Independence of total species richness and richness difference are not the same thing

Leprieur and Oikonomou (2014) criticized that a replacement index β_− 3, a partitioned component of Jaccard index β_jac, was not richness independent and should not be used in biogeographic and ecological studies. However, Leprieur and Oikonomou failed to recognize the difference between richness and richness difference. Independence of total species richness is not equal to independence of richness difference. Theoretically and ideally, it is true that β_− 3 (and β_jac as well) is not independent of richness difference while Simpson index (β_sim) is fully independent of richness difference. However, all these indices actually are independent of total species richness. At last, it is worth mentioning that the ideal independence studied here is easily violated in computational simulation and real-world settings.     

Effects of woody plant species richness on mammal species richness in southern Africa

Aim To determine the relationship between the species richness of woody plants and that of mammals after accounting for the effect of environmental variables. Location Southern Africa, including Namibia, South Africa, Lesotho, Swaziland, Botswana, Zimbabwe, and part of Mozambique. Methods We used a comprehensive dataset including the species richness of mammals and of woody plants and environmental variables for 118 quadrats (each of 25,000 km²) across southern Africa, and used structural equation models (SEMs) and spatial regressions to examine the relationship between the species richness of woody plants and of mammal trophic guilds (herbivores, insectivores, carni/omnivores) and habitat guilds (aquatic/fossorial, ground‐living, climbers, aerial), after controlling for environment. We compared the results of SEMs with those of single‐predictor regressions (without controlling for environment) and of spatial regressions (controlling for both environment and residual spatial autocorrelation). Results The geographical variation of mammal species richness in southern Africa was strongly and positively related to that of woody plant species richness, and this relationship held for most mammal guilds even when the influence of environment and spatial autocorrelation had been accounted for. However, the effect of woody plant species richness on the richness of aquatic/fossorial species almost disappeared after controlling for environment, suggesting that the congruence in species richness patterns between these two groups results from similar responses to the same environmental variables. For many mammal guilds, the relative role of environmental predictors as measured by standardized partial regression coefficients changed depending on whether non‐spatial single‐predictor regressions, non‐spatial SEMs, or spatial regressions were used. Main conclusions Woody plants are important determinants of the species richness of most mammal guilds in southern Africa, even when controlling for environment and residual spatial autocorrelation. Environmental correlates with animal species richness as measured by simple correlations or single‐predictor regressions might not always reflect direct effects; they might, at least to some degree, result from indirect effects via woody plants. Interpretations of the strength of the effect of environmental variables on mammal species richness in southern Africa depend largely on whether spatial or non‐spatial models are used. We therefore stress the need for caution when interpreting environmental ‘effects’ on broad‐scale patterns of species richness if spatial and non‐spatial methods yield contrasting results.     

Measuring richness and evenness

Surveying Natural Populations by L-A.C. Hayek and M.A. Buzas Columbia University Press, 1997. $69.00/￡48.00 hbk, $28.00/￡19.00 pbk (xvi+563 pages) ISBN 0 231 10240 2/0 231 10241 0.     

Plant species richness under

Exotic pine plantations constitute a significant landscape feature in the North Island of New Zealand but their conservation value for native plant species is not often documented. Pine stem density, height and basal area of nine plantations of Pinus radiata ranging in age from 6 to 67 years in Kinleith Forest was determined. Pines reached heights of 60 m, and stand basal areas up to 183 ± 14 m(2)ha(-1). The abundance of woody shrubs, tree ferns and ground ferns was assessed in each stand. Understorey composition of shrubs and ferns was reflected on the first two axes of DCA ordinations and correlated with the age of the pines. Adventive shrubs predominated in stands < 20 years old. Light-demanding native shrubs with bird dispersed fruits predominated in older stands, with more shade-tolerant species in the oldest site. Species richness increased rapidly in the first 11 years, but thereafter more slowly. Twelve native shrub species and 22 ferns were recorded from the most diverse stands. Richness and species composition were related to stand age, and probably also to topographical heterogeneity and aspect. Tree ferns reached densities of 2000—2500 ha(-1) and basal areas of 20—30 m(2)ha(-1) in the older stands. Initially the tree fern population was strongly dominated by Dicksonia squarrosa, which comprised 84% of individuals overall. Five species were present by 29 years. The faster growing Cynthea medullaris and C. smithii achieved greater heights than the Dicksonia spp., and their relative biomass was greatest in the oldest stands.     

A richness that cures

A study in Nature by Fischer et al. shows that environmental enrichment or increasing histone acetylation rescue the ability to form new memories and re-establish access to remote memories even in the presence of brain degeneration. Chromatin remodeling may be the final gate environmental enrichment opens to enhance plasticity and represents a promising target for therapeutical intervention in neurodegenerative diseases.     

Dependence of broad-scale geographical variation in fleshy-fruited plant species richness on disperser bird species richness

Aim We analysed the interdependence of avian frugivore‐ and fruited plant‐species richness at the scale of major river basins across Europe, taking into account several environmental factors along different spatial gradients. Location Continental Europe and the British Isles. Methods We focused on wintering birds and autumn/winter fruiting plants, and used major river basins as geographical units and Structural Equation Modelling as the principal analytical tool. Results The statistical influence of disperser species richness on fleshy‐fruited plant species richness is roughly double that of the reverse. Broad‐scale variation in frugivore richness is more dependent on environmental factors than on fruited plant richness. However, the influence of disperser richness on plant richness is four times higher than the influence of environmental factors. Environmental influences on both birds and plants are greater than purely spatial influences. Main conclusions Our results are interpreted as indicating that biotic dispersal of fruits strongly affects broad‐scale geographical trends of fleshy‐fruited plant species richness, whereas richness of fruited plants moderately affects frugivore richness.     

Species richness of Colorado riparian vegetation

Abstract. The probable causes of spatial variation in the diversity of plant communities on a global and local scale have been widely investigated, but the regional scale has received little attention. It remains unclear how disturbance affects diversity in wetlands andriparian vegetation. This study examines the hypothesis that regional variation in the richness of riparian wetlands is related to variation in macro-environment and flood potential. Vascular plant species richness was sampled in 0.1 ha plots at 115 riparian sites scattered over a 300 km length of the western slope of the Rocky Mountains in western Colorado, USA. The relationship between macro-environmental variables (e.g. drainage basin area), disturbance indicators, and species richness was analyzed using correlation analysis and multiple regression analysis. Total richness varied between 20 and 87 species (average 50.6) per 0.1 ha, and was highest in subalpine riparian forests from 2600–3650 m a.s.l. (57.8 species / 0.1 ha). Tree and shrub richness were highest in lower elevation, larger drainage basins, forb and graminoid richness were highest in higher elevation, smaller drainage basins. These opposing trends resulted in no net trend in total richness with elevation. Regression models for total richness were poor, suggesting that other variables must be important. The intermediate disturbance hypothesis and other single-factor hypotheses are not supported as explanations of the regional pattern of variation in richness.     

Functional richness outperforms taxonomic richness in predicting ecosystem functioning in natural phytoplankton communities

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Habitat fragmentation and species richness

In a recent article in this journal, Fahrig (2013, Journal of Biogeography, 40 , 1649–1663) concludes that variation in species richness among sampling sites can be explained by the amount of habitat in the ‘local landscape’ around the sites, while the spatial configuration of habitat within the landscape makes little difference. This conclusion may be valid for small spatial scales and when the total amount of habitat is large, but modelling and empirical studies demonstrate adverse demographic consequences of fragmentation when there is little habitat across large areas. Fragmentation effects are best tested with studies on individual species rather than on communities, as the latter typically consist of species with dissimilar habitat requirements. The total amount of habitat and the degree of fragmentation tend to be correlated, which poses another challenge for empirical studies. I conclude that fragmentation poses an extra threat to biodiversity, in addition to the threat posed by loss of habitat area.     

Helminth parasite richness among vertebrates

The numbers of intestinal helminth species (parasite richnesS) recorded from each of 488 vertebrate host species are compared using data compiled from the published literature. Associations between parasite richness, sampling effort, host size and host habitat (aquatic versus terrestrial) are assessed using a method designed to control for phylogenetic association. Parasite richness increases with the number of surveys on which each estimate of parasite richness is based (sampling effort). When the effects of sampling effort are controlled for, there remains a strong positive relationship between parasite richness and host body size. There is no tendency for aquatic hosts to harbour more parasite species than terrestrial hosts independently of differences in sampling effort and body size. The results are interpreted in the context of hosts representing habitats for parasite colonization, resource allocation between parasite species, and the age of the major mammalian radiations.     

Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing

Variation in plant species richness has been described using only aboveground vegetation. The species richness of roots and rhizomes has never been compared with aboveground richness in natural plant communities. We made direct comparisons of grassland plant richness in identical volumes (0.1 × 0.1 × 0.1 m) above and below the soil surface, using conventional species identification to measure aboveground richness and 454 sequencing of the chloroplast trnL(UAA) intron to measure belowground richness. We described above- and belowground richness at multiple spatial scales (from a neighbourhood scale of centimetres to a community scale of hundreds of metres), and related variation in richness to soil fertility. Tests using reference material indicated that 454 sequencing captured patterns of species composition and abundance with acceptable accuracy. At neighbourhood scales, belowground richness was up to two times greater than aboveground richness. The relationship between above- and belowground richness was significantly different from linear: beyond a certain level of belowground richness, aboveground richness did not increase further. Belowground richness also exceeded that of aboveground at the community scale, indicating that some species are temporarily dormant and absent aboveground. Similar to other grassland studies, aboveground richness declined with increasing soil fertility; in contrast, the number of species found only belowground increased significantly with fertility. These results indicate that conventional aboveground studies of plant richness may overlook many coexisting species, and that belowground richness becomes relatively more important in conditions where aboveground richness decreases. Measuring plant belowground richness can considerably alter perceptions of biodiversity and its responses to natural and anthropogenic factors.     

Relative influence of regional species richness vs local climate on local species richness in China's forests

Disentangling the relative effects of local and regional processes on local species richness (LSR) is critical for understanding the mechanisms underlying large‐scale biodiversity patterns. In this study we used 1098 forest plots from 41 mountains across China, together with regional flora data, to examine the relative influence of local climate vs regional species richness (RSR) on LSR patterns. Both RSR and LSR for woody species and all species combined decreased with increasing latitude, while richness of herbaceous species exhibited a hump‐shaped pattern. The major climatic orrelates of species richness differed across spatial scales. At the regional scale, winter coldness was the best predictor of RSR patterns for both woody and herbaceous species. At the local scale, however, productivity‐related climatic indices were the best predictors of LSR patterns. Local climate and RSR together explained 48, 54 and 23% of the variation in LSR, for overall, woody and herbaceous species, respectively. Both local climate and RSR independently influenced LSR in addition to their joint effects, suggesting that LSR patterns were shaped by local and regional processes together. Local climate and RSR affected LSR of woody species mainly through their joint effects, while there were few shared effects of climate and RSR on the LSR of herbaceous species. Our findings suggest that while geographic RSR patterns are mainly determined by winter coldness, the ecological processes driven by productivity may be critical to the filtering of regional flora into local communities. We also demonstrate that biogeographic region is not a good surrogate for regional richness, at least for our dataset. Consequently, whether biogeographic region can effectively reflect regional effects needs further examination.     

Distribution of vascular plant species richness and endemic richness along the Himalayan elevation gradient in Nepal

Aim Species richness and endemic richness vary along elevation gradients, but not necessarily in the same way. This study tests if the maxima in gamma diversity for flowering plants and the endemic subset of these plants are coherent or not. Location The study was conducted in Nepal, between 1000 and 5000 m a.s.l. Methods We used published data on distribution and elevational ranges of the Nepalese flora to interpolate presence between maximum and minimum elevations. Correlation, regression and graphical analyses were used to evaluate the diversity pattern between 1000 and 5000 m a.s.l. Results The interval of maximum species endemic to Nepal or the Himalayas (3800–4200 m) is above the interval of maximum richness (1500–2500 m). The exact location of maximum species density is uncertain and its accuracy depends on ecologically sound estimates of area in the elevation zones. There is no positive statistically significant correlation between log‐area and richness (total or endemic). Total richness is positively correlated with log‐area‐adjusted, i.e. estimated area adjusted for the degree of topographic heterogeneity. The proportion of endemic species increases steadily from low to high elevations. The peak in endemism (c. 4000 m) corresponds to the start of a rapid decrease in species richness above 4000 m. This may relate to the last glacial maximum (equilibrium line at c. 4000 m) that penetrated down to 2500–3000 m. This dynamic hard boundary may have caused an increase in the extinction rate above 4000 m, and enhanced the probability of isolation and facilitated speciation of neoendemics, especially among genera with a high proportion of polyploids. Main conclusions The results reject the idea of corresponding maxima in endemic species and species richness in the lowlands tentatively deduced from Stevens’ elevational Rapoport effect. They confirm predictions based on hard boundary theory, but hard‐boundaries should be viewed as dynamic rather than static when broad‐scale biogeographical patterns with a historical component are being interpreted.     

Different relationships between galling and non-galling herbivore richness and plant species richness: a meta-analysis

The plant richness hypothesis (PRH) is used to explain herbivorous insect richness based on the number of plant species, predicting a positive relationship. However, the influence of plant richness on insect distribution can become stronger with greater levels of specialization of herbivores. In this meta-analysis, I tested whether there is any difference in the correlation force recorded between studies that investigated endophagous versus exophagous herbivores, and galling versus non-galling guilds, in order to determine whether more specialized groups have a stronger relationship. Furthermore, I calculated whether effect sizes were homogeneous between galling studies carried out at local and regional scales, and between tropical and temperate regions. A total of 52 correlations were analyzed between plant species richness and herbivore species richness, with 18 correlations derived from galling herbivores and 34 from non-galling herbivores. The effect sizes were significant and positive in all studies, being higher for endophages than for exophages, and for galling than for non-galling studies. These results provide evidence that groups of insects with a higher level of host specialization and specificity (e.g., endophagous and galling) exhibit a greater dependence on plant richness. There was no difference in effect sizes for galling studies between the local and regional level or between tropical and temperate groups. Despite the large variability found for galling studies, effect sizes were consistent independently of climatic region and latitudinal variation. These results suggest that the PRH for galling insects can be generalized to most ecosystem and vegetation types.     

Regional species richness,hydrological characteristics and the local species richness of assemblages of North American stream fishes

1. Local assemblage structure, from a deterministic perspective, is presumably dictated by the regional species pool as well as regulated by local factors. We examined the relationships of the regional species pool and local hydrological characteristics to local species richness of North American freshwater fishes using data sets collected during the National Water Quality Assessment program conducted by the United States Geological Survey. 2. We predicted that local species richness is ultimately constrained by the composition of the regional species pool and further associated with local hydrological factors. Moreover, we predicted that variation in local species richness within major families can be explained by different combinations of hydrological characteristics that represent lineage‐specific responses to the environment. 3. Daily discharge and regional and local species richness data were assembled from 41 stream localities across the United States. Multiple stepwise regressions were conducted to predict local species richness, based on regional species richness, mean discharge and hydrological characteristics quantified by nine variables characterising flow variability. Species richness at each site was calculated for the entire assemblage as well as within the four most species‐rich families in the data set (Catostomidae, Centrarchidae, Cyprinidae and Percidae). 4. Local species richness was best predicted by a combination of regional species richness and discharge magnitude when all species were considered. Regional species richness was a significant explanatory variable of local species richness for three of four families (Catostomidae, Centrarchidae, Cyprinidae), but not for Percidae. Local richness in Centrarchidae and Cyprinidae was positively correlated with temporal flow variability as well as high and low flow duration, respectively, while richness in Catostomidae and Percidae tended to be associated with discharge volume. In addition, local species richness for three of the four major families was positively correlated with species richness of the other families in the assemblage, potentially suggesting the influence of local habitat quality and heterogeneity. 5. Results suggest the importance of the combined influences of the regional species pool and local hydrological characteristics on local richness in freshwater fishes, with variation in richness within each family predicted by different characteristics of flow regimes.