dispersal kernel-weighted metrics commonly used in metapopulation theory. Population connectivity mediated the persistence of conservation target species in new ponds, suggesting source-sink dynamics in newly established populations. Population density captured this effect well and could be used by practitioners for site selection. Ponds created where there were 2-4 occupied ponds within a radius of ∼0.5km had >3.5 times higher incidence of target species (median) than isolated ponds. Species had individual preferences regarding pond characteristics, but breeding sites with larger (≥100m2) total water surface area, that temporarily dried, and that were in surroundings with maximally 50% forest benefitted multiple target species. Pond diversity will foster amphibian diversity at the landscape scale.

Microplastics in anoxic/aerobic membrane bioreactor (A/O-MBR): Characteristics, biofilms, degradation and carrier for antibiotic resistance genes

Wastewater treatment plants (WWTPs)are proposed as one of the ways for microplastics (MPs) to enter the water environment. MPs as the carrier of other pollutants, the inevitable aging process will change the characteristics and fate of MPs. Herein, the physicochemical property alteration, microbial community evolution and antibiotic resistance genes (ARGs) occurrence of the aged MPs surface were analyzed in A/O-MBR system. Remarkable alteration in MPs surface properties, which included the decrease in hydrophobicity and the increase in oxygen-containing functional groups, led to aging of MPs. Aging MPs are more likely to grow biofilms, which further increased the probability of microbial colonization. The genera Hydrogenophaga, Exiguobacterium, Enterobacter, Vibrio, Flavobacterium and Bacillus on MPs surface showed higher degradation potential. ARGs determination results indicated that MPs could enrich ARGs on their surface, and the relative abundance of β-lactam ARGs on different MPs surfaces was the highest. The above research results indicated that MPs in sewage treatment systems not only undergo aging, but also carry ARGs, causing further harm to the environment.

Probabilistic assessment of existing shield tunnel longitudinal responses to tunnelling

AbstractThis paper proposes a probabilistic‐based framework to assess the failure probability of the existing shield tunnel owing to undercrossing tunnelling. A novel deterministic model using the two‐phase analysis method is presented to evaluate the longitudinal behaviours of the in‐service shield tunnel. First, the tunnelling‐induced settlement is estimated using the Loganathan and Poulos’ method; second, the longitudinal beam‐spring model (LBSM), which can explicitly consider the circumferential joints, is applied to reflect the performances of the existing shield tunnel. Two well‐documented case histories are selected to validate the effectiveness of the deterministic analysis model. The predictions are also compared with previous analytical methods. Afterward, to improve the computational efficiency, a surrogate model is then established to replace deterministic model and perform the global sensitivity analysis (GSA). A probabilistic analysis is further performed to explore the tunnelling‐induced deformation characteristics of the shield tunnel by means of Monte Carlo simulation (MCS) method. Parametric analyses are further performed to explore the influences of key variables on the failure probabilities of the existing shield tunnel. The results show the proposed deterministic model gives a satisfactory prediction in tunnelling‐induced responses of the existing shield tunnel. The LBSM can reflect the segmental ring and joint deformations more realistically. The uncertainties in the ground elastic modulus, joint rotation stiffness and the joint shearing stiffness dominate the tunnel settlement, joint opening and dislocation, respectively. The failure probability of tunnel settlement is more sensitive to volume loss than that of the joint opening and dislocation. The whole system failure probability is identical to that of the tunnel settlement failure mode. By increasing the coefficient of variation (COV) of random variables, probability density function (PDF) curves for neutral and pessimistic conditions become lower and wider, and the maximum joint opening and dislocation positions corresponding to the peaks of PDF apparently deviate from that of the determinate results. Increasing the two tunnel clearances, the allowable volume loss for opening and dislocation increase linearly, but it has insignificant influence on the tunnel failure mode. However, enlarge the new tunnel diameter leads to rapid decrease in the allowable volume loss for all failure modes.

Long‐term occupancy monitoring reveals value of moderate disturbance for an open‐habitat specialist, the Stephens' kangaroo rat (Dipodomys stephensi)

AbstractFor species of conservation concern, long‐term monitoring is vital to properly characterize changes in population distribution and abundance over time. In addition, long‐term monitoring guides management decisions by informing and evaluating the efficacy of management actions. A long‐term monitoring initiative for the federally threatened Stephens' Kangaroo rat (Dipodomys stephensi, SKR) was established in 2005, across 628 hectares within Marine Corps Base Camp Pendleton (MCBCP), San Diego, California, USA. From 2005 to 2018, we tracked trends in area occupied by SKR, trends in relative SKR densities within occupied habitat, and modeled probabilities of SKR occupancy, colonization, extinction, with habitat, climate, and disturbance covariates. Area occupied by SKR increased almost 2‐fold from 2005 to 2018 on MCBCP, while density in occupied habitat increased almost 3‐fold. Increased area occupied was correlated with increases in estimated density among years, indicating SKR population growth occurs by expansion into suitable habitat patches, as well as increases in numbers within occupied habitat. SKR occupancy was positively associated with gentle slopes (&lt;10%) and moderate open ground (40–80%) and forb cover (&gt;40%). They were more likely to colonize previously unoccupied habitat when there were moderate levels of open ground (40–80%) and low shrub cover (&lt;20%), while more likely to go locally extinct in areas with high slopes (&gt;10%), less open ground (&lt;20%), and increased non‐native grass cover (&gt;40%). Additionally, probabilities of SKR occupancy and colonization were higher in areas with moderate levels of disturbance, which was positively associated with open ground and forb cover. We conclude that long‐term occupancy and density monitoring is effective in informing status and trends of spatially dynamic species and that moderate habitat‐based disturbance is compatible with the management of SKR.

Changes in Wolf Occupancy and Feeding Habits in the Northern Apennines: Results of Long-Term Predator-Prey Monitoring.

The comprehension of the factors that have influenced the recent changes in wolf (Canis lupus) range and diet that have occurred in our study area, characterized by a highly heterogeneous landscape, can shed light on their current process of expansion toward the plain. Wolf presence was monitored using a standardized protocol from 2007 to 2022 by carrying out eight monitoring sessions organized in seasonal surveys, during which, we collected wolf presence data. To model wolf range dynamics, we used dynamic occupancy models considering land cover types and wild ungulate abundances as covariates. Moreover, we studied the wolf diet through scat analysis, identifying the consumed items from undigested remains. Wolf occupancy in the study area progressed from mountains to lower hills gradually; the observed range dynamics were driven by prey abundance and human presence: in particular, the probability of colonization increased with roe deer (Capreolus capreolus) abundance, whereas the probability of extinction increased with urban areas. The wolf diet showed a gradual shift from the prevalent consumption of wild boar (2007-2008 and 2011-2012) to the prevalent consumption of roe deer (continuously increasing from 2015 onward). Our results might be related to a specific adaptation of the predator to the local ecology of the most consumed species: the roe deer.

Water-filled leaf axils in teasel plants: A study of often overlooked aquatic habitats

Teasels (Dipsacus spp.) are among the few European plant species that can create small aquatic ecosystems, known as phytotelmata, in their leaf axils. However, these unique environments have received little research attention. We performed the first detailed study of phytotelmata in teasels, aiming to describe the physical habitat and macroinvertebrate communities across different leaf axil levels. We explored 64 phytotelmata on 20 teasel plants in Slovakia (Central Europe). These small aquatic ecosystems contained less than 100 ml of water, exhibited a pH ranging from slightly acidic to neutral, had very low oxygen content, and showed highly variable conductivity. We collected more than 1000 larvae of Diptera, representing at least ten aquatic invertebrate taxa. The dominant species found in these communities were the chironomid Metriocnemus eurynotus (Holmgren, 1883), followed by ceratopogonids of the genus Dasyhelea. The oldest, bottom-situated phytotelmata showed the highest invertebrate density and species richness, suggesting an important role of ecosystem age and the probability of colonization in the community assembly process. These highly replicated ecosystems with simple communities may serve as useful models for studying various ecological phenomena such as metacommunity dynamics, succession, community assembly, biodiversity-ecosystem functioning or mutualistic interactions.

Occupancy, relative abundance and activity patterns of three sympatric deer in ponds of Calakmul Biosphere Reserve, Campeche

Calakmul Biosphere Reserve is one of the largest tropical forests in the Americas, home to three species of deer, the white-tailed deer, Odocoileus virginianus, the Yucatan brown brocket deer, Odocoileus pandora, and the Central American red brocket deer, Mazama temama. Important ecological aspects on the conservation of these species have been poorly studied. The aim of this study was to determine the occupancy, relative abundance and activity patterns of these species through 9 years of camera-trapping in ponds of a Neotropical Forest in southern Mexico, contributing to the understanding of the ecological patterns and conservation of Neotropical deer. To determine abundance, occupancy and activity patterns, 18 ponds were monitored from 2014 to 2022. The general relative abundance index was used to calculate abundance and the temporal kernel density was used to evaluate the overlap in daily activity of the species. The dynamic occupancy model was used to obtain the occupancy, colonization, extinction and detection of deer, while species co-occurrence occupancy models were used to assess the interaction of water and species. White-tailed deer were the most abundant (Table 1) during the nine years of the study, with low pond occupancy, but with a high probability of colonization. The brown brocket deer was the one with the highest probability of occupancy, showing a low abundance (Table 1), followed by the red brocket deer, with a very low occupancy and abundance (Table 1). Interaction with water was positive in two of the three analyzed species and activity was diurnal for Odocoileus species and cathemeral for Mazama (Fig. 3). The use of ponds by deer is varied in quantity and activity, but they are important places for their development. The protection of the ponds should be fundamental for the conservation of the species in the area, being one of the few semi-perennial water sources and places of food and shelter for wildlife.

Capsular gene distribution and RAPD typing of Streptococcus agalactiae isolated from pregnant women

Streptococcus agalactiae has different virulence factors, from which the capsule has the most significant role in the pathogenesis of this organism. We aimed to investigate the distribution of more prevalent capsular genes among different Random Amplified Polymorphic DNA (RAPD) types of S. agalactiae isolated from pregnant women. A total of 106 isolates were collected from 420 vaginal and rectal swabs obtained from pregnant women. The specimens were transferred using Todd Hewitt Broth and were cultured on a blood agar containing antibiotics. The S. agalactiae isolates were identified by the standard microbiological and biochemical tests. The genomic DNAs of S. agalactiae isolates were extracted using an extraction kit. Then, the PCR method was used to detection of the capsular genes. Moreover, The RAPD PCR was used to genotyping of the isolates. The colonization rate of the pregnant women was 25.23%, and there was a statistically significant correlation between the weeks of gestation and the probability of colonization (p-value < 0.05). Also, 31 (29.24%) and 18 (16.98%) pregnant women had a history of abortion and membrane rupture, respectively. In addition, 20 (18.86%), 32 (30.18%), 4 (3.77%), and 6 (5.66%) isolates carried genes encoding capsular types Ia, Ib, III, and V, respectively. None isolates had the type II capsular gene, and other 44 isolates were non-typeable. Nine clones (clusters) of S. agalactiae were observed in the present study with 70% similarity, and 53 different types were identified among the isolates. Except for capsular types III and V that belonged to clones 3, 5, 7, and 9, other capsular types were detected in different RAPD types. We found that the capsular types Ib and Ia were predominant among pregnant women in this area, indicating their significance for vaccine designation. Also, our isolates showed a lower genotypic diversity in RAPD typing. This may be due to the same sources of most isolates.

Disentangling fine‐ and large‐scale colonization processes in metapopulation dynamics: a case study on a threatened epiphytic bryophyte

Understanding the colonization process of species living in a dynamic fragmented habitat is essential to assess their persistence. In the metapopulation theory, the colonization of a species can be quantified using the turnover of occupancy in habitat patches. However, this approach is often limited by the feasible size of surveyed areas. Because many species are capable of long‐distance dispersal, such areas often constitute open systems undergoing colonization of propagules coming from outside, the ‘background deposition'. We focus on disentangling background deposition from local colonization among surveyed patches when analyzing turnover. We consider two spatial scales: 1) focal areas where all patches are monitored over time; 2) a larger extent, encompassing the focal areas, over which the distribution of the target species is quantified with a coarse spatial grain. Our key idea is to use the regional connectivity of focal areas within the larger scale as a covariate when analyzing colonization events within focal areas. A positive effect of regional connectivity on the colonization probability of patches may indicate background deposition. We applied this approach to the epiphytic bryophyte Dicranum viride in a managed temperate deciduous forest, considering phorophyte trees as patches, forest stands as focal areas and the whole forest as the larger scale. We combined a fine‐grained turnover survey of occupied trees within three forest stands (~ 3 ha) with a coarse‐grained snapshot of D. viride distribution over the forest (~ 15 000 ha). Regional connectivity came out as the most significant factor, with a strong positive effect on colonization probability within stands. However, it was attributed to sources in the immediate vicinity of focal stands, suggesting a short‐ranged colonization process occurring across stands' borders rather than long‐distance background deposition. Our results thus call for maintaining a stepping‐stone of habitat across the forest through time to improve D. viride persistence.

Estimating landscape spread of a low‐prevalence disease using multiple surveillance methods

Abstract Diseases occurring at low prevalence in free‐ranging wildlife can be difficult to study and predict at a landscape scale. This problem is compounded by imperfect pathogen detection. We used data from multiple surveillance methods to determine factors influencing spread of a low‐prevalence disease, bovine tuberculosis (bTB), among white‐tailed deer (Odocoileus virginianus) in a bTB endemic area over a 10‐year period. We fit dynamic occupancy models to predict spatial spread of bTB through a county in Michigan, USA, within the bTB endemic area, while accounting for imperfect detection and a suite of ecological processes potentially driving bTB spread. Detection by all surveillance methods was low overall (posterior mean detection probabilities 0.01–0.03). Probability of bTB occurrence was 1.46 times as likely in the historical centre of the outbreak compared to outside. Deer density had a weakly positive effect on bTB spread. The probability of a site being newly infected with bTB annually was low (posterior mean colonization probabilities 0.08–0.27), while the probability of persistence after initial infection was high (posterior mean persistence probability 0.67). Synthesis and applications: We used three surveillance methods to estimate probability of presence and spread of a low‐prevalence pathogen at a landscape scale under incomplete sampling coverage. Our methods are relevant for determining spatial risk of any wildlife disease that is monitored using multiple methods of surveillance, which is important for prioritization of management actions.

Do cuckoo calls affects red-backed shrike settlement pattern? An experimental approach

Birds select breeding territories by assessing territory quality and considering predation pressure. However, in many small passerines, brood parasitism may also play an important role in territory occupancy. Settlement decisions are made under time pressure, especially for late migrants. An example of late migrants is the red-backed shrike Lanius collurio, a species wintering in sub-tropical Africa, which serves as a host for the common cuckoo Cuculus canorus and arrives in territories a few days later than their brood parasite. We expected that arriving red-backed shrikes avoided territories with common cuckoo presence. Then, we tested how experimentally provided artificial playback calls of the common cuckoo and woodpigeon (treated as control) affected the probability of red-backed shrike settlement. In the breeding season 2021, we observed 279 red-backed shrike territories to assess the effect of playback of common cuckoo calls on their host presence. Moreover, we adopt information on shrike territories collected in previous years to establish territory quality, measured by occupancy pattern over years. Each of these places was also checked for the presence of corvids, which are predators of shrike nests. We did not find difference with lower preference of shrikes towards cuckoo calls and to pigeon calls Columba columbus, what suggest the human presence and manipulation in the territories during experiments with recorders should be incorporated as an important factor to understanding shrikes’ settlement behaviour. What is interesting we found no negative effect of corvids (jay Garrulus glandarius) in control territories. However, shrike territories where cuckoo calls were emitted and where the presence of corvids was found were less likely to be inhabited by shrikes. Therefore, territory quality, human presence enhanced by nest predators, is an important factor affecting host–parasite interactions.

Decomposing biodiversity change to processes of extinction, colonization, and recurrence across scales

Temporal biodiversity change involves colonization, extinction, and recurrence of species. These processes vary with spatial grain (i.e. the area at which biodiversity is assessed), but there is little theory to explain this. Here, we present theoretical scenarios showing that colonization, extinction, and recurrence of species can either increase or decrease in strength across grain size. We tested for these patterns in empirical data on Czech birds over 30 years, and several orders of magnitude of spatial grain. We found that colonization increased from local to national scales, while extinctions followed a hump‐shaped pattern, leading to a higher temporal increase of richness towards coarse grains. Probabilities of colonization and extinction decreased with grain size, with a steeper decrease for extinction. Our results hold independently across two time periods (1985–2002 and 2002–2017), and colonization is the dominant process behind temporal change of richness. This decomposition of biodiversity change allowed us to identify scale‐wise ecological mechanisms driving biodiversity change, and explain seemingly confusing directions of biodiversity change at different spatial scales.