Nonmetric Multidimensional Scaling (nonmetric + multidimensional_scaling)

Distribution by Scientific Domains
Distribution within Life Sciences

Selected Abstracts

Moist lower montane rainforest classification: a case study from Bwindi Impenetrable National Park, Uganda

Tomas Chaigneau
Abstract Moist lower montane vegetation has rarely been classified beyond broad zonational belts over large altitudinal ranges due to highly diverse species composition and structure. This study shows it is possible to further classify such forest types within Bwindi-Impenetrable National Park (BINP), and that these assemblages can be explained by a combination of environmental conditions and past management. Botanical and environmental data were collected along some 4000 m of linear transects from the area surrounding Mubwindi Swamp, BINP. Ordination using Nonmetric Multidimensional Scaling (NMDS) and classification using Two-way Indicator Species Analysis (TWINSPAN) successfully identified four different species assemblages. These forest types were then named on the basis of the ecological characteristics of the species within the group, and the environmental conditions influencing the distribution and past disturbance of the forest. The techniques used were in agreement for three out of the four forest types identified. Analysis using an environmental overlay showed a significant association between forest type and altitude. The results of this study indicate that a regional classification of forest types within moist lower montane forest belt using only tree species is possible, and that the forest types identified can be explained by environmental conditions and past management. Résumé La végétation humide de basse montagne a rarement été classée au-delà de larges ceintures de zonage portant sur des étendues de grandes amplitudes altitudinales, en raison de compositions et de structures d'espèces extrêmement diverses. Cette étude montre qu'il est possible de classer plus précisément de tels types forestiers dans le Parc National de la Forêt Impénétrable de Bwindi (BINP), et que l'on peut expliquer ces assemblages par une combinaison de conditions environnementales et de gestion passée. Des données botaniques et environnementales ont été collectées le long de quelque 4,000 m de transects linéaires à partir de la zone entourant le Marais de Mubwindi, au BINP. L'ordination par la Gradation non métrique multidimensionnelle et la classification utilisant l'Analyse TWINSPAN (Two-way Indicator Species Analysis) ont réussi à identifier quatre assemblages d'espèces différents. Ces types forestiers furent alors nommés en se basant sur les caractéristiques écologiques des espèces au sein du groupe ainsi que sur les conditions environnementales qui influencent la distribution et des perturbations anciennes des forêts. Les techniques utilisées se sont montrées cohérentes pour trois des quatre types de forêt identifiés. L'analyse utilisant une superposition environnementale a révélé une association significative entre type forestier et altitude. Les résultats de cette étude indiquent qu'une classification régionale des types forestiers dans la ceinture forestière humide qui entoure la basse montagne est possible en n'utilisant que trois espèces d'arbres, et que les types forestiers identifiés peuvent s'expliquer par les conditions environnementales et par la gestion antérieure. [source]

Elevated air temperature alters an old-field insect community in a multifactor climate change experiment

Abstract To address how multiple, interacting climate drivers may affect plant,insect community associations, we sampled insects that naturally colonized a constructed old-field plant community grown for over 2 years under simultaneous CO2, temperature, and water manipulation. Insects were sampled using a combination of sticky traps and vacuum sampling, identified to morphospecies and the insect community with respect to abundance, richness, and evenness quantified. Individuals were assigned to four broad feeding guilds in order to examine potential trophic level effects. Although there were occasional effects of CO2 and water treatment, the effects of warming on the insect community were large and consistent. Warming significantly increased Order Thysanoptera abundance and reduced overall morphospecies richness and evenness. Nonmetric multidimensional scaling found that only temperature affected insect community composition, while a Sørensen similarity index showed less correspondence in the insect community between temperature treatments compared with CO2 or soil water treatments. Within the herbivore guild, elevated temperature significantly reduced richness and evenness. Corresponding reductions of diversity measures at higher trophic levels (i.e. parasitoids), along with the finding that herbivore richness was a significant predictor of parasitoid richness, suggest trophic-level effects within the insect community. When the most abundant species were considered in temperature treatments, a small number of species increased in abundance at elevated temperature, while others declined compared with ambient temperature. Effects of temperature in the dominant insects demonstrated that treatment effects were limited to a relatively small number of morphospecies. Observed effects of elevated CO2 concentration on whole-community foliar N concentration did not result in any effect on herbivores, which are probably the most susceptible guild to changes in plant nutritional quality. These results demonstrate that climatic warming may alter certain insect communities via effects on insect species most responsive to a higher temperature, contributing to a change in community structure. [source]

Nonmetric multidimensional scaling with clustering of subjects

Kohei Adachi
A new nonmetric multidimensional scaling method is devised to analyze three-way data concerning inter-stimulus similarities obtained from many subjects. It is assumed that subjects are classified into a small number of clusters and that the stimulus configuration is specific to each cluster. Under this assumption, the classification of subjects and the scaling used to derive the configurations for clusters are simultaneously performed using an alternating least-squares algorithm. The monotone regression of ordinal similarity data, the scaling of stimuli and the K -means clustering of subjects are iterated in the algorithm. The method is assessed using a simulation and its practical use is illustrated with the analysis of real data. Finally, some extensions are considered. [source]

Aspen succession and nitrogen loading: a case for epiphytic lichens as bioindicators in the Rocky Mountains, USA

Paul C. Rogers
Abstract Question: Can lichen communities be used to assess short- and long-term factors affecting seral quaking aspen (Populus tremuloides) communities at the landscape scale? Location: Bear River Range, within the Rocky Mountains, in northern Utah and southern Idaho, USA. Method: Forty-seven randomly selected mid-elevation aspen stands were sampled for lichens and stand conditions. Plots were characterized according to tree species cover, basal area, stand age, bole scarring, tree damage, and presence of lichen species. We also recorded ammonia emissions with passive sensors at 25 urban and agricultural sites throughout an adjacent populated valley upwind of the forest stands. Nonmetric multidimensional scaling (NMS) ordination was used to evaluate an array of 20 variables suspected to influence lichen communities. Results: In NMS, forest succession explained most variance in lichen composition and abundance, although atmospheric nitrogen from local agricultural and urban sources also significantly influenced the lichen communities. Abundance of nitrophilous lichen species decreased with distance from peak ammonia sources and the urban center in all aspen succession classes. One lichen, Phaeophyscia nigricans, was found to be an effective bioindicator of nitrogen loading. Conclusions: Lichen communities in this landscape assessment of aspen forests showed clear responses to long-term (stand succession) and short-term (nitrogen deposition) influences. At the same time, several environmental factors (e.g. tree damage and scarring, distance to valley, topography, and stand age) had little influence on these same lichen communities. We recommend further use of epiphytic lichens as bioindicators of dynamic forest conditions. [source]

Plant Community Structure in Tropical Rain Forest Fragments of the Western Ghats, India,

BIOTROPICA, Issue 2 2006
S. Muthuramkumar
ABSTRACT Changes in tree, liana, and understory plant diversity and community composition in five tropical rain forest fragments varying in area (18,2600 ha) and disturbance levels were studied on the Valparai plateau, Western Ghats. Systematic sampling using small quadrats (totaling 4 ha for trees and lianas, 0.16 ha for understory plants) enumerated 312 species in 103 families: 1968 trees (144 species), 2250 lianas (60 species), and 6123 understory plants (108 species). Tree species density, stem density, and basal area were higher in the three larger (> 100 ha) rain forest fragments but were negatively correlated with disturbance scores rather than area per se. Liana species density, stem density, and basal area were higher in moderately disturbed and lower in heavily disturbed fragments than in the three larger fragments. Understory species density was highest in the highly disturbed 18-ha fragment, due to weedy invasive species occurring with rain forest plants. Nonmetric multidimensional scaling and Mantel tests revealed significant and similar patterns of floristic variation suggesting similar effects of disturbance on community compositional change for the three life-forms. The five fragments encompassed substantial plant diversity in the regional landscape, harbored at least 70 endemic species (3.21% of the endemic flora of the Western Ghats,Sri Lanka biodiversity hotspot), and supported many endemic and threatened animals. The study indicates the significant conservation value of rain forest fragments in the Western Ghats, signals the need to protect them from further disturbances, and provides useful benchmarks for restoration and monitoring efforts. [source]

Beta diversity of geometrid moths (Lepidoptera: Geometridae) in an Andean montane rainforest

Gunnar Brehm
Abstract. Turnover in species composition of the extremely species-rich family Geometridae (Lepidoptera) was investigated along an elevational gradient ranging from 1040 m to 2677 m above sea level. Moths were sampled using weak light traps (30 W) in three field periods in 1999 and 2000 in an Andean montane rainforest in the province of Zamora-Chinchipe in southern Ecuador. A total of 13 938 specimens representing 1010 species were analysed. Similarities of ensembles of all geometrid moths and of the subfamilies Ennominae and Larentiinae were calculated using the NESS index (with mmax). Ordinations performed using nonmetric multidimensional scaling (NMDS) and correspondence analysis depicted a gradual change of the ensembles along the altitudinal gradient. Extracted ordination scores significantly correlate with altitude (,0.97 , r , ,0.95, P < 0.001) and with ambient air temperature (0.93 , r , 0.97, P < 0.001). Temperature is therefore assumed to be the most important abiotic determinant responsible for the species turnover among the moths. Matrix correlation tests were performed in order to compare faunal matrices with matrices derived from available environmental factors. Both tree diversity and vegetation structure significantly correlate with faunal data, but tree diversity explains considerably more of the data variability (range: Mantel r = 0.81,0.83, P < 0.001) than vegetation structure (range: Mantel r = 0.35, P < 0.005 to r = 0.43, P < 0.001). Tree diversity also changes gradually and scores of the first NMDS dimension are highly significantly correlated with altitude (r = 0.98, P < 0.001). A common underlying factor such as ambient temperature might also be responsible for such vegetation changes. Additionally, simulated model data was developed that assumed a constant turnover of moth species and equal elevational ranges of all species involved. Despite the simplicity of the models, they fit empirical data very well (Mantel r > 0.80 and P < 0.001 in all models). [source]

Autosomal microsatellite variability of the Arrernte people of Australia

M. A. Alfonso-Sánchez
The genomic diversity of the Arrernte people of Australia or caterpillar people was investigated utilizing 13 autosomal short tandem repeat (STR) markers. Significant departures from Hardy,Weinberg equilibrium were detected at the D18S51, TPOX and CSF1PO loci, which persisted after applying the Bonferroni correction. Gene diversity values oscillate between 0.6302 (CSF1PO) and 0.8731 (D21S11). Observed heterozygosity (Ho) ranges from 0.2632 (D18S51) to 0.8333 (vWA) and is lower than the expected heterozygosity (He) for 12 of the 13 loci analyzed. The genetic relationships of the Arrernte with Middle Eastern, East Asian, South Asian and Indian populations were analyzed by distance-based methods, including Neighbor-Joining trees and nonmetric multidimensional scaling. In addition, the genetic contribution of the populations included in the analysis to the Arrernte gene pool was estimated utilizing weighted least square coefficients. Although the Arrernte population exhibits a remarkable level of genetic differentiation, results of the phylogeographic analyses based on autosomal microsatellite data suggest a certain degree of genetic relatedness between the Arrernte tribe of Australia and populations from the Indian subcontinent. In contrast, the STR diversity analyses failed to detect substantial East Asian contribution to the genetic background of the Arrernte group. Am. J. Hum. Biol., 2008. © 2007 Wiley-Liss, Inc. [source]

Mesoscale Patterns in the Floristic Composition of Forests in the Central Western Ghats of Karnataka, India

BIOTROPICA, Issue 4 2010
B. R. Ramesh
ABSTRACT We describe the mesoscale floristic patterns in the central Western Ghats of Karnataka, India, through combined analysis of woody species abundance and stand structure data from a network of ninety-six 1-ha sampling plots spread across 22,000 km2. A total of 61,906 individuals (,10 cm gbh) comprising 400 plant species from 254 genera and 75 families were recorded. Euphorbiaceae, Rubiaceae, Lauraceae and Moraceae families constituted 23.5 percent of the total number of species encountered. The relative dominance of species was skewed with Poecilonueron indicum, Xylia xylocarpa, Terminalia tomentosa and Anogeissus latifolia being dominant in some plots. Correspondence analysis (CA) and a nonmetric multidimensional scaling (NMDS) of plots by species abundances data showed similar arching patterns, with significant correlation between the first axis of CA and NMDS (r=0.77). Hierarchical clustering of plot scores along the three first CA axes resulted in splitting the plots into five different categories that broadly reflect the major bioclimatic features of the region. A multiscale bootstrapping test indicated that categorization of the wettest (wet evergreen group 1 and 2) and driest (dry deciduous) groups were robust (P<0.05 with 1000 bootstraps), while the remaining two transitional groups were uncertain (P=0.12 and 0.26 for moist deciduous and semi-evergreen group, respectively). Principal component analysis revealed that plots with similar floristic composition can encompass contrastingly different physiognomic structures (canopy cover, canopy height and mean tree diameter) probably in relation to their levels of disturbance. Observed patterns in the floristic composition have been discussed in the light of the complex interaction between the bioclimatic and disturbance regimes that characterize the region. [source]