Multi-response Permutation Procedure Research Articles

Long-Term Cumulative Effect of Management Decisions on Forest Structure and Biodiversity in Hemiboreal Forests

We evaluated the long-term impacts of various forest management practices on the structure and biodiversity of Estonian hemiboreal forests, a unique ecological transition zone between temperate and boreal forests, found primarily in regions with cold winters and moderately warm summers, such as the northern parts of Europe, Asia, and North America. The study examined 150 plots across stands of different ages (65–177 years), including commercial forests and Natura 2000 habitat 9010* “Western Taiga”. These plots varied in stand origin—multi-aged (trees of varying ages) versus even-aged (uniform tree ages), management history—historical (practices before the 1990s) and recent (post-1990s practices), and conservation status—protected forests (e.g., Natura 2000 areas) and commercial forests focused on timber production. Data on forest structure, including canopy tree diameters, deadwood volumes, and species richness, were collected alongside detailed field surveys of vascular plants and bryophytes. Management histories were assessed using historical maps and records. Statistical analyses, including General Linear Mixed Models (GLMMs), Multi-Response Permutation Procedures (MRPP), and Indicator Species Analysis (ISA), were used to evaluate the effects of origin, management history, and conservation status on forest structure and species composition. Results indicated that multi-aged origin forests had significantly higher canopy tree diameters and deadwood volumes compared to even-aged origin stands, highlighting the benefits of varied-age management for structural diversity. Historically managed forests showed increased tree species richness, but lower deadwood volumes, suggesting a biodiversity–structure trade-off. Recent management, however, negatively impacted both deadwood volume and understory diversity, reflecting short-term forestry consequences. Protected areas exhibited higher deadwood volumes and bryophyte richness compared to commercial forests, indicating a small yet persistent effect of conservation strategies in sustaining forest complexity and biodiversity. Indicator species analysis identified specific vascular plants and bryophytes as markers of long-term management impacts. These findings highlight the ecological significance of integrating historical legacies and conservation priorities into modern management to support forest resilience and biodiversity.

Determinants of microbial community structure in supraglacial pool sediments of monsoonal Tibetan Plateau.

Supraglacial pools are prevalent on debris-covered mountain glaciers, yet only limited information is available on the microbial communities within these habitats. Our research questions for this preliminary study were: (1) What microbes occur in supraglacial pool sediments of monsoonal Tibet?; (2) Which abiotic and biotic habitat variables have the most influence on the microbial community structure?; and (3) Does microbial composition of supraglacial pool sediments differ from that of glacial-melt stream pool sediments? We collected microbial samples for 16S rRNA sequencing and invertebrates for enumeration and identification and measured 14 abiotic variables from 46 supraglacial pools and nine glacial-melt stream pools in 2018 and 2019. Generalized linear model analyses, small sample Akaike information criterion, and variable importance scores were used to identify the best predictor variables of microbial community structure. Multi-response permutation procedure (MRPP) was used to compare taxa composition between supraglacial pools and stream pools. The most abundant phyla in supraglacial pool sediments were Proteobacteria, Actinobacteria, Bacteroidota, Chloroflexi, and Cyanobacteria. Genera richness, indicator genera richness, and Polaromonas relative abundance were best predicted by Chironomidae larvae abundance. Angustibacter and Oryzihumus relative abundance were best predicted by pH, Acidiphilium relative abundance was best predicted by turbidity, and Sphingomonas relative abundance was best predicted by glacier zone. Taxa composition was similar between supraglacial and stream pools at the class, genus, and ASV taxonomic levels. Our results indicate that Chironomidae larvae may play a keystone species role in shaping bacterial communities of supraglacial pools on debris-covered glaciers.IMPORTANCEGlacier meltwater habitats (cryoconite holes, supraglacial pools, supraglacial ponds and lakes, glacial streams) and their biota have not been well-studied, especially on debris-covered glaciers in temperate monsoonal regions. Our study is the first to document the microbial community-habitat relationships in supraglacial pools on a debris-covered glacier in Tibet. Microbial genera richness, indicator genera richness, and Polaromonas relative abundance declined with increasing larval Chironomidae abundance, which is a novel finding that highlights the importance of larval insects in structuring microbial communities in supraglacial pools.

Microbial diversity in dairy manure environment under liquid-solid separation systems

ABSTRACT In dairy manure, a wide array of microorganisms, including many pathogens, survive and grow under suitable conditions. This microbial community offers a tremendous opportunity for studying animal health, the transport of microbes into the soil, air, and water, and consequential impacts on public health. The aim of this study was to assess the impacts of manure management practices on the microbial community of manure. The key novelty of this work is to identify the impacts of various stages of manure management on microbes living in dairy manure. In general, the majority of dairy farms in California use a flush system to manage dairy manure, which involves liquid-solid separations. To separate liquid and solid in manure, Multi-stage Alternate Dairy Effluent Management Systems (ADEMS) that use mechanical separation systems (MSS) or weeping wall separation systems (WWSS) are used. Thus, this study was conducted to understand how these manure management systems affect the microbial community. We studied the microbial communities in the WWSS and MSS separation systems, as well as in the four stages of the ADEMS. The 16S rRNA gene from the extracted genomic DNA of dairy manure was amplified using the NovoSeq Illumina next-generation sequencing platform. The sequencing data were used to perform the analysis of similarity (ANOSIM) and multi-response permutation procedure (MRRP) statistical tests, and the results showed that microbial communities among WWSS and MSS were significantly different (p < 0.05). These findings have significant practical implications for the design and implementation of manure management practices in dairy farms.

Natura 2000 network enhances the protection of rare epiphytic lichens: evidence from forest sites of Central Italy

AbstractAlthough epiphytic lichens are widely adopted as environmental indicators, they are not yet included among the target species listed in Annex II of the Habitats Directive, to which the system of protected areas of the Natura 2000 network refers. In this work, we aim to test the effectiveness of this system, mainly designed for the conservation of other groups of species, in protecting lichen species richness. For this purpose, we considered a case study (Central Italy) with half of the territory included in protected areas. Statistical differences in species richness and lichen communities were tested between sites located in 16 Protected Areas (PA) and 11 Non-Protected Areas (NPA) using non-parametric tests, multi-response permutation procedures (MRPP), non-metric multidimensional scaling (NMDS) and Indicator Species Analysis (ISA). Despite the broad overlap between epiphytic lichen communities of NPAs and PAs and a similar number of total and common species, PAs contain a significantly higher number of nationally rare and extremely rare species, including cyanolichens. These results are also confirmed by the indicator analysis. Although the Natura 2000 network does not explicitly address the conservation of lichens, the protected areas in our study can play a role in protecting the diversity of epiphytic lichens, especially nationally rare and endangered species. However, the future inclusion of red-listed epiphytic lichens among the target species of Annex II of the Habitats Directive would be welcome to better protect these organisms on a European level.

Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture.

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.

Peaking hydropower and fish assemblages: an example from the Tallapoosa River, AL

AbstractDams alter many aspects of riverine environments and can have broad effects on aquatic organisms and habitats both upstream and downstream. While dams and associated reservoirs can provide many services to people (hydropower, recreation, flood control, and navigation), they can also negatively affect riverine ecosystems. In particular, hydropeaking dams affect downstream fish habitats by increasing variability in discharge and temperature. To assess the effects of Harris Dam on the Tallapoosa River, AL, operating under an adaptive management plan implemented in 2005, we sampled fish for community analyses from four sites on the river: three in the regulated reach downstream of the dam, and one unregulated site upstream. Fish were collected every other month using boat/barge electrofishing. We used Shannon's H, nonmetric multidimensional scaling (NMDS), a multiresponse permutation procedure (MRPP), and indicator species analysis to quantify patterns in fish assemblage structure and determine how assemblages varied among sites. NMDS and MRPP indicated significant fish assemblage differences among sites, with the tailrace fish assemblage being distinct from the other downstream sites and sites becoming more similar to the upstream, unregulated site (relative to fish assemblages) with distance downstream of the tailrace. The tailrace fish assemblage included higher proportions of rheophilic species that may be better suited to variable and/or high flows. Altered fish assemblages demonstrated continued effects of Harris Dam on the downstream aquatic systems, particularly close to the dam. These effects may indicate that further mitigation should be considered depending on conservation and management goals.

Soil microarthropod distribution on the urban–rural gradient of Riga city: a study with robust sampling method application

AbstractTo address the new challenge of bringing more nature into the urban environment and developing adequate green infrastructure management methods, it is necessary to clarify the regularities of the distribution of the main ecosystem components—soil organism communities on the urban gradient. Microarthropods—collembolans and mites—are the most diverse soil animals and bioindicators of soil conditions. However, no suitable approaches exist so far to help reduce the high workload of soil zoological studies and make the data acquisition for soil assessment faster. To get closer to a solution to this problem, we propose a robust sampling approach using one pooled sample per site with surface area 58 cm2. This was tested in a microarthropod distribution study on the urban gradient of Riga city (Latvia) in six urban habitat types at 21 sites. The use of classical statistical methods for the processing of soil microarthropod data is limited because these data do not meet model requirements on which classical methods are based, first of all, conformity to the normal distribution. These problems are circumvented by bootstrapping methodology, which thanks to increasing computer performance now is implemented in the most modern program packages. We tested a set of such methods: one-way bootstrap-based analysis of variance, nonmetric multidimensional scaling (NMS), nonparametric multiplicative regression (NPMR), multi-response permutation procedure and Chao bootstrap-based rarefaction curves. NMS in combination with NPMR gave the best results providing statistically significant species distribution curves along the urban gradient which were broadly in line with species traits found by other studies.

A Comparison of Two Macroinvertebrate Multi-Plate Sampling Methods to Inform Great Lakes Monitoring and Remediation Efforts.

Hester-Dendy (HD) multi-plate samplers have been widely used by state and federal government agencies for bioassessment of water quality through use of macroinvertebrate community data. To help guide remediation and restoration efforts at the Niagara River Great Lakes Area of Concern site, a multi-agency study was conducted in 2014 to assess the contribution of seven major urban tributaries on the US side of the river toward the impairment of the Niagara River. As part of this study, macroinvertebrate communities were sampled using two co-located versions of HD samplers: one version used by the New York State Department of Environmental Conservation (NYSDEC) and another by the US Environmental Protection Agency Office of Research and Development. Samplers were deployed in tributaries in highly developed watersheds with high percent impervious surface. The two sampling methods varied in terms of number and size of plates, between-plate spacing, and deployment method. Comparison of the similarity/grouping of communities with multivariate ordination techniques, Nonmetric Multidimensional Scaling and Multi-Response Permutation Procedure, showed that both methods were able to detect differences in communities at stations, despite some grouping by month and method. The indices and metrics derived from the two HD methods were found to give comparable but not identical assessments of water quality. Despite their differences, the methods were robust with respect to water quality categories derived from indices used nationally (HBI) and by NY state (BAP). For the common richness metrics, total taxa and EPT richness, there was no statistical difference between means from 3 samplings. Some metrics, especially percent tolerant collector-gatherer individuals, did show significant differences at certain stations. Indicator Species Analysis showed some taxa associated with each method. The observed community differences were thought mostly due to the difference in sampler deployment position.

Composition, abundance and biodiversity of terrestrial arthropods in pastures and their relationship with landscaping plants

We investigated the association of landscaping plants with the communities of ground-dwelling arthropods within pastures and tested the hypothesis that arthropod biodiversity increases with vegetation heterogeneity. The community characterization and biodiversity of arthropods in a pasture were compared with those within communities with landscaping plants, including forest remnants, Forsythia koreana and Prunus serotina. The total abundance of mites was greater within the forest remnants than within the pasture; however, the abundance of insects and spiders did not differ. Nonmetric multidimensional scaling and the multiresponse permutation procedure revealed that the community composition of insects and spiders differed according to vegetation type. The abundance of Teleogryllus emma was highest within the forest remnant community, which suggested the species’ dependency on vegetation type. Species richness and the Shannon index of insects increased within F. koreana but not within P. serotina compared with the pasture. This suggested that belts of shrubs might have a greater promoting effect on insect biodiversity than belts of trees. Species richness of spiders did not differ by vegetation type. The total number of insect and spider species within the study area increased by 2.8 and 3.5 times, respectively, by establishing three types of vegetation. These results suggested that increasing vegetation heterogeneity by establishing landscaping plants is a good option for conserving insect and spider biodiversity in pastures.

Understory plant dynamics following a wildfire in southern Patagonia

Historically, wildfires have occurred infrequently in the Subantarctic forests on the island of Tierra del Fuego in southern Argentina: wildfires on the landscape are sporadic and exclusively human-caused. As a result of this, post-fire effects on native vegetation are largely unknown. In November of 2008, a wildfire started near a sawmill in the central part of the island. Six pre-established research plots located in Nothofagus antarctica (ñire) dominated forests burned, impacting a long-term study of understory vegetation dynamics. In 2008 (pre-fire), two 10 m long permanent transects were established per plot (n = 12), where we evaluated species richness and plant cover using a point intersection method at 20 cm intervals, resulting in 50 points per transect. After the fire, we continued sampling to evaluate post-fire understory response in burned and unburned plots. The first post-fire sampling occurred in January 2009, and was repeated semi-annually in burned and unburned plots (2010–2014, 2016, 2018, 2020, and 2021). Data were analyzed using GLMMs (Generalized Linear Mixed Models) and multivariate analyses (Nonmetric Multidimensional Scaling, Multi-Response Permutation Procedures). Total species richness and cover decreased the year following the fire, but recovered by 2010, eventually surpassing pre-fire levels. Increases in species diversity were due principally to an increase in exotic species richness (F = 4.73; p < 0.001) and cover (F = 51.59; p < 0.001). For native species, richness followed the same trend as total vegetation, but cover decreased drastically following the fire (F = 19.77; p < 0.001) and had not recovered to pre-fire levels by 2021. MRPP revealed that plant assemblage in burned plots differed from those in unburned plots the season following the fire (p < 0.001) and still differed 7–12 years post-fire (p < 0.001). Wildfire in Tierra del Fuego produces changes in understory dynamics that create non-forest plant assemblages dominated by exotic species; these changes last many years and pose a significant threat to the forests and native plant species of the island. Without active restoration, forests impacted by wildfire may be permanently lost along with the ecosystem services and habitat they provide.

Rhizosphere soil microbial community and its response to different utilization patterns in the semi-arid alpine grassland of northern Tibet

As the link between plants and soils, rhizosphere soil microorganisms play an important role in the element cycle. This study aimed to understand the response of the rhizosphere soil microbial community structure and interaction network to grassland utilization in the alpine steppe of the northern Tibet Plateau. High-throughput sequencing was employed to study the composition, diversity, and species interaction network of rhizosphere soil microbial communities under grazing, mowing, and enclosing treatments. Proteobacteria (47.19%) and Actinobacteria (42.20%) were the dominant bacteria in the rhizosphere soil. There was no significant difference in relative abundance among rhizosphere soil microorganisms at phylum and genus levels, but differences were found in Chlorobi, Ignavibacteriae, and Micromonospora. The alpha diversity index based on Shannon, Chao1, and Simpson indices revealed that except for a significant difference in the Shannon index of the Artemisia nanschanica group, the richness and evenness of rhizosphere soil microbial communities among all groups were similar. Non-metric multidimensional scaling (NMDS) and multi-response permutation procedure (MRPP) analyses showed that the inter-group differences of three plants (Stipa purpurea, Carex moorcroftii, and Artemisia nanschanica) were greater than the differences within the groups; however, only the inter-group difference with the Stipa purpurea group was significant. The microbial interaction network showed that the network complexity of the Artemisia nanschanica group and the enclosing treatment, which were not easily influenced by external factors, were higher than those of the other groups and treatments; this again demonstrated that Proteobacteria and Actinobacteria were the network core microbial species in alpine steppe of the northern Tibet Plateau and were crucial for maintaining stability of the microbial communities. Findings from this study provide a theoretical basis for the restoration of degraded alpine grassland and the development of microbial functions.

Evaluating the temporal and spatio-temporal niche partitioning between carnivores by different analytical method in northeastern Japan

Temporal and spatio-temporal niche partitioning is an important strategy for carnivore coexistence. Camera-trap data has been analyzed through several methods to assess the temporal and spatio-temporal niche partitioning. However, different analytical approaches used to may evaluate niche partitioning detect different results. In this study, we evaluated the temporal or spatio-temporal partitioning among sympatric medium-sized carnivores, red foxes, raccoon dogs, and Japanese martens, based on three analytical methods—the temporal overlap, temporal co-occurrence, and time-to-encounter analysis—to evaluate. From May to October 2019 and 2020, we obtained the activity of the target species using camera-traps in northeastern Japan. We analyzed the data with the coefficient of temporal overlap, probabilistic co-occurrence analysis, checkerboard score, and multi-response permutation procedures. The results of the assessment of the niche partitioning differed depending on the analytical methods based on temporal and spatio-temporal partitioning. Therefore, we conclude that the choice of analytical approach is important for evaluating the temporal and spatio-temporal niche partitioning.

Changes in soil chemical properties and plant species composition during primary succession on an oceanic island

AbstractQuestionsWhat is the influence of time and environmental factors such as climate and topography on soil chemical properties and composition of vascular plants during primary succession on lava flows of an oceanic island? How is compositional change characterized and which successional stages can be distinguished?LocationLa Palma, Canary Islands.MethodsWe sampled soil properties and vascular plants in 72 plots on a long‐term chronosequence of 10 lava flows ranging in age between 40 and over 20,000 years in the semi‐arid lowlands of La Palma Island. Soil properties were analyzed by general least‐squares models (GLS), while canonical correspondence analysis (CCA), cluster analysis and multiresponse permutation procedures (MRPP) were applied to investigate compositional change.ResultsSoil characteristics and plant species composition during primary succession were strongly affected by substrate age but also by climatic and topographic factors. Values of most soil properties increased with lava flow age, while pH decreased. Soil organic matter, phosphorus, exchangeable calcium and ammonium revealed a positive correlation with mean annual precipitation. Lava flow age was always the most important independent factor determining plant assembly followed by mean annual precipitation. Four successional stages and their composition of indicator species, life strategies and species status could be defined. Alien species did not alter successional trajectories.ConclusionTime, climate and topography simultaneously affect soil properties and plant composition during primary succession on lava flows. The climatic windward–leeward gradient on La Palma Island influences plant colonization and soil development in the semi‐arid coastal areas. Favorable conditions (moisture) can speed up primary succession. Compositional changes suggest convergence during primary succession. During the entire colonization process, dominant successional shrubs are endemics, highlighting the importance of evolutionary adaptation to volcanic disturbances.

Diversity and Seasonal Occurrence of Native and Nonnative Ants (Hymenoptera: Formicidae) in Long-Term Experimental Chinese Privet (Lamiales: Oleaceae) Plots in Georgia, USA

Diversity and Seasonal Occurrence of Native and Nonnative Ants (Hymenoptera: Formicidae) in Long-Term Experimental Chinese Privet (Lamiales: Oleaceae) Plots in Georgia, USA

Quantifying Mesophotic Fish Assemblages of Hawai‘i’s Au‘au Channel: Associations With Benthic Habitats and Depth

Mesophotic reefs (30–150 m) occur in the tropics and subtropics at depths beyond most scientific diving, thereby making conventional surveys challenging. Towed cameras, submersibles, and mixed-gas divers were used to survey the mesophotic reef fish assemblages and benthic substrates of the Au‘au Channel, between the Hawaiian Islands of Maui and Lāna‘i. Non-parametric multivariate analysis: Non-metric Multidimensional Scaling (NMDS), Hierarchical Cluster Analysis (HCA), Multi-Response Permutation Procedure (MRPP), and Indicator Species Analysis (ISA) were used to determine the association of mesophotic reef fish species with benthic substrates and depth. Between 53 and 115-m depths, 82 species and 10 genera of fish were observed together with 10 types of benthic substrate. Eight species of fish (Apolemichthys arcuatus, Centropyge potteri, Chaetodon kleinii, Chromis leucura, Chromis verater, Forcipiger sp., Naso hexacanthus, and Parupeneus multifasciatus) were positively associated with increasing depth, Leptoseris sp. coral cover, and hard-bottom cover, and one species (Oxycheilinus bimaculatus) of fish was positively associated with increasing Halimeda sp. algae cover. Fish assemblages associated with rubble were not significantly different from those associated with sand, Montipora coral beds and Leptoseris coral beds, but were distinct from fish assemblages associated with hard bottom. The patterns in the data suggested two depth assemblages, one “upper mesophotic” between 53 and 95 m and the other deeper, possibly part of a “lower mesophotic” assemblage between 96 and 115 m at the edge of the rariphotic and bottomfish complex.

Forest fires have long-term effects on the composition of vascular plants and bryophytes in Scots pine forests of hemiboreal Estonia

Since fire frequency is expected to increase globally due to climate change, it is important to understand its effects on forest ecosystems. We studied the long-term patterns in species diversity, cover and composition of vascular plants and bryophytes after forest fire and the site-related factors behind them. Research was carried out in northwestern Estonia, using a chronosequence of Scots pine ( L.) stands, located on nutrient poor sandy soils, where fires had occurred 12, 23, 38, 69, 80 and 183 years ago. In every stand three 100 m vegetation plots were established to collect floristic and environmental information. The effects on floristic characteristics of time since fire, light, and soil variables were evaluated with linear mixed models, followed by backward variable selection. Compositional variation was analysed with non-metric multidimensional scaling, Multi-response Permutation Procedures, and Indicator Species Analysis. Altogether, 31 vascular plant and 39 bryophyte species were found in vegetation plots. The cover of the vascular plant and bryophyte layers increased with a longer time since fire. Soil and light variables impacted the richness of several vascular plant and bryophyte groups, whereas only the richness of liverworts and dwarf-shrubs correlated with time since fire. Considerable compositional differences were observed in vascular plant and bryophyte assemblages between recently vs. long-time ago burned stands. To conclude, time since fire significantly impacted compositional patterns of vascular plants and bryophytes in pine forests on nutrient poor soils, although time-related trends in species richness were less evident.Pinus sylvestris2

Species richness, diversity, density and spatial distribution of soil seed banks in the riparian woodland along the Thamalakane River of the Okavango Delta, northern Botswana

Soil seed banks serve as reservoirs of seeds for subsequent regeneration of plants. Soil seed banks were investigated along the Thamalakane Riparian Woodlands (hereafter referred to as TRWs) of the Okavango Delta, northern Botswana, from January-July 2015 and January-July 2016. The study aimed at examining species richness and diversity, determining densities, assessing the spatial distribution of seeds in the soil and comparing the similarity in species composition between the standing vegetation and soil seed bank flora. The vegetation was sampled in 71 plots (20 × 50 m) and soil samples were collected from 568 subplots. Agglomerative hierarchical cluster analysis was used to determine soil seed bank communities. Indicator species analysis was used to calculate indicator values for species in each community of germinated seeds and across different soil layers. Multi-response permutation procedures (MRPP) were used to compare similarity in soil seed bank composition. Bray-Curtis ordination was used to infer spatial relationships of soil layers in terms of soil seed bank composition. A total of 109 plant species were identified in the litter and top 9 cm soil layers with a mean density of 2101 seeds m−2. Herbs, grasses, sedges and woody plants were represented by 68, 19, 9 and 13 species, respectively, in 30 families and 87 genera. The overall total diversity and evenness of the soil seed bank in the TRWs was 3.25 and 0.69, respectively. Four plant communities were identified from the soil seed bank, namely Setaria verticilata-Amaranthus hybridus, Acanthospermum hispidum-Setaria sagittifolia, Digitaria eriantha-Eclipta prostrata and Cyperus longus-Fimbristylis dichotoma. Bray-Curtis ordination showed that there was overlap between these communities in terms of seed bank composition. However, MRPP analysis showed that there was significant (P < 0.05) separation between germinated soil seed bank communities. The overall horizontal distribution of seeds varied among sampling quadrats while the vertical distribution of seeds exhibited the highest densities occurring in the upper 3 cm of the soil and gradually decreasing densities with increasing depth. Relatively high densities also occurred in the litter layer. There were large differences in depth distribution between species, suggesting differences in seed longevity. The similarity in species composition between the soil seed flora and standing vegetation was low (27%). The results demonstrated that many species in TRWs store quantities of seeds in the soil. The fact that most of the woody species do not accumulate more seeds in the soil suggests that their regeneration from seeds would be unlikely if mature individuals disappeared (die or are harvested). Because of its diverse seed banks, the herbaceous flora would have a better chance of re-establishing in the event of anthropogenic or natural disturbances. Therefore, the future of the TRW woody flora seems to depend on the successful conservation of the standing vegetation.

Variable importance assessments and backward variable selection for multi-sample problems

Variable selection for multi-sample problems is of great interest in statistics. Existing methods for addressing this problem have some limits or disadvantages. In this paper, we propose distance-based variable importance measures to deal with these problems, which are inspired by the Multi-response permutation procedure (MRPP), Energy distance (ED) and Distance components (DISCO) analysis. The proposed variable importance assessments can effectively measure the importance of an individual dimension by quantifying its influence on the differences between multivariate distributions across treatment groups. An importance-measure-based backward selection (IM-BWS) algorithm is developed that can be used in variable selection for multi-sample problems to discover important variables. We propose a modified MRPP based on the IM-BWS procedure for improving the power performance of the original MRPP. Our proposed methods are model-free, work for high-dimensional data, and can capture important variables under different models. Both simulations and real data applications demonstrate that our proposed method enjoys good properties and has advantages over other existing methods.

Plant Species Composition and Interactions within Communities Invaded by Persicaria perfoliata (Polygonaceae)

Persicaria perfoliata (Mile-a-Minute Weed), an invasive vine, forms monocultural patches of various sizes within infested landscapes among patches also containing other plants. We compared the species composition of P. perfoliata-dominated patches and adjacent nondominated patches in 2 topographically homogeneous sites using 20 paired plots, nonmetric multidimensional scaling, multi-response permutation procedure, and indicator species analyses. Richness and diversity were lower in the P. perfoliata-dominated patches but both patch types had uncommon native plants present. The patch types differed significantly in composition, and the nondominated patches were dominated by another nonnative invader, Microstegium vimineum (Japanese Stiltgrass), or a native weed, Ambrosia artemisiifolia (Common Ragweed). Documenting potentially interacting native and exotic species within an invaded landscape will help predict likely restoration success in response to targeted nonnative-invasive plant removal.

Space use of cougars at the northern edge of their range

AbstractThe space use strategies animals use to acquire resources needed for survival and reproduction reflect life history traits and individual behaviors. For large solitary carnivores, such as cougars (Puma concolor), prey, mates, and safe habitat in which to raise offspring, are resources that influence space use. Most animal home range studies investigate differences between sexes but fail to explore the space use patterns among individuals. We first used 95% minimum convex polygon (MCP), kernel density estimate (KDE), and Brownian bridge estimator (BB), to estimate the home range of 43 cougars satellite-collared in west-central Alberta, Canada, in 2016–2018. We found that adult males (MCP = 498 km2; KDE = 623 km2; BB = 547 km2) had home ranges that were more than twice the size of those of adult females (MCP = 181 km2; KDE = 273 km2; BB = 217 km2). We then used net squared displacement, path segmentation analysis, and multi-response permutation procedure, to examine the space use patterns of 27 female and 16 male cougars. We constructed a decision tree and found that 23% of cougars were dispersers (12% of females and 44% of males), 47% were residents (58% of females and 31% of males), 9% were seasonal home range shifters (12% of females and 6% of males), and 19% shifted to a new area during the study period (19% of females and 19% of males). We learned that dispersers all were subadults, whereas all residents, seasonal shifters, and shifters, were adults, except for one subadult male. Our study provides insights on animal home ranges with methods to categorize different space use strategies which could be used to help assess the dynamics of a population.