More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy

The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the subject of debate. Vast increases in gene number are now possible due to advances in genomics, but large numbers of genes will be available for only modest numbers of taxa, raising the question of whether such genome-scale phylogenies will be robust to the addition of taxa. To examine the relative benefit of increasing taxon number or gene number to phylogenetic accuracy, we have developed an assay that utilizes the symmetric difference tree distance as a measure of phylogenetic accuracy. We have applied this assay to a genome-scale data matrix containing 106 genes from 14 yeast species. Our results show that increasing taxon number correlates with a slight decrease in phylogenetic accuracy. In contrast, increasing gene number has a significant positive effect on phylogenetic accuracy. Analyses of an additional taxon-rich data matrix from the same yeast clade show that taxon number does not have a significant effect on phylogenetic accuracy. The positive effect of gene number and the lack of effect of taxon number on phylogenetic accuracy are also corroborated by analyses of two data matrices from mammals and angiosperm plants, respectively. We conclude that, for typical data sets, the number of genes utilized may be a more important determinant of phylogenetic accuracy than taxon number.     

Autochthonous leaf assemblages as records of deciduous forest communities: an actualistic study

How well do autochthonous leaf assemblages reflect live plant communities? How do leaf assemblages accumulating over different time scales compare in paleoecologic information content? Forest-floor leaf assemblages accumulating over ten-day intervals (referred to here as short-term assemblages) and over a five-month season of leaf abscission (referred to here as a long-term assemblage) were compared with the surrounding community in a modern temperate deciduous forest in northern Ohio. Leaf number in the long-term leaf assemblage is strongly correlated with the abundance of taxa (stem number) around the accumulation site and weakly correlated with both average taxon size (stem circumference) and average taxon distance from the accumulation site. Of the variance in leaf number, 45% is explained solely by stem number and 67% by stem number and average distance together. Average size explains an insignificant amount of the variance in leaf number. Like the long-term assemblage, leaf number in the short-term leaf assemblages is usually strongly correlated with stem number and usually weakly correlated with average taxon size and average taxon distance. However, these patterns are not consistent, and the correlations are highly variable. Similarly, there is high variability in the degree to which stem number, average taxon size and average taxon distance account for variance in leaf number. Short-term leaf assemblages are characterized by great fluctuations in taxonomic relative abundance, caused by seasonal variation in the timing and rate of leaf abscission among taxa. While autochthonous leaf assemblages accumulating over several months can reflect the surrounding community with fair accuracy, leaf assemblages accumulating over shorter time spans are inconsistent records of the surrounding community. The depositional circumstances producing short-term assemblages (i.e. event burial) may result in well-preserved specimens, but community data from such assemblages should be treated with caution and, if possible, compared with data from contemporaneous long-term assemblages.Paleobotany, taphonomy, actualism, paleocommunity reconstruction, time-averaging. Keith H. Meldahl, Damon Scott and Karen Carney, Department of Geology, Oberlin College, Oberlin, Ohio, 44074, USA; 6th June, 1994; revised 8th February, 1995.     

THE QUANTIFICATION OF SOME PLANT-TAXA CIRCUMSCRIPTIONS

Intrataxon variability is estimated by the technique of numerical taxonomy. Taxa which had been determined by orthodox taxonomic methods are subjected to analyses by numerical phenetics. Comparisons are made of the amounts of cohesion among the members of different taxa in the Bromeliaceae at several taxonomic levels by computing the degrees of similarities between members of the same taxon and of different taxa. Results of these comparisons with several taxa reveal that the variability of a taxon in terms of phenetic distance computed with a large number of characters does not necessarily agree with a subjective appraisal of variability. The method facilitated difficult taxonomic determinations and provided an estimate of the relative evolutionary ages of different taxonomic groups.     

Historical vs. ecological factors influencing global patterns of scarabaeine dung beetle diversity

Abstract. There has been much debate concerning the relative influence on biodiversity of historical vs. current ecological factors. Although both are important, we suggest that historical influences might be greater at higher taxonomic level, since one is looking further back into evolutionary history than at lower taxonomic level. Although we are unable to separate ecological from historical effects in the present global study on scarabaeine dung beetles, we are able to demonstrate differences in correlations between major environmental influences (climatic area, numbers of dung types) and major components of diversity (taxon richness, taxon diversity, functional composition) at different taxonomic levels (tribe, genus, species). Current global variation in taxon richness is correlated strongly to current biogeographical variation in the area of suitable climate at all three taxonomic levels. However, generic and species richness is correlated most strongly to climatic combinations which include tropical and warm summer rainfall climate types (I, II). In contrast, tribal richness is correlated most strongly to climatic combinations which include both warm summer rainfall and temperate climate types (II, VI, X). Regional variation in the number of available dung types shows a strong positive correlation to regional variation in taxon richness at higher tribal level but not at lower generic and species levels. Similarly, biogeographical differences in the number of available dung types show a strong negative correlation to dominance indices for taxon diversity at tribal level (distribution of generic numbers between tribes) but none at generic level (species numbers per genus). As functional diversification is linked closely to taxonomic diversification at tribal level, proportions of both ball‐rolling genera and ball‐rolling species also show strong negative correlations to the number of dung types available in each region. In conclusion, the presence of dung type correlations only at higher taxonomic level may reflect historical effects on scarabaeine taxon diversification, whereas differences in correlations to climate type with taxonomic level may reflect both current ecological and historical effects.     

Regional variation in the historical components of global avian species richness

Aim Using a global data base of the distribution of extant bird species, we examine the evidence for spatial variation in the evolutionary origins of contemporary avian diversity. In particular, we assess the possible role of the timing of mountain uplift in promoting diversification in different regions. Location Global. Methods We mapped the distribution of avian richness at four taxonomic levels on an equal‐area 1° grid. We examined the relationships between richness at successive taxonomic levels (e.g. species richness vs. genus richness). We mapped the residuals from linear regressions of these relationships to identify areas that are exceptional in the number of lower taxa relative to the number of higher taxa. We use generalized least squares models to test the influence of elevation range and temperature on lower‐taxon richness relative to higher‐taxon richness. Results Peaks of species richness in the Neotropics were congruent with patterns of generic richness, whilst peaks in Australia and the Himalayas were congruent with patterns of both genus and family richness. Hotspots in the Afrotropics did not reflect higher‐taxon patterns. Regional differences in the relationship between richness at successive taxonomic levels revealed variation in patterns of taxon co‐occurrence. Species and genus co‐occurrence was positively associated with elevational range across much of the world. Taxon occurrence in the Neotropics was associated with a positive interaction between elevational range and temperature. Conclusions These results demonstrate that contemporary patterns of richness show different associations with higher‐taxon richness in different regions, which implies that the timing of historical effects on these contemporary patterns varies across regions. We suggest that this is due to dispersal limitation and phylogenetic constraints on physiological tolerance limits promoting diversification. We speculate that diversification rates respond to long‐term changes in the Earth's topography, and that the role of tropical mountain ranges is implicated as a correlate of contemporary diversity, and a source of diversification across avian evolutionary history.     

Disentangling the effects of local and regional processes on biodiversity patterns through taxon‐contingent metacommunity network analysis

Metacommunity theory, which has gained a central position in ecology, accounts for the role of migration in patterns of diversity among communities at different scales. Community isolation has a main role in this theory, but is difficult to estimate empirically, partly due to the taxon‐dependent nature of dispersal. Landscapes could be perceived as either fragmented or connected for organisms with contrasting dispersal abilities. Indeed, the dispersal ability of a taxon, and the spatial scale at which eco‐evolutionary processes shape local diversity, determine a taxon‐dependent metacommunity network. In this paper, we introduce a methodology using graph theory to define this taxon‐dependent metacommunity network and then to estimate the isolation of local communities. We analyzed the relative importance of local conditions versus community isolation as determinants of community richness for 25 taxa inhabiting 18 temporary ponds. Although local factors have been the foci of most previous empirical and theoretical considerations, we demonstrate that the metacommunity network is an equally important contributor to local diversity. We also found that the relative effect of local conditions and the metacommunity network depend on body size and taxon abundance. Local diversity of larger species was more affected by patch isolation, while taxon abundances were associated with positive or negative effects of isolation. Our results provide empirical support for the proposed role of metacommunity networks as determinants of community diversity and show the taxon‐dependent nature of these networks.     

Behavioural flexibility predicts species richness in birds, but not extinction risk

The number of species varies greatly among taxa. In birds, for example, the parvorder Passerida contains 3556 species while the Odontophorida contains only six species. This uneven distribution of species among bird groups is not a consequence of random branching patterns and therefore warrants an explanation. According to the behavioural drive hypothesis, behavioural innovation coupled with social transmission of the new skill to other members of the population may lead to accelerated rates of evolution, and could therefore account for differences in species richness. In this paper, we test the behavioural drive hypothesis by examining the link between behavioural flexibility and the number of species per taxon. We estimate flexibility with relative brain size and feeding innovation rate and predict that both will be positively associated with the number of species per taxon. Since the number of species at any given time results from a balance between speciation and extinction rates, we also examine the link between flexibility and the number of species threatened with extinction. We predict that the two flexibility correlates will be negatively associated with the number of species at risk. In simple regressions, both flexibility correlates were significantly associated with species number per taxon. However, only innovation rate remained in the final model. Relative brain weight dropped out of the multiple regression due to its association with innovation rate. Relative brain weight, innovation rate and species number per taxon were all significantly correlated with the number of threatened species in the simple regression, but only the latter remained significant in the final model. The same results were obtained on independent contrasts, indicating that behavioural flexibility predicts richness but not extinction risk in birds. Copyright 2003 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour.      

Indole alkaloids as systematic markers of the Apocynaceae

Indole alkaloids can be characterized by skeletal specialization (S), determined upon consideration of their relative position on a biogenetic map and the number of their naturally occurring substitutional derivatives, as well as by oxidation level (O). The mean (S) and (O) for contained alkaloids of a given plant taxon are taken to represent evolutionary advancement parameters, respectively EA_s and EA_o.A correlation of these EA_s/EA_o values for tribes of the Apocynaceae-Plumerioideae reveals a chemical gradient, given by gradually increasing EA_s and EA_o values, to link Carisseae-Alstonieae-Rauvolfieae-Tabernaemontaneae.     

水稻无脊椎动物多样性的K-L变换编目分析

K-L变换可消除样品各特征间的相关性,去除信息量较少或信息虚假的坐标轴,降低特征空间的维数,用较少量的特征描述样品,是目前最为有效的数据信息压缩抽取方法。利用K-L变换,样品之间变化较小的分类单元（目或功能群等）,不会作为重要特征保留下来。因此,数量上占优势、或害虫防治中有重要地位的分类单元并不一定是识别样品的重要特征。可以藉K-L变换明确构成样品变异的主要分类单元,从而对不同地区、不同季节的取样实践有一定的指导意义、用通常的多样性指数分析及多样性差异显著性分析无法解决这个问题。用K-L变换可大大压缩数据存储空间。对数据量很大的生物多样性分析有较大的应用价值。反映样品所携信息量的热带水稻田无脊椎动物目主要是半翅目,中腹足目,以及表腹亚目。其中,在旱季半翅目占主要地位,而在雨季中腹足目占主要地位。就无脊椎动物目的组成而言,它们是构成样品变异的主要类群,是取样中需要得到特别注意的目。反映样品信息的无脊椎动物功能群主要是外部植食类,植食多食性类,半水生水面爬行类,粗粒残物取食类,以及陆生爬行、跳跃或猎者类,是取样中要重点考虑的一些类群。     

ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE

Abstract — Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re-investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.     

A CLADISTIC TEST OF THE TAXON CYCLE AND TAXON PULSE HYPOTHESES

Abstract— A species' habitat preference is intcrpretablc both as a response to present-day conditions and as a result of evolutionary response to historical conditions. The taxon cycle and taxon pulse have been proposed as hypotheses that allow prediction of patterns of habitat specialization within a lineage. Both are based on common assumptions: (1) habitat specialization is largely irreversible in a lineage, (2) ecological specializations arise in a center of origin, and (3) dispersal events leading to current distributions can be ascertained. Eight taxa of Antillean, Mexican, and Central American Carabidae, for which cladistic hypotheses of relationship have been proposed, are used to test the generality of the taxon cycle and pulse. The patterns of habitat utilization predicted by the taxon cycle and taxon pulse hypotheses are tested by comparing cladistic transformations of habitat preference to randomly generated patterns of data generated under a null hypothesis. Evolutionary changes in habitat are interpreted using Camin-Sokal coding, which assumes irreversible habitat shifts and a predetermined ecological ground state (assumptions of the taxon cycle and taxon pulse). An observed pattern is considered to demonstrate the taxon cycle or pulse when it results in an explanation of the habitat shifts that is more parsimonious than 95 % of the randomly generated patterns. Of the eight carabid groups, only one exhibits a statistically significant pattern supporting the taxon cycle and pulse. The failure of the taxon cycle and pulse as generally predictive hypotheses may be due to historical changes in climate that permit episodes of range expansion for species previously restricted to small ranges, and habitat shifts and specialization that do not progress in a linear transformation series. Habitat shifts are also analyzed using Farris optimization, resulting in the most parsimonious transformation series of habitats, subject to a predefined ordering of habitats, while allowing reversals. Significance of an observed pattern of habitat shifts under Farris optimization implies habitat constancy relative to cladogenesis, and step-wise changes in habitat preference. Two of the eight groups exhibit significant patterns of habitat utilization under Farris optimization, indicating that vicariance of areas of like habitat has been the predominant factor generating species diversity in these groups. The other groups do not exhibit habitat constancy, suggesting rapid changes in habitat preference relative to speciation.     

Taxon age,origination, and extinction through geologic time

Changes in the taxon ages of fossil marine families that are alive and those that become extinct in each stage of the Phanerozoic reflect changes in the origination rate, differences in the extinction rate of families with different taxon ages, and mass extinction events. Extinct families are generally much younger than the population from which they were drawn. Periods dominated by higher numbers of younger families are more susceptible to larger size extinctions and greater variation in extinction size. As a result the relative size of extinction peaks must be viewed with regard to the taxon age structure of the population. Mass extinctions cause little change in the taxon age of the fauna. However, adaptive radiations cause a large drop in the average age of the families that are alive at any given time. Families must be treated as dynamic entities in macroevolutionary studies because their probabilities of extinction change over time.     

How wide to cast the net? Cross‐taxon congruence of species richness,community similarity and indicator taxa in ponds

1. Broad‐scale assessments of biodiversity often rely on the use of surrogate taxa, whose reliability has rarely been tested, particularly in freshwater systems. Here we use data from 46 ponds in two regions of the U.K. to explore the performance of macroinvertebrate taxa as surrogates for the rapid assessment of pond biodiversity. For the four dominant taxonomic groups in these ponds (Chironomidae, Coleoptera, Gastropoda and Trichoptera) we explore cross‐taxon species richness relationships in each of the two regions, and also determine the degree of concordance between the different taxa in accurately representing the similarity relationships between pond assemblages. 2. Patterns of cross‐taxon congruence in species richness were highly variable among taxa and study sites, making the use of a single taxon as a predictor of overall macroinvertebrate species richness problematic. In contrast, all four taxa show >70% congruence with the pattern of community similarity between sites resulting from the entire macroinvertebrate dataset, this result being consistent within and between regions. Canonical correspondence analysis demonstrated that all taxa were related in a similar manner to measured environmental parameters, meaning that limited additional ecological information is gained by including a wider range of pond taxa in rapid site assessment. 3. Single taxonomic groups can, therefore, perform consistently as indicators of community similarity between ponds, and no one taxon dramatically outperforms any other in this respect. The relative merits of the four focal taxa as surrogates for pond invertebrate assemblage composition are discussed with reference to ease of survey, ease of identification and ecological range occupied. 4. It is suggested that Coleoptera have a number of advantages as a surrogate taxon, being diverse, easily sampled, readily identified, taxonomically stable, ecologically well understood and occurring across a wide spectrum of pond types. They are therefore recommended for use as a focal group in rapid pond biodiversity assessments, employing an approach such as ours, which examines patterns of assemblage similarity, rather than species richness alone.     

Fossil plankton depth zones

Varied evidence from the known depth correlated distribution of benthic shelly facies communities in the Ordovician and Silurian clearly shows that graptolite taxonomic diversity increased from the nearshore regions to the shelf margin regions, as well as into the deeper portions of epicontinental basinal areas. We then consider a method for determining the depth distribution of individual graptolite taxa. This method depends on correlating the first appearance of graptolite taxa as one departs from shoreline in terms of the underlying benthos, arrayed in benthic assemblages. The first appearance departing from shoreline corresponds with the upper depth limits of each taxon in terms of the underlying depth indicated by the underlying, associated benthos. The depth of maximum abundance for each taxon should correspond to that point in the increasing relative abundance of that taxon where relative increase in abundance ceases. The lower depth limit of each taxon should correspond to that point on the relative abundance curve where increase in total relative abundance ceases.Using information about the stratigraphic ages indicated by the graptolite faunas, zone-by-zone, combined with that provided by the communities present within the associated and formerly underlying benthic assemblages should provide a more refined stratigraphic zonation than that obtained without combining both.     

Assessing the value of DNA barcodes for molecular phylogenetics: effect of increased taxon sampling in lepidoptera

Background

A common perception is that DNA barcode datamatrices have limited phylogenetic signal due to the small number of characters available per taxon. However, another school of thought suggests that the massively increased taxon sampling afforded through the use of DNA barcodes may considerably increase the phylogenetic signal present in a datamatrix. Here I test this hypothesis using a large dataset of macrolepidopteran DNA barcodes.

Methodology/Principal Findings

Taxon sampling was systematically increased in datamatrices containing macrolepidopteran DNA barcodes. Sixteen family groups were designated as concordance groups and two quantitative measures; the taxon consistency index and the taxon retention index, were used to assess any changes in phylogenetic signal as a result of the increase in taxon sampling. DNA barcodes alone, even with maximal taxon sampling (500 species per family), were not sufficient to reconstruct monophyly of families and increased taxon sampling generally increased the number of clades formed per family. However, the scores indicated a similar level of taxon retention (species from a family clustering together) in the cladograms as the number of species included in the datamatrix was increased, suggesting substantial phylogenetic signal below the ‘family’ branch.

Conclusions/Significance

The development of supermatrix, supertree or constrained tree approaches could enable the exploitation of the massive taxon sampling afforded through DNA barcodes for phylogenetics, connecting the twigs resolved by barcodes to the deep branches resolved through phylogenomics.     

The nonidentity of invariable positions in the cytochromes c of different species

This study answers the question: Are the variable and invariable codons of cytochrome c largely the same in all species? A method is presented for estimating the number of invariable (as opposed to unvaried) codons common to two taxa. The two taxa in this study were comprised of four fungi and four metazoans. Given the number of mutations fixed in each taxon, one calculates the number of codons that would be expected to have fixed mutations in both taxa, in one taxon only, in the other taxon only, and in neither taxon. This expectation depends upon the number of invariable codons that are assumed to be common to both taxa. In the present example, the assumption of 41 invariable codons in common leads to estimates that deviate by less than 2% from the values actually observed. This leads to the conclusion that there are 46 positions that are variable in one taxon but invariable in the other, thereby demonstrating that the invariable codons are not largely the same between the fungi and the metazoans.     

Phylogeny of Paragnathorhynchus Meixner and Aculeorhynchus Schilke (Turbellaria, Kalyptorhynchia)

Paragnathorhynchus subterraneus Meixner is redescribed and identified with Prognathorhynchus stilofer Schilke. The paired tubular extracapsular secretory sacs in the proboscis apparatus of Aculeorhynchus glandulis Schilke are interpreted as evolutionary derivatives of intracapsular secretory vesicles in the proboscis of some Gnathorhynchidae. Aculeorhynchus Schilke is interpreted as an apomorph sister taxon of a group of taxa in the Gnathorhynchidae.     

Comparisons among colonization of artificial substratum types and natural substratum by benthic macroinvertebrates

A field study was designed to concurrently evaluate differences in colonization by benthic macroinvertebrates on a range of artificial substratum types (single particles of natural rock or clay brick and baskets of natural substratum) after three colonization periods (1, 8 and 29 days). Fauna on the artificial substrata were compared to natural substratum and the effect of natural epilithic cover on colonization by zoobenthos was determined. Densities of total number of organisms and the seven most abundant taxa, total number of taxa and quantity of organic material were greater on the natural substratum than on the artificial substratum types. Relative abundances of taxa on pairs of the artificial substratum types, unlike pairs of each artificial substratum type and the natural substratum, were statistically correlated. Among the artificial substratum types densities of total number of organisms and about one-half of the most abundant taxa, total number of taxa and quantity of organic material were greatest in the substratum baskets. Natural epilithic cover on the single rock particles and substratum baskets affected the densities of total number of organisms and two of the seven most abundant taxa. These taxonomic groups were at approximately two to six-fold greater densities on the substrata with fine sediment. consistent patterns in densities of the zoobenthos on the substrata were found after each colonization period. In our study all measures of the macroinvertebrate assemblages (densities of each taxon, total number of organisms, total number of taxa and relative abundances of taxa), with few exceptions, were different between each artificial substratum type and natural substratum. This result showed the abundance and composition of the macroinvertebrate fauna on artificial substratum types were different from the natural substratum. Therefore, the choice of using artificial substrata instead of direct sampling of the natural substratum should be carefully made. Among the artificial substratum types relative abundances of taxa were similar on the single substratum particles and substratum baskets indicating single particles instead of baskets might be used to sample the zoobenthos. Investigators should consider the potential effect of the natural epilithic cover of substratum particles on colonization by zoobenthos when choosing the type of artificial substratum.     

The importance of globalisation in driving the introduction and establishment of alien species in Europe

Understanding the role of globalisation in promoting introduction and establishment of alien species is an important step towards successful management of biological invasions. We aimed to quantify the taxon‐dependent association of globalisation with the introduction and establishment of alien species in Europe. The availability of the KOF index of globalisation that measures all economic, social and political dimensions of global connectivity enables a study of this factor. Based on an extensive database of alien species, we used model selections based on the Akaike information criterion and hierarchical partitioning to identify the importance of globalisation in predicting the number of all introduced species and established species of ten mainly terrestrial taxa in countries across Europe. The association of globalisation with alien species establishment varied depending on taxon type. While the gross domestic product (GDP) of countries was a strong predictor for all but one taxon, globalisation was also found to be an important predictor for three taxa including those of high (e.g. insects) and low mobility (e.g. magnoliophyta). Globalisation explained 3.1 to 22% independently, and 5.5 to 35% jointly with other variables, of among‐country variations in the number of established alien species. The effect of globalisation on the distribution of all introduced species is not substantially different from that on the established alien species. This study highlights how globalisation among habitat availability and environmental conditions can determine the patterns of alien species introduction and establishment across Europe. The results also emphasise the varying degree of importance between different taxa. Knowledge of the relative significance of various pathways with regard to different taxa is important for correctly focusing efforts to reduce the spread of these species.     

Factors Affecting Macroinvertebrate Richness and Diversity in Portuguese Streams: a Two‐Scale Analysis

We analysed the spatial patterns in macroinvertebrate taxon richness and abundance at two scales: sampling unit and basin. We sampled 12 stream sites in three zones of Portugal, differing in climate geomorphology and water chemistry. At a sampling unit scale, substratum organic matter content, depth and the dominant size of substratum particles were correlated with numbers of taxa and individuals. We propose that the number of taxa at a small scale depends on the number of individuals, which in turn is the result of organic matter accumulation, hydrologic and substratum characteristics. The environmental parameters better explaining the large‐scale biological data were temperature, minimum size of substratum particles and pH. Regardless of the relative importance of variable types and mechanisms regulating stream invertebrates along the climatic gradient, rivers from the North and Centre appeared to be richer in taxa than the typically Mediterranean streams in the South.