Improving phenological event identification in trees using manually measured dendrometer data: conventional approaches vs. the novel two-stage threshold approach

The facultative bimodal growth pattern in Quercus ilex – A simple model to predict sub-seasonal and inter-annual growth

As climate change continues, cities are experiencing more heat and drought, causing further deterioration of growing conditions for urban trees. We investigated the growth of the commonly planted urban tree species Tilia cordata, Acer platanoides and Robinia pseudoacacia. The growth analyses are based on dendrometer data from permanent tree laboratories in two German cities with different precipitation levels: Munich with 940 mm/year and Würzburg with 570 mm/year. Species-specific growth patterns (quantity, growth initiation and duration) and the effects of site microclimate on stem increment were analyzed. Due to the high temporal resolution of the dendrometer data and the long recording periods of over 5 years, both long-term trends over several years and short-term reactions of the trees to external influences can be analyzed.Additional to the species-specific differences, with lowest annual growth rates for T. cordata, significant trends show that precipitation and urbanization strongly dictate where trees grow the best. For both cities, cooler and greener sites revealed higher stem increment compared to warmer, highly sealed sites in the historic city centre. During 2021 more precipitation was registered (14 to 19% higher than the long-term average) in both cities. The most beneficial effect on tree growth is clearly shown for Munich, with approximately 50% higher increment for A. platanoides and 30% higher increment of T. cordata compared to the drier year 2022.These results can support planning decisions on the selection of suitable tree species for urban locations.

Plastic bimodal growth in a Mediterranean mixed-forest of Quercus ilex and Pinus halepensis

Solid-state nanoporesequencing has shown impressive performancesin several research scenarios but is still challenging, mainly dueto the ultrafast speed of DNA translocation and significant noisesembedded in raw signals. Hence, event detection, aiming to locateprecisely these translocation events, is the fundamental step of dataanalysis. However, existing event detection methods use either a user-definedglobal threshold or an adaptive threshold determined by the data,assuming the baseline current to be stable over time. These disadvantageslimit their applications in real-world application scenarios, especiallyconsidering that the results of different methods are often inconsistent.In this study, we develop an automated adaptive method called AutoNanopore,for fast and accurate event detection in current traces. The methodconsists of three consecutive steps: current trace segmentation, currentamplitude outlier identification by straightforward statistical analyses,and event characterization. Then we propose ideas/metrics on how toquantitatively evaluate the performance of an event detection method,followed by comparing the performance of AutoNanopore against twostate-of-the-art methods, OpenNanopore and EventPro. Finally, we examineif one method can detect the overlapping events detected by the othertwo, demonstrating that AutoNanopore has the highest coverage ratio.Moreover, AutoNanopore also performs well in detecting challengingevents: e.g., those with significantly varying baselines.

The consequences for growth and phenology of early selection for height or its growth components were evaluated in 160 open-pollinated families of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) from southwestern Oregon. Seedlings from two inland and two coastal populations (40 families each) were grown for two growing seasons in a common garden. Predicted response to selection suggests that risk of low juvenile–mature correlation and maladaptation with early selection would be less in the inland than in the coastal region. A phenological event that influences a common growth pattern seems to account for the difference in response. Early bud set in the 1st year was genetically correlated with larger overwintering buds in seedlings from both inland and coastal regions. These larger buds yielded a large increment of predetermined growth in the 2nd year, followed by little or no free growth and early bud set. Seedlings with late bud set in the 1st year had the converse pattern. Inland seedlings set buds much earlier on the average than did coastal seedlings; hence seedlings from the two regions had different growth patterns. Risks that can attend early selection for height generally would be decreased in both regions by selecting for predetermined growth, but several qualifications are discussed.

Phenology of High-Arctic Arthropods: Effects of Climate on Spatial, Seasonal, and Inter-Annual Variation

A robust method for microseismic event detection based on automatic phase pickers

Increasingly, the analysis of biological data involves collection of data over time, especially when the phenomena of interest concern identification of patterns of differential growth or response to long-term environmental stressors. When different patterns over time can be identified, they may indicate the presence of different survival strategies in a population of interest, species-specific responses to stressors, or may be markers for as yet unidentified subspecies in the population. In this chapter, two techniques for the analysis of biological data over time are described. The first technique is a two-stage analysis of data over time in which polynomial regressions are conducted to identify distinct growth patterns in the data. These growth curve patterns are then used in subsequent structural models to identify the correlates of growth curves. The second technique, the method of “Tuckerized” growth curves, proposes identification of growth curves by an eigenvalue decomposition. This solution is then rotated to make the solution conceptually interpretable within the context of overall growth over time. Factor scores from this rotated solution are then used to investigate whether such growth patterns differ as a function of environmental or species classification. Both techniques are compared and contrasted using longitudinal data on tree circumference taken from three species of trees located in the wetlands of two North American states, South Carolina and Louisiana. Rather than being competing models of growth over time, these two techniques represent complementary analyses, which differ in terms of their assumptions of categorization and growth curve processes over time.

Light, as a primary source of energy, directly or indirectly influences virtually all morphological modifications occurring in both shoots and roots. A pot experiment was conducted to assess the growth patterns of one-year-old Pleioblastus pygmaeus plants’ rhizome-root systems and their responses to different light intensities from 11 March to 26 December 2016. The experiment design scheme was 3.87% (L1), 11.25% (L2), 20.25% (L3), 38.76% (L4), 60.70% (L5), and 100% full sunlight (control CK). The results indicated that along the growing period from March to December, eight of the eleven studied parameters of the rhizome-root system showed significant variability and diverse growth patterns. In addition, light intensity is a key factor for determining P. pygmaeus plants’ rhizome and root growth. Specifically, the light intensity had a significant, positive, and linear/or almost linear impact on the number of old and new rhizomes, old rhizome length, new rhizome diameter, as well as the culm root diameter. A nonlinear and positive relationship was found between light intensity and the listed three parameters, i.e., new rhizome length, new rhizome internode length, and rhizome root length. The value of the above-mentioned three parameters significantly increased when affected from 0% to 40–60% of full sunlight and then gradually increased until 100% of full sunlight. The ratio of aboveground dry weight to underground dry weight (A/U ratio) showed a single peak curve with increasing light intensity and presented the highest value under ca. 55% full sunlight. Furthermore, 40% full sunlight (equal to an average light of 2232 lux) might be the threshold for P. pygmaeus rhizome-root system growth. When the light intensity was below 40%, the generalized additive models (GAMs) predicted value of most studied parameters decreased to lower than zero. In conclusion, current study provides a solid basis for understanding the dynamic growth and development of P. pygmaeus rhizome-root system, and its responses to different light conditions, which could be used as inputs to P. pygmaeus plant cultivation.

A bimodal radial growth (RG) pattern, i.e., growth peaks in spring and autumn, was repeatedly found in trees in the Mediterranean regions, where summer drought causes reduction or cessation of cambial activity. In a dry inner Alpine valley of the Eastern Alps (Tyrol, Austria, 750 m asl), Pinus sylvestris shows unimodal RG with onset and cessation of cambial activity in early April and late June, respectively. A resumption of cambial activity after intense summer rainfall was not observed in this region. In a field experiment, we tested the hypothesis that early cessation of cambial activity at this drought-prone site is an adaptation to limited water availability leading to an early and irreversible switch of carbon (C) allocation to belowground. To accomplish this, the C status of young P. sylvestris trees was manipulated by physical blockage of phloem transport (girdling) 6 weeks after cessation of cambial cell division. Influence of manipulated C availability on RG was recorded by stem dendrometers, which were mounted above the girdling zone. In response to blockage of phloem flow, resumption of cambial activity was detected above girdling after about 2 weeks. Although the experimentally induced second growth surge lasted for the same period as in spring (c. 2 months), the increment was more than twice as large due to doubling of daily maximum RG rate. After girdling, wood anatomical traits above girdling no longer showed any significant differences between earlywood and latewood tracheids indicating pronounced effects of C availability on cell differentiation. Below girdling, no reactivation of cambial activity occurred, but cell wall thickness of last formed latewood cell was reduced due to lack of C supply after girdling. Intense RG resumption after girdling indicates that cessation of cambial activity can be reversed by manipulating C status of the stem. Hence, our girdling study yielded strong support for the hypothesis that belowground organs exert high C sink strengths on the drought-prone study site. Furthermore, this work highlights the need of in-depth experimental studies in order to understand the interactions between endogenous and exogenous factors on cambial activity and xylem cell differentiation more clearly.

Anticipating future impacts of climate warming and aridification on drylands requires understanding how coexisting woody plant species respond to climate variability. However, we lack knowledge of the growth resilience capacity of Mediterranean shrubs. Do coexisting trees and shrubs differ in their response to climate? Do coexisting shrub species have comparable post‐drought growth resilience? This study was conducted in two Mediterranean shrublands with sparse trees in semi‐arid north‐eastern Spain. We selected sites situated in formerly agricultural or grassland areas in two regions subjected to semi‐arid Mediterranean climate conditions. We sampled six shrubs' species ( Juniperus phoenicea , Juniperus oxycedrus , Pistacia lentiscus , Pistacia terebinthus , Rhamnus lycioides and Rhamnus alaternus ) and one tree species ( Pinus halepensis ) to measure their radial growth and to reconstruct their past growth patterns using dendrochronology. We quantified climate–growth relationships of trees and shrubs, as well as the growth resilience capacity after drought events of the six shrubs. Growth patterns differed between species but a prevalent trade‐off between growth and longevity was found. Growth responses to climate were comparable between species but differed between sites. Most species responded positively to precipitation and negatively to temperature. The most negative correlations of growth with drought severity were found at the driest Valcuerna site. Shrubs differed in their resilience capacity. Across sites, species were more resistant and resilient in Alcubierre, the wettest site. The shrubs P. terebinthus and R. lycioides were more resistant and resilient than the rest of species, which required longer growth recovery times and accumulated stronger growth reductions, particularly J. phoenicea . Synthesis . These results highlight the importance of drought as a driver of growth in Mediterranean scrublands. Growth resilience strategies differed between species with junipers being less resilient to drought than other coexisting shrubs. Further research should investigate how this difference in post‐drought resilience is related to functional traits, particularly those related with plant water‐use strategies.

SUMMARYThe objective of the current study was to assess the use of nonlinear mixed model methodology to fit the growth curves (weightv.time) of two dairy goat genotypes (Alpine, +A and Saanen, +S). The nonlinear functions evaluated included Brody, Von Bertalanffy, Richards, Logistic and Gompertz. The growth curve adjustment was performed using two steps. First, random effectsu1,u2andu3were linked to the asymptotic body weight (β1), constant of integration (β2) and rate constant of growth (β3) parameters, respectively. In addition to a traditional fixed-effects model, four combinations of models were evaluated using random variables: all parameters associated with random effects (u1,u2andu3), onlyβ1andβ2(u1andu2), onlyβ1andβ3(u1andu3) and onlyβ1(u1). Second, the fit of the best adjusted model was refined by using the power variance and modelling the error structure. Residual variance ($\sigma _e^2 $) and the Akaike information criterion were used to evaluate the models. After the best fitting model was chosen, the genotype curve parameters were compared. The residual variance was reduced in all scenarios for which random effects were considered. The Richards (u1andu3) function had the best fit to the data. This model was reparameterized using two isotropic error structures for unequally spaced data, and the structure known in the literature as SP(MATERN) proved to be a better fit. The growth curve parameters differed between the two genotypes, with the exception of the constant that determines the proportion of the final size at which the inflection point occurs (β4). The nonlinear mixed model methodology is an efficient tool for evaluating growth curve features, and it is advisable to assign biologically significant parameters with random effects. Moreover, evaluating error structure modelling is recommended to account for possible correlated errors that may be present even when using random effects. Different Richard growth curve parameters should be used for the predominantly Alpine and Saanen genotypes because there are differences in their growth patterns.

Climate change is altering the timing of seasonal events for many taxa. There is limited understanding of how northward/southward songbird migration follows or is limited by the latitudinal progression of seasonal transitions. Consistent environmental conditions that migrating birds encounter across latitudes likely represent or correlate with important resources or limiting factors for migration. We tested whether migratory passage-observed via radar-consistently tracked land surface variables and phenophases across latitudes in the US Central Flyway in both spring and fall. The daily temperatures, precipitation and vegetation greenness occurring on 10%, 50% and 90% cumulative passage dates changed substantially with latitude, indicating that most migrants experienced rapidly changing conditions as they headed north or south. Temperature did not limit the progression of migration in either season. Peak spring migration in the southern US occurred nearly 40 days after the spring green wave, the northward progression of vegetation growth, but nearly caught up to green-up at 48° N. Spring migration phenology may have evolved to prioritize earlier arrival for breeding. Across all latitudes, peak fall migration coincided with the same land surface phenophase, an interval of 26 days prior to dormancy onset. Migrants may rely on phenological events in vegetation during fall stopovers. Considering that (a) migratory passage tracked fall land surface phenology across latitudes at a continental scale, (b) previous studies at local scales have demonstrated the importance of fruit during fall migratory stopover and (c) fruiting phenology in North America is occurring later over time while fall migration is advancing, the potential for mismatch between fall fruiting and bird migration phenology urgently needs further investigation.

In the transition between Mediterranean forest and the arid subtropical shrublands of the southeastern Iberian Peninsula, humans have transformed habitat since ancient times. Understanding the role of the original mosaic landscapes in wildlife species and the effects of the current changes as pine forest plantations, performed even outside the forest ecological boundaries, are important conservation issues. We studied variation in the density of the endangered spur-thighed tortoise (Testudo graeca) in three areas that include the four most common land types within the species’ range (pine forests, natural shrubs, dryland crop fields, and abandoned crop fields). Tortoise densities were estimated using a two-stage modeling approach with line transect distance sampling. Densities in dryland crop fields, abandoned crop fields and natural shrubs were higher (>6 individuals/ha) than in pine forests (1.25 individuals/ha). We also found large variation in density in the pine forests. Recent pine plantations showed higher densities than mature pine forests where shrub and herbaceous cover was taller and thicker. We hypothesize that mature pine forest might constrain tortoise activity by acting as partial barriers to movements. This issue is relevant for management purposes given that large areas in the tortoise’s range have recently been converted to pine plantations.

This paper presents a Simple and effective unsupervised adaptation method for Robust Object Detection (SimROD). To overcome the challenging issues of domain shift and pseudo-label noise, our method integrates a novel domain-centric data augmentation, a gradual self-labeling adaptation procedure, and a teacher-guided fine-tuning mechanism. Using our method, target domain samples can be leveraged to adapt object detection models without changing the model architecture or generating synthetic data. When applied to image corruptions and high-level cross-domain adaptation benchmarks, our method outperforms prior baselines on multiple domain adaptation benchmarks. SimROD achieves new state-of-the-art on standard real-to-synthetic and cross-camera setup benchmarks. On the image corruption benchmark, models adapted with our method achieved a relative robustness improvement of 15-25% AP50 on Pascal-C and 5-6% AP on COCO-C and Cityscapes-C. On the cross-domain benchmark, our method outperformed the best baseline performance by up to 8% and 4% AP50 on Comic and Watercolor respectively. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup>