Median Tree Research Articles

Exact median-tree inference for unrooted reconciliation costs

BackgroundSolving median tree problems under tree reconciliation costs is a classic and well-studied approach for inferring species trees from collections of discordant gene trees. These problems are NP-hard, and therefore are, in practice, typically addressed by local search heuristics. So far, however, such heuristics lack any provable correctness or precision. Further, even for small phylogenetic studies, it has been demonstrated that local search heuristics may only provide sub-optimal solutions. Obviating such heuristic uncertainties are exact dynamic programming solutions that allow solving tree reconciliation problems for smaller phylogenetic studies. Despite these promises, such exact solutions are only suitable for credibly rooted input gene trees, which constitute only a tiny fraction of the readily available gene trees. Standard gene tree inference approaches provide only unrooted gene trees and accurately rooting such trees is often difficult, if not impossible.ResultsHere, we describe complex dynamic programming solutions that represent the first nonnaïve exact solutions for solving the tree reconciliation problems for unrooted input gene trees. Further, we show that the asymptotic runtime of the proposed solutions does not increase when compared to the most time-efficient dynamic programming solutions for rooted input trees.ConclusionsIn an experimental evaluation, we demonstrate that the described solutions for unrooted gene trees are, like the solutions for rooted input gene trees, suitable for smaller phylogenetic studies. Finally, for the first time, we study the accuracy of classic local search heuristics for unrooted tree reconciliation problems.

The ordered median tree of hubs location problem

In this paper, we propose the Ordered Median Tree of Hub Location Problem (OMTHL). The OMTHL is a single-allocation hub location problem where p hubs must be placed on a network and connected by a non-directed tree. Each non-hub node is assigned to a single hub and all the flow between origin–destination pairs must cross at least one hub. The objective is to minimize the sum of the ordered weighted averaged collection and distribution costs plus the sum of the interhub flow costs. We present different MILP formulations for the OMTHL based on the properties of the Minimum Spanning Tree Problem, the ordered median optimization and on the different ways of modeling flow within the network. Given that ordered median hub location problems are rather difficult to solve, we have improved the OMTHL solution performance by introducing covering variables in two valid reformulations. In addition, we have developed two pre-processing phases to reduce the size of these formulations. We establish an empirical comparison between these new formulations and we also provide enhancements that together with a proper formulation allow to solve medium-size instances on general random graphs.

Variation in Eucalyptus delegatensis post-fire recovery strategies: The Tasmanian subspecies is a resprouter whereas the mainland Australian subspecies is an obligate seeder

Eucalyptus delegatensis is native to the Australian Alps (subsp. delegatensis) and montane Tasmania (subsp. tasmaniensis). Post-fire regeneration mechanisms of the obligate-seeder subspecies on the Australian mainland are well-known, but less is known about the resprouter Tasmanian subspecies. In January 2016, large tracts of Eucalyptus delegatensis forests in central Tasmania, logged at different intensities, were burnt by low- and high-severity fire. We used statistical modelling to understand how tree survival, vegetative regeneration and seedling recruitment differed according to understorey type, fire severity, logging intensity and tree size (DBH). Fire severity, defined as unburnt, low-severity (fire scarring on the stem and/or lower canopy burnt) and high-severity (full canopy burnt), affected tree survival: 84% of trees were alive in unburnt transects, compared with 43% in low-severity transects and 36% in high-severity transects. Epicormic resprouting was the dominant mode of vegetative recovery, with < 1% of total trees recovering solely by basal resprouting. Fire severity significantly affected epicormic resprouting, with 70% of live stems resprouting post-fire in low-severity transects and 99% in high-severity transects, compared with 4% in unburnt transects. Tree survival was strongly influenced by tree size: in high-severity transects, 24% of trees with DBH < 20 cm were alive, compared with 88% of trees with DBH ≥ 20 cm. These differences in survival were primarily because large trees were more likely to resprout epicormically, with epicormic shoots present on 24% of live trees with DBH < 20 cm, compared with 79% of live trees with DBH ≥ 80 cm. The strong effect of tree size renders clear-felled forests especially vulnerable to fire during the several decades when all the regenerating trees are small (DBH < 20 cm). Seedling recruitment was uncommon, independent of understorey type and logging intensity, but with higher occurrence on high-severity (54%) than low-severity (19%) or unburnt (15%) transects. When present, seedling densities were typically low: median = 400 and maximum = 4·104 seedlings ha−1. This study highlights that mature forests of Eucalyptus delegatensis in Tasmania are more resilient (able to return to pre-disturbance conditions) to single high-severity fires than their mainland counterparts, because they can recover more quickly through epicormic resprouting. However, clear-felling reduces this resilience for several decades because it decreases median tree size and, hence, leads to higher post-fire mortality. It is difficult to predict how the Tasmanian subspecies will respond to an increased frequency of high-severity fires associated with a projected warmer and drier climate.

Pruning of genetic programming trees using permutation tests

We present a novel approach based on statistical permutation tests for pruning redundant subtrees from genetic programming (GP) trees that allows us to explore the extent of effective redundancy . We observe that over a range of regression problems, median tree sizes are reduced by around 20% largely independent of test function, and that while some large subtrees are removed, the median pruned subtree comprises just three nodes; most take the form of an exact algebraic simplification. Our statistically-based pruning technique has allowed us to explore the hypothesis that a given subtree can be replaced with a constant if this substitution results in no statistical change to the behavior of the parent tree—what we term approximate simplification. In the eventuality, we infer that more than 95% of the accepted pruning proposals are the result of algebraic simplifications, which provides some practical insight into the scope of removing redundancies in GP trees.

Spatial characteristics and economic value of threatened species (Khaya ivorensis)

Khaya ivorensis (K. ivorensis), one of the most valuable tropical hardwood species indigenous to West and Central Africa, has been classified as a threatened tree species. However, information on its remaining population and distribution are limited. We mapped the current K. ivorensis spatial distribution, modelled the spatial autocorrelation and estimated its economic value using volume estimation and market pricing. The study was conducted in Odigbo and Irele local government areas (LGA), Ondo State, Nigeria. Spatially, localities of 97 K. ivorensis were identified across the study area and can be added into a wide range of datasets from local to global inventories. Large trees in diameter and height were statistically clustered in the north of Odigbo and assumed to relate with forest reserve management. Estimated median tree volumes were 0.39 m3 and 0.31 m3 in accordance with the allometric volume function and specific volume function, respectively. The economic values of wood varied approximately from US$111,208 to US$72,081. Findings from this study are a valuable resource for conserving this species and other threatened tree species.

Ageing culturally significant relic trees in southeast Queensland to support bushfire management strategies

SummaryAppropriate fire management strategies are needed to protect forests and large old ecologically and culturally significant trees in natural landscapes. The aim of this study was to determine the age of large old and relic trees of cultural significance that included Cypress Pine (Callitris columellaris F. Muell.), a species that is sensitive to crown scorching fires in a fire‐prone landscape, and to calibrate a tree‐growth‐rate method for estimating tree age. Twelve large trees were dated using radiocarbon (14C) dating. The trees are located on North Stradbroke Island (Indigenous name: Minjerribah), southeast Queensland (Australia) in a fire‐prone landscape where recent wildfires have destroyed many large trees. The median tree ages ranged from 155 to 369 years. These results suggest an important role of past Indigenous land management practices in protecting Cypress Pine from crown scorching fires. The tree‐growth‐rate‐based method for estimating tree age generally overestimated the age derived from radiocarbon dating. Bias correction factors were developed for correcting various measures of periodic growth rates. This study provides evidence that appropriate low‐intensity fire strategies have the potential to contribute to the survival of forests and conserve large old trees.

Residential urban tree canopy is associated with decreased mortality during tuberculosis treatment in California

Trees can sequester air pollutants, and air pollution is associated with poor tuberculosis outcomes. However, the health impacts of urban trees on tuberculosis patients are unknown. To elucidate the effects of urban tree canopy on mortality during tuberculosis treatment, we evaluated patients diagnosed with active tuberculosis in California from 2000 through 2012, obtaining patient data from the California tuberculosis registry. Our primary outcome was all-cause mortality during tuberculosis treatment. We determined percent tree cover using 1 mresolution color infrared orthoimagery categorized into land cover classes, then linked tree cover to four circular buffer zones of 50–300 m radii around patient residential addresses. We used the Kaplan-Meier method to estimate survival probabilities and Cox regression models to determine mortality hazard ratios, adjusting for demographic, socioeconomic, and clinical covariates. Our cohort included 33,962 tuberculosis patients of median age 47, 59% male, 51% unemployed, and 4.9% HIV positive. Tuberculosis was microbiologically confirmed in 79%, and 1.17% were multi-drug resistant (MDR). Median tree cover was 7.9% (50 m buffer). Patients were followed for 23,280 person-years with 2370 deaths during tuberculosis treatment resulting in a crude mortality rate of 1018 deaths per 10,000 person-years. Increasing tree cover quintiles were associated with decreasing mortality risk during tuberculosis treatment in all buffers, and the magnitude of association decreased incrementally with increasing buffer radius: In the 50 m buffer, patients living in neighborhoods with the highest quintile tree cover experienced a 22% reduction in mortality (HR 0.78, 95%CI 0.68–0.90) compared to those living in lowest quintile tree cover; whereas for 100, 200, and 300 m buffers, a 21%, 13%, and 11% mortality risk reduction was evident. In conclusion, urban tree canopy was associated with decreased mortality during tuberculosis treatment even after adjusting for multiple demographic, socioeconomic, and clinical factors, suggesting that trees might play a role in improving tuberculosis outcomes.

Structural Characteristics of Tree Cover and the Association with Cardiovascular and Respiratory Health in Tampa, FL.

Urban tree cover can provide several ecological and public health benefits. Secondary datasets for Tampa, FL, including sociodemographic variables (e.g., race/ethnicity), health data, and interpolated values for features of tree cover (e.g., percent canopy and leaf area index) were analyzed using correlation and regression. Percent canopy cover and leaf area index were inversely correlated to respiratory and cardiovascular outcomes, yet only leaf area index displayed a significant association with respiratory conditions in the logistic regression model. Percent racial/ethnic minority residents at the block group level was significantly negatively correlated with median income and tree density. Leaf area index was also significantly lower in block groups with more African-American residents. The percentage of African Americans (p = 0.101) and Hispanics (p < 0.001) were positively associated with respiratory outcomes while population density (p < 0.001), percent canopy (p < 0.01), and leaf area index (p < 0.01) were negatively associated. In multivariate models, higher tree density, leaf area index, and median income were significantly negatively associated with respiratory cases. Block groups with a higher proportion of African Americans had a higher odds of displaying respiratory admissions above the median rate. Tree density and median income were also negatively associated with cardiovascular cases. Home ownership and tree condition were significantly positively associated with cardiovascular cases.

L1-NORM FITTING OF ELLIPTIC PARABOLOIDS WITH PRIOR INFORMATION FOR ENHANCED CONIFEROUS TREE LOCALIZATION IN ALS POINT CLOUDS

Abstract. Airborne laser scanning (ALS) is an established tool for deriving various tree characteristics in forests. In some applications, an accurate pointwise estimate of the tree position is required. For dense data acquired by TLS or UAV-mounted scanners, this can be achieved by locating the stem, whose center coordinates are then used for deriving the planimetric tree position. However, in case of standard ALS data this is often not an option due to the low probability of obtaining stem hits in operational scenarios of forest mapping campaigns. This paper presents an alternative, indirect approach where the tree position is approximated as the center of a quadric surface which best represents the tree crown shape. The study targets coniferous trees due to their distinct crown shape which may be approximated by an elliptic paraboloid. It is assumed that individual tree point clusters are given and the task is to find the tree center for each cluster. We first consider the general problem of fitting an elliptic paraboloid with a known axis and an L1 residual norm error criterion, which is more robust to outliers compared to least-squares fitting. We formulate this problem as a quadratically constrained quadratic program (QCQP), and show how prior knowledge on the crown shape and center position can be incorporated. Next, a computationally simpler problem is considered where the paraboloid semiaxis lengths are constrained to be equal, and a corresponding linear program is constructed. Experiments on ALS datasets of forest plots from Bavaria, Germany and Oregon, USA reveal that a reduction in median tree position error of up to 20% can be attained compared to both least-squares fitting and other baseline techniques, resulting in an absolute error of ca. 22 cm on both datasets.

Effect of lianas on forest‐level tree carbon accumulation does not differ between seasons: Results from a liana removal experiment in Panama

AbstractLianas are prevalent in Neotropical forests, where liana‐tree competition can be intense, resulting in reduced tree growth and survival. The ability of lianas to grow relative to trees during the dry season suggests that liana‐tree competition is also strongest in the dry season. If correct, the predicted intensification of the drying trend over large areas of the tropics in the future may therefore intensify liana‐tree competition resulting in a reduced carbon sink function of tropical forests. However, no study has established whether the liana effect on tree carbon accumulation is indeed stronger in the dry than in the wet season.Using 6 years of data from a large‐scale liana removal experiment in Panama, we provide the first experimental test of whether liana effects on tree carbon accumulation differ between seasons. We monitored tree and liana diameter increments at the beginning of the dry and wet season each year to assess seasonal differences in forest‐level carbon accumulation between removal and control plots.We found that median liana carbon accumulation was consistently higher in the dry (0.52 Mg C ha−1year−1) than the wet season (0.36 Mg C ha−1year−1) and significantly so in three of the years. Lianas reduced forest‐level median tree carbon accumulation more severely in the wet (1.45 Mg C ha−1year−1) than the dry (1.05 Mg C ha−1year−1) season in all years. However, the relative effect of lianas was similar between the seasons, with lianas reducing forest‐level tree carbon accumulation by 46.9% in the dry and 48.5% in the wet season.Synthesis.Our results provide the first experimental demonstration that lianas do not have a stronger competitive effect on tree carbon accumulation during the dry season. Instead, lianas compete significantly with trees during both seasons, indicating a large negative effect of lianas on forest‐level tree biomass increment regardless of seasonal water stress. Longer dry seasons are unlikely to impact liana‐tree competition directly; however, the greater liana biomass increment during dry seasons may lead to further proliferation of liana biomass in tropical forests, with consequences for their ability to store and sequester carbon.

Cophenetic Median Trees.

Median tree inference under path-difference metrics has shown great promise for large-scale phylogeny estimation. Similar to these metrics is the family of cophenetic metrics that originates from a classic dendrogram comparison method introduced more than 50 years ago. Despite the appeal of this family of metrics, the problem of computing median trees under cophenetic metrics has not been analyzed. Like other standard median tree problems relevant in practice, as we show here, this problem is also NP-hard. NP-hard median tree problems have been successfully addressed by local search heuristics that are solving thousands of instances of a corresponding (local neighborhood) search problem. For the local neighborhood search problem under a cophenetic metric, the best known (naïve) algorithm has a time complexity that is typically prohibitive for effective heuristic searches. Building on the pioneering work on path-difference median trees, we develop efficient algorithms for Manhattan and Euclidean cophenetic search problems that improve on the naïve solution by a linear and a quadratic factor, respectively. We demonstrate the performance and effectiveness of the resulting heuristic methods in a comparative study using benchmark empirical datasets.

EVIDENCE OF TWO COCIRCULATING CANINE DISTEMPER VIRUS STRAINS IN MESOCARNIVORES FROM NORTHERN COLORADO, USA.

Canine distemper virus (CDV) is a highly contagious pathogen that principally infects wildlife and domestic carnivores. Peridomestic species such as raccoons ( Procyon lotor) experience outbreaks with high mortality. Clinical signs of infection include anorexia, fever, respiratory infection, and neurologic complications. Although not zoonotic, CDV poses a high risk to unvaccinated domestic animals and the conservation of endangered species. During 2013-16, we opportunistically collected wild and domestic carnivore specimens through a rabies surveillance program in northern Colorado, US. Brainstem and cerebellar tissue samples were independently tested for rabies and CDV by fluorescent antibody test. We tested a total of 478 animals for CDV, comprised of 10 wild and domestic carnivore species. A total of 15% (72/478) of all animals sampled tested positive for CDV, consisting of 24% (71/300) of raccoons and 4% (1/26) of coyotes ( Canis latrans), but coinfection with rabies virus was not observed among CDV-positive animals. We extracted RNA from positive tissues, and a reverse-transcription PCR was used to create complementary DNA. We amplified and sequenced the hemagglutinin gene from 60 CDV-positive tissues, and a median joining network and maximum likelihood phylogenetic tree revealed two major lineages among samples. Phylogenetic analysis indicated that our sequences were most similar to the America-2 ( n=55) and the America-3 ( n=5) CDV lineages circulating in North America. Our results indicated two distinct and distantly related clades of CDV overlapping geographically and temporally among raccoon populations in northern Colorado.

Land surveys show regional variability of historical fire regimes and dry forest structure of the western United States.

An understanding of how historical fire and structure in dry forests (ponderosa pine, dry mixed conifer) varied across the western United States remains incomplete. Yet, fire strongly affects ecosystem services, and forest restoration programs are underway. We used General Land Office survey reconstructions from the late 1800s across 11 landscapes covering ~1.9million ha in four states to analyze spatial variation in fire regimes and forest structure. We first synthesized the state of validation of our methods using 20 modern validations, 53 historical cross-validations, and corroborating evidence. These show our method creates accurate reconstructions with low errors. One independent modern test reported high error, but did not replicate our method and made many calculation errors. Using reconstructed parameters of historical fire regimes and forest structure from our validated methods, forests were found to be non-uniform across the 11 landscapes, but grouped together in three geographical areas. Each had a mixture of fire severities, but dominated by low-severity fire and low median tree density in Arizona, mixed-severity fire and intermediate to high median tree density in Oregon-California, and high-severity fire and intermediate median tree density in Colorado. Programs to restore fire and forest structure could benefit from regional frameworks, rather than one size fits all.

Managing mangrove forests from the sky: Forest inventory using field data and Unmanned Aerial Vehicle (UAV) imagery in the Matang Mangrove Forest Reserve, peninsular Malaysia

Abstract Retrieval of biophysical properties of mangrove vegetation (e.g. height and above ground biomass) has typically relied upon traditional forest inventory data collection methods. Recently, the availability of Unmanned Aerial Vehicles (UAV) with different types of sensors and capabilities has proliferated, opening the possibility to expand the methods to retrieve biophysical properties of vegetation. Focusing on the Matang Mangrove Forest Reserve (MMFR) in Perak Province, Malaysia, this study aimed to investigate the use of UAV imagery for retrieving structural information on mangroves. We focused on a structurally complex 90-year-old protective forest zone and a simpler 15-year-old productive forest zone that had been silviculturally managed for charcoal production. The UAV data were acquired in June 2016. In the productive zone, the median tree stand heights retrieved from the UAV and field data were, respectively, 13.7 m and 14 m (no significant difference, p-value = .375). In the protective zone, the median tree stand heights retrieved from the UAV and field data were, respectively, 25.8 and 16.5 m (significant difference, p-value = .0001) taking into account only the upper canopy. The above ground biomass (AGB) in the productive zone was estimated at 217 Mg ha−1 using UAV data and 238 Mg ha−1 using ground inventory data. In the protective zone, the AGB was estimated at 210 Mg ha−1 using UAV data and 143 Mg ha−1 using ground inventory data, taking into account only upper canopy trees in both estimations. These observations suggested that UAV data were most useful for retrieving canopy height and biomass from forests that were relatively homogeneous and with a single dominant layer. A set of guidelines for enabling the use of UAV data for local management is presented, including suggestions as to how to use these data in combination with field observations to support management activities. This approach would be applicable in other regions where mangroves occur, particularly as these are environments that are often remote, inaccessible or difficult to work in.

Estimating Transmission from Genetic and Epidemiological Data: A Metric to Compare Transmission Trees

Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data from pathogens. The logic behind such approaches is that isolates that are nearly genetically identical are more likely to have been recently transmitted than those that are very different. A number of methods have been developed to perform this inference. However, testing their convergence, examining posterior sets of transmission trees and comparing methods’ performance are challenged by the fact that the object of inference—the transmission tree—is a complicated discrete structure. We introduce a metric on transmission trees to quantify distances between them. The metric can accommodate trees with unsampled individuals, and highlights differences in the source case and in the number of infections per infector. We illustrate its performance on simple simulated scenarios and on posterior transmission trees from a TB outbreak. We find that the metric reveals where the posterior is sensitive to the priors, and where collections of trees are composed of distinct clusters. We use the metric to define median trees summarising these clusters. Quantitative tools to compare transmission trees to each other will be required for assessing MCMC convergence, exploring posterior trees and benchmarking diverse methods as this field continues to mature.

Canopy of advantage: Who benefits most from city trees?

Urban tree canopy provides a suite of ecological, social, and economic benefits to the residents of urban areas. With an expanding recognition of these benefits among city residents, there is growing concern that access to these benefits is not distributed equally and may represent the presence of an environmental injustice. This study examines the spatial relationship between median household income and tree canopy variables, specifically realized tree canopy cover and potential tree canopy cover, for Toronto, Canada. Toronto provides a strong empirical focus as it is a densely populated urban setting reported to be exhibiting an increase in the geographic polarization of residents based upon household income. Spatial relationships between median household income and tree canopy variables are evaluated using the bivariate Moran's I statistic, a specialized local indicator of spatial autocorrelation (LISA). This method explicitly identified where statistically significant spatial clusters of high and low household income coincide with significant clusters of high and low urban tree canopy, providing the basis for an examination of the policies and management decisions that led to this temporal snapshot. The importance of these spatial clusters is examined from the perspective of understanding the impact of urban change (both socio-demographic and built form), and from the standpoint of improving equality of access to city trees and their benefits resulting from future tree planting decisions.

Bijective Diameters of Gene Tree Parsimony Costs.

Synthesizing median trees from a collection of gene trees under the biologically motivated gene tree parsimony (GTP) costs has provided credible species tree estimates. GTP costs are defined for each of the classic evolutionary processes. These costs count the minimum number of events necessary to reconcile the gene tree with the species tree where the leaf-genes are mapped to the leaf-species through a function called labeling. To better understand the synthesis of median trees under these costs, there is an increased interest in analyzing their diameters. The diameters of a GTP cost between a gene tree and a species tree are the maximum values of this cost of one or both topologies of the trees involved. We are concerned about the diameters of the GTP costs under bijective labelings. While these diameters are linear time computable for the gene duplication and deep coalescence costs, this has been unknown for the classic gene duplication and loss, and for the loss cost. For the first time, we show how to compute these diameters and proof that this can be achieved in linear time, and thus, completing the computational time analysis for all of the bijective diameters under the GTP costs.

Implementing and managing urban forests: A much needed conservation strategy to increase ecosystem services and urban wellbeing

Megacities contain at least 10 million people whose wellbeing largely depends on ecosystem services provided by remote natural areas. What is, however, most often disregarded is that nature conservation in the city can also contribute to human wellbeing benefits. The most common mind set separates cities from the rest of nature, as if they were not special kinds of natural habitats. Instead, awareness that urban systems are also nature and do host biodiversity and ecosystem services opportunities, should push urban people towards increased urban forest conservation and implementation strategies. This research estimated existing and potential, tree cover, and its contribution to ecosystem services in 10 megacity metropolitan areas, across 5 different continents and biomes. We developed estimates for each megacity using local data to transform i-Tree Eco estimates of tree cover benefits to reductions in air pollution, stormwater, building energy, and carbon emissions for London, UK. The transformation used biophysical scaling equations based on local megacity tree cover, human population, air pollution, climate, energy use, and purchasing power parity. The megacity metropolitan areas ranged from 1173 to 18,720 sq km (median value 2530 sq km), with median tree cover 21%, and potential tree cover another 19% of the city. Megacities had a median tree cover density of 39m2/capita, much smaller than the global average value of 7800m2/capita, with density lower in desert and tropical biomes, and higher in temperate biomes. The present median benefit value from urban trees in all 10 megacities can be estimated as $482 million/yr due to reductions in CO, NO2, SO2, PM10, and PM2.5, $11 million/yr due to avoided stormwater processing by wastewater facilities, $0.5 million/yr due to building energy heating and cooling savings, and $8 million/yr due to CO2 sequestration. Planting more trees in potential tree cover areas could nearly double the benefits provided by the urban forest. In 2016 there were 40 megacities, totaling 722 million residents, nearly 10% of the human population, who would benefit from nature conservation plans where they work and live. Nature conservation strategies in megacities should work to sustain and grow the benefits of the urban forest, and improve accounting methods to include additional ecosystem services provided by the urban forest.

Growth responses of trees and understory plants to nitrogen fertilization in a subtropical forest in China

Abstract. Reactive nitrogen (N) increase in the biosphere has been a noteworthy aspect of global change, producing considerable ecological effects on the functioning and dynamics of the terrestrial ecosystems. A number of observational studies have explored responses of plants to experimentally simulated N enrichment in boreal and temperate forests. Here we investigate how the dominant trees and different understory plants respond to experimental N enrichment in a subtropical forest in China. We conducted a 3.4-year N fertilization experiment in an old-aged subtropical evergreen broad-leaved forest in eastern China with three treatment levels applied to nine 20 m × 20 m plots and replicated in three blocks. We divided the plants into trees, saplings, shrubs (including tree seedlings), and ground-cover plants (ferns) according to the growth forms, and then measured the absolute and relative basal area increments of trees and saplings and the aboveground biomass of understory shrubs and ferns. We further grouped individuals of the dominant tree species, Castanopsis eyrei, into three size classes to investigate their respective growth responses to the N fertilization. Our results showed that the plot-averaged absolute and relative growth rates of basal area and aboveground biomass of trees were not affected by N fertilization. Across the individuals of C. eyrei, the small trees with a DBH (diameter at breast height) of 5–10 cm declined by 66.4 and 59.5 %, respectively, in N50 (50 kg N ha−1 yr−1) and N100 fertilized plots (100 kg N ha−1 yr−1), while the growth of median and large trees with a DBH of &gt; 10 cm did not significantly change with the N fertilization. The growth rate of small trees, saplings, and the aboveground biomass of understory shrubs and ground-cover ferns decreased significantly in the N-fertilized plots. Our findings suggested that N might not be a limiting nutrient in this mature subtropical forest, and that the limitation of other nutrients in the forest ecosystem might be aggravated by the enhanced N availability, potentially resulting in an adverse effect on the development of natural subtropical forest.

Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach.

Median tree problems are powerful tools for inferring large-scale phylogenetic trees that hold enormous promise for society at large. Such problems seek a median tree for a given collection of input trees under some problem-specific distance. Here, we introduce a median tree problem under the classic Manhattan path-difference distance. We show that this problem is NP-hard, devise an ILP formulation, and provide an effective local search heuristic that is based on solving a local search problem exactly. Our algorithm for the local search problem improves asymptotically by a factor of $n$n on the best-known (naïve) solution, where $n$n is the overall number of taxa in the input trees. Finally, comparative phylogenetic studies using considerably large empirical data and an accuracy analysis for smaller phylogenetic trees reveal the ability of our novel heuristic.