Instability of ordination results under changes in input data order: explanations and remedies

Abstract. Correspondence analysis (CA) and its Detrended form (DCA) produced by the program CANOCO are unstable under reordering of the species and sites in the input data matrix. In CA, the main cause of the instability is the use of insufficiently stringent convergence criteria in the power algorithm used to estimate the eigenvalues. The use of stricter criteria gives results that are acceptably stable. The divisive classification program TWINSPAN uses CA based on a similar algorithm, but with extremely lax convergence criteria, and is thus susceptible to extreme instability. We detected an order-dependent programming error in the non-linear rescaling procedure that forms part of DCA. When this bug is corrected, much of the instability in DCA disappears. The stability of DCA solutions is further enhanced by the use of strict convergence criteria. In our trials, much of the instability occurred on axes 3 and 4, but one should not assume that published two-dimensional ordinations are sufficiently accurate. Data sets which have pairs of almost equal eigenvalues among the first three axes could suffer from marked instability in the first two dimensions. We recommend that a debugged, strict version of CANOCO be released. Meanwhile, users can check the stability of their CA and DCA ordinations using the software that we have made available on the World Wide Web ( http://www.helsinki.fi/jhoksane/ ). An accurate program for CA, a debugged, strict version of DECORANA (for DCA) and a strict version of TWINSPAN are also available at our site.     

Lebensgemeinschaften koexistierender Arten der Wasserkäfergattung Hydroporus aus zwei norddeutschen Untersuchungsgebieten (Coleoptera; Dytiscidae)

The community structure of 15 species of the genus Hydroporus was investigated in various pools with the multivariate software DECORANA, TWINSPAN and CANOCO. Abiotic values measured at 22 bog pools were correlated to DECORANA-data. Typical communities in the Ohemoor (near Hamburg) are related to the factors shaddow, absorption, calcium, and sodium. Data of coexisting Hydroporus species (including other small Dytiscidae, Haliplidae, Noteridae) from 93 pools (near Seedorf/Schleswig-Holstein) could be devided into 4 typical communities (bog, wood, sand-pit, agricultural areas).     

长白山北坡木本植物分布与环境关系的典范对应分析

 在长白山北坡海拔700～2 600 m的坡面上,海拔每上升100 m设立一个样点,共计20个样点。调查每个样点中木本植物的生态重要值,并计测样点内包括气候、土壤、林冠郁闭度在内的13个环境因子。应用CANOCO3.12软件对获得的数据进行了典范对应分析(CCA),应用CANODRAW3.0作出了种类     

Chironomid microdistribution in gravel of an English chalk river

1. The study aimed to determine the relative importance of certain environmental variables to the distribution of instars of chironomid species in mid-stream gravels of the River Pang. 2. Core samples of gravel substrata were collected over 1 year. Water depth, current, particle size distribution, substratum porosity and detritus were recorded for each sample. The four principal components from a linear ordination of the environmental variables were used to constrain the ordination of chironomid data using the program CANOCO. 3. Microdistribution was principally related to a temporal gradient of water depth, current and substratum heterogeneity. There was significant spatial separation of instars along a gradient of fine detritus, silt and substratum porosity. The distributions of early instars of three taxa were also significantly related to particle size. There was a significant relationship between the size distribution of larvae and the spatial distribution of fine sediments and detritus. This relationship was strengthened when restricted to larvae classified as scrapers.     

Environmental factors affecting chemical variability of essential oils in Thymus piperella L.

Environmental factors affecting essential oils variability in Thymus piperella L. are studied. The relationship between the bioclimatics index and edaphic factors with three chemotypes is determined through the application of multivariate analysis (CANOCO) and other statistical processes to both ecological and the essential oil data set components. Chemotype p-cymene γ-terpinene carvacrol shows a positive relationship with the aridity index (I_a) and Altitude. The p-cymene thymol chemotype is related to factors affecting water balance in both the soils and plants. The influence of climatic factors over p-cymene carvacrol is less evident. The compound p-cymene, common to the three chemical groups and the most abundant of all, presents positive correlation with the organic matter in the soil.     

Filamentous algal communities related to pH in streams in The Trossachs, Scotland

• 1 A survey of acidified streams in the Loch Ard area of The Trossachs, Scotland, was carried out between 1986 and 1988, to determine the influence of physical and chemical factors on the distribution of benthic algae. Samples were taken on thirty-five occasions from fifteen sites on ten streams. Forty-nine operational taxa of filamentous algae were distinguished. Relative abundance of taxa in samples was scored on a seven-point scale. Estimates of standing crop were made by pigment extraction and ash-free dry weight (AFDW) determination from biomass developed on artificial substrata.
• 2 No evidence was found for seasonality in standing crop, nor for an increase in standing crop with a decrease in pH. Seasonality in relative abundance was evident for few taxa. Species richness and diversity were highly correlated with pH and correlated chemical variables.
• 3 Canonical correspondence analysis (CCA) carried out using the CANOCO program ordinates species and sites and relates them directly to environmental variables. The most important variable was found to be pH (or an acidification-related variable that is highly correlated with pH), with percentage forest cover and total oxidized nitrogen being of secondary importance. The effect of subdividing the data set, using data based on presence-absence as well as estimated relative abundance, was tested. A comparison of the effects on the distribution of site and species values on the pH vector showed that the results are robust, confirming the value of this semi-quantitative sampling method for use with a difficult algal group. It was possible to infer pH from algal community structure using CANOCO.
• 4 The pH ranking of species derived from CCA revealed that larger cell diameter taxa do not predominate at low pH, implying that reduction of invertebrate grazing was not an important determinant of algal community composition.

     

Picea abies- and Fraxinus excelsior-dominated wetland forest communities in Latvia

This paper reports on the syntaxonomical structure, the ecological, physiognomical and phytogeographical differentiation of wetland forests in Latvia dominated by Picea abies and Fraxinus excelsior. Data were collected following the Braun-Blanquet approach and treated by the GROUPAGE, TWINSPAN and CANOCO programs. Spruce forests (Sphagno girgensohnii-Piceetum var. Crepis paludosa, S.g.-P. myrtilletosum) form a well-defined community mostly in shallow and medium deep (0.2–1.3 m) peatland. Assemblages of spruce wetlands in NEE Europe point to amazing similarity and little variation from NE Poland and Fennoscandia over the Baltic States to the central parts of Russia. Ash-dominated wetlands (Carici elongatae-Alnetum, Carici remotae-Fraxinetum) refer only to particular localities of the country and lie on wet mineral, gleyey soils, usually along brooks and on undulating ground rich in subsoil streams, mostly in sites without an evident accumulation of peat. In Latvia, these reach the northernmost limit of distribution and are poorer in species compared with the ash wetlands of Central Europe.     

On the surrogate value of red-listed butterflies for butterflies and grasshoppers: a case study in Grammos site of Natura 2000, Greece

We tested the surrogate value of butterflies, red-listed butterflies and grasshoppers for each other in terms of diversity patterns congruence and complementarity at a site in the NATURA 2000 network. Grammos Mountain is proposed as a new Prime Butterfly Area for Greece: it supports a total of 56 grasshopper species and 112 butterfly species, 24 of which are of European conservation concern (SPEC) and two of Prime Butterflies Area Project. We found a strong congruence in the species richness patterns of SPEC butterflies, butterflies and grasshoppers, because three common ecological factors influenced them: number of flower heads, altitude, and cover of low trees or bushes (Redundancy Analysis, CANOCO). Each complementarity network maintained quite well the species richness of the other two target groups (<18% average species loss). SPEC butterflies were the best surrogate group overall and therefore we propose that they should be monitored on a permanent basis.     

Ecology of terrestrial testate amoebae assemblages from coastal Lowlands on Devon Island (NWT,Canadian Arctic)

Summary Fifty-seven taxa belonging to 17 genera of testate rhizopods were recorded in samples of mosses, soils and lichens, collected from the Truelove and Sparbo Hardy Lowlands on the high arctic Devon Island (NWT, Canada). Different groups of habitats are characterized by particular assemblages of Testacea species, with the quantity and quality of the available water as important ecological parameters. The Assulina muscorum-Corythion dubium assemblage characterizes the most dry and acidic moss habitats, while the Paraquadrula irregularis assemblage is to be found in wet and rather neutral habitats. The sedge moss meadows with their more moderately coarse textured and poorly drained soils, bear a Plagiopyxis callida-Plagiopyxis declivis soil-dwelling testate amoebae assemblage. The Centropyxis minuta assemblage lives in the most coarsely textured soils. pH seems to play a subordinate role, not only in the mosses but also in the soils. Multivariate methods (cluster analysis and CANOCO) have been used to separate these different assemblages.     

辽东栎林不同层植物沿海拔梯度分布的DCCA分析

 为研究北京东灵山辽东栎（Quercus liaotungensis）不同层植物的分布与环境因子之间的关系,对东灵山辽东栎林进行了植物群落学调查。沿 海拔梯度在乔木层、灌木层和草本层各调查119个样方,同时调查了每个样方的环境因子如海拔、坡度和坡位。物种数据采用二元属性数据,对 非数值环境因子进行赋值。对东灵山辽东栎林和各环境因子进行去趋势典范对应分析（Detrended canonical correspondence analysis, DCCA）,结果表明：DCCA 第一轴基本上反映了植物群落所处环境的海拔的梯度变化,第二轴基本上反映了坡位的梯度变化。同时发现辽东栎林 大多数植物分布在低海拔区域。乔木层的物种分布比较均匀。草本层的物种分布重叠率是最大的,说明草本植物的生境相似性很高。低海拔区 域的生物多样性要高于高海拔区域的生物多样性。结合环境因子间的相关关系和DCCA排序结果,发现海拔是影响东灵山辽东栎林物种分布的主 要环境因子。     

Biogeographical zonation of the western Iberian peninsula on the basis of the distribution of earthworm species

We used TWINSPAN and CANOCO to investigate the biogeography of the western Iberian Peninsula on the basis of the distribution of earthworms among ninety areas of Galicia, Portugal, Asturias, León, Zamora, Salamanca, Cáceres, Badajoz and Huelva. This part of Iberia is clearly divisible into a Eurosiberian Region in the north and west and a Mediterranean Region in the south and east. For earthworm faunas, however, the limit between these regions is considerably further south than is conventionally accepted on the basis of Rivas Martinez's (1987) vegetation-type classification. Species character- istic of the Eurosiberian Region include Dendrobaena madeirensis, D. octaedra, Allolobophora caliginosa and various species of the genus Lumbricus . Within this region the earthworm fauna of Asturias is clearly distinct from that of Galicia and northern Portugal. Species characteristic of the Mediterranean Region include Allolobophora caliginosa , A. chlorotica and A. rosea , but inventories from this region are most easily identified by the absence or scarcity of those species characteristic of the Eurosiberian Region. Many areas show intermediate characteristics between the two major regions, and in some cases one region 'intrudes' into the other.     

Drivers of macrophyte development in rivers in an agricultural area: indicative species reactions

The ecological drivers of macrophyte development in a lowland agricultural area were tested based on a 2008 survey on the Wkra River catchment. Our survey was carried out in the rivers of an agricultural area with relatively high concentrations of both nitrates and phosphates in the water. By using the Polish macrophyte method, we were able to calculate several botanical metrics. Canonical ordination analyses used to relate biological data to environmental variables such as physical and chemical parameters of water, surface water velocity or river width, were carried out using CANOCO for Windows. Redundancy analysis (RDA) showed that pH and alkalinity were the parameters best correlated with the distribution of macrophytes and values of macrophyte indices. The recorded values of the Macrophyte Index for River in the Wkra River and its tributaries reflected their good and moderate ecological status (the Water Framework Directive scale). Despite the fact that nutrient concentrations in the water were relatively high and that most of the sites represented eutrophic conditions, the results of this survey showed that non-nutrient parameters may play an important role in explaining aquatic plant occurrence in rivers that have been subjected to eutrophication.     

Magnitude of mesozooplankton variability: a case study from the Marginal Ice Zone of the Barents Sea in spring

Zooplankton was studied on eight stations in the marginal icezone (MIZ) of the Barents Sea, in May 1999, along two transectsacross the ice edge. On each station, physical background measurementsand zooplankton samples were taken every 6 h over a 24 h periodat five discrete depth intervals. Cluster analysis revealedseparation of open water stations from all ice stations as wellas high similarity level among replicates belonging to particularstation. Based on five replicates per station, analysis of variance(ANOVA) confirmed significant differences (P < 0.05) in abundancesof the main mesozooplankton taxa among stations. Relations betweenthe zooplankton community and environmental parameters wereestablished using redundancy analysis (CANOCO). In total, 55%of mesozooplankton variability within studied area was explainedby eight variables with significant conditional effects: depthstratum, fluorescence, temperature, salinity, bottom depth,latitude, bloom situation, and ice concentration. GLM modelssupported supposition about clear and negative relationshipbetween concentration of Oithona similis, and overall mesozooplanktondiversity. The analyses showed a dynamic relationship betweenmesozooplankton distribution and hydrological conditions onshort-term scale. Furthermore, our study demonstrated that variabilityin the physical environment of dynamic MIZ of the Barents Seahas measurable effect on the Arctic pelagic ecosystem.     

人工滩涂湖泊滴水湖浮游藻类群落特征

于2009年3月—2010年2月逐月对中国最大人工滩涂湖泊——滴水湖的浮游藻类群落特征进行研究。利用CANOCO4.5软件对浮游藻类数据和环境因子数据进行典范对应分析(CCA),以揭示浮游藻类对生态环境的响应。结果表明:全年共检测到浮游藻类186种及变种,隶属于8门92属,其中绿藻门种类最多,其次是蓝藻门和硅藻门;主要优势种为小席藻、微小平裂藻、银灰平裂藻、不定微囊藻、弱细颤藻、啮蚀隐藻、四尾栅藻、扁圆卵形藻;藻类的年均丰度和年均生物量分别为(4552.29±4591.33)×104cells·L-1和8.15±6.63mg·L-1,藻类现存量各月份间差异极显著(P<0.01),但站点间差异不显著;多样性分析显示,藻类物种多样性较好;典范对应分析表明,水温、总氮等是影响滴水湖藻类群落结构的主要因素。     

Plant characteristics determine insect borer assemblages on Protea species in the Cape Fynbos, and importance for conservation management

The influence of regional climate, biotope and host-plant variables on the frequency of occurrence of insect borers associated with infructescences of Protea species in the species-rich flora of the Cape Fynbos was investigated. Large samples of infructescences (n=1000) were collected on a seasonal basis and borers identified and quantified. Data were analysed using DECORANA and CANOCO so as to correlate environmental variables with borer occurrence. Distinct differences in frequency of occurrence of the various insect taxa were recorded on the various plant species studied. These differences were primarily accounted for by physical host-plant characteristics (infructescence and seed set variables), and secondarily, by biotope variables and climatic factors. Fynbos plant characteristics therefore play a major role in determining insect abundance. Plant diversity in the Fynbos is maintained by burning. These management burns, however, should not be applied too frequently or over areas large enough to extirpate any borer species. As these borers are excellent umbrellas for many other insects, their conservation covers Fynbos insect diversity in general.     

Effects of land use on black fly assemblages (Diptera: Simuliidae) in submontane rivers (West Carpathians, Slovakia)

The effects of land use on black fly assemblages were investigated in submontane rivers (the Ľubochnianka River, the Revúca River, upper Váh River catchment) in the Carpathians. We recorded 11 black fly species in the Ľubochnianka River and 10 species in the Revúca River. Land use differs between the catchments; the Ľubochnianka is a primarily forested catchment, and the Revúca is markedly deforested catchment. Fifteen environmental variables were analysed. Based on the results provided by CANOCO, phosphorus level and stream slope are the most important variables and have significant influences on the variability of black fly assemblages. In spring, Prosimulium rufipes occurred along the entire lengths of the streams. The black fly assemblage of the Revúca River differs from the assemblage of the Ľubochnianka River mainly by its higher abundances of Simulium variegatum and Simulium ornatum, by the presence of Simulium carthusiense, and by the absence of Prosimulium hirtipes.     

Classification and ordination analysis of herbaceous flora in district Tor Ghar,western Himalaya

District Tor Ghar is phytosocilogically unexplored region in the western Himalaya. Present study was conducted in district Tor Ghar during the summers of 2012 and 2013 to study floristic diversity of herbaceous flora in the region. The district Tor Ghar is located on 34° 32′ - 34° 50′ N, and 72° 48′ - 72°58′ E. A total of 229 herb species belonging to 168 genera and 66 families were identified. Herbaceous vegetation was sampled from 1 × 1 m quadrats. For vegetation classification into plant communities, presence, absence (1,0) data on 229 herbaceous species and 64 locations were analyzed in PCORD version 5 via Cluster and Two Way Cluster Analyses. Six plant communities were established. Plant abundance data were treated in CANOCO version 4.5 to measure the ecological gradient of plant species and communities of the region. Detrended Correspondence Analysis (DCA) a type of indirect gradient analysis reconfirmed the results of Cluster and Two way Cluster Analysis. Moreover the study furnishes useful information for improvement, protection and management of present vegetation status for future generation. A comprehensive conservation measure with practical implementation is utmost necessary for conservation of rapidly depleting plant resources of the area.     

Hydrology and substrates: determinants of oligochaete distribution in lowland streams (The Netherlands)

In most soft-bottomed, lowland streams in the Netherlands discharge regimes largely follow the precipitation pattern. Winter discharges are higher and much more dynamic then summer discharges, although rain storms throughout the year cause unexpected peak flows. Minimal precipitation, reduced stream flow and droughts can occur during the summer months. Lowland stream habitat, particularly in The Netherlands, is hydrologically dynamic, with substrates frequently moved or disturbed. Differences in discharge patterns in Dutch soft-bottomed lowland streams are expected to affect distribution patterns of macroinvertebrates and thus oligochaetes. Ten small to medium sized lowland streams, differing from one another in hydrological regime, were studied. Five major habitats in each stream were assessed on three occasions over a 15-month period. Each habitat sampled with a micro-macrofauna shovel; during each sampling period, several environmental parameters, especially hydrological and substrate parameters, were measured. Ordination (CANOCO) (Ter Braak, 1989) and statistical tests (chi-squared test) (Lindgren & McElrath, 1970) were used to determine the major oligochaete distribution patterns between streams as well as between habitats within each stream. Each stream was characterized by its oligochaete assemblage; general distribution patterns and individual oligochaete–substratum relationships were documented. Hydro-morphological parameters together explained the differences in major distribution patterns. Preferences of oligochaetes for specific structural habitats are discussed.     

Hordeumgeniculatum in the Pannonian Basin: Ecological requirements and grassland vegetation on salt-affected soils

Hordeum geniculatum is considered as an obligate halophyte, but exact data about ecological requirements of the species are lacking. Therefore, species response curves of H. geniculatum were obtained for soil reaction and nutrients using Borhidi's indicator values and LOESS smoother response model in the programme CANOCO. Our data showed that H. geniculatum can be regarded as an obligate halophyte preferring slightly to moderately saline soils with relatively high content of nutrients. The Hordeetum hystricis association, indicating grazed vegetation on salt-rich soils, is a plant community that occurs only in central and southeastern Europe. Because this plant community has only been documented in a relatively small area, details about its vegetation ecology are inaccurate. Therefore, the ecology and species composition of this community were studied in three countries within the Pannonian Basin (Hungary, Serbia and Slovakia). A detrended correspondence analysis of 95 relevés from the Pannonian Basin confirmed that the community is characterised by the cover of H. geniculatum above 25%, which may even reach 75%. The association was species-rich; we sampled 91 taxa in 95 relevés. The widespread presence of many accessory species was dependent on environmental conditions, particularly the nutrient and salt content and animal disturbance.