Measuring dominance and diversity in ecological communities: choosing the right variables

Abstract. Although there are many studies in searching for the most useful community diversity index, the importance of choosing an appropriate parameter has been neglected. Here, we examined dominance and diversity in early post-fire chaparral communities using different variables, i.e. plant density, cover and biomass. Significant different results were produced by applying different parameters and the difference may be caused by the inconsistency in density, cover, and biomass allocated in each life form. Among the three parameters, biomass was most successful in detecting differences among communities because the apportionment of biomass among species was more variable than that of density. Although the three species variables represent different aspects of community properties and their relative performance may vary among communities, we recommend the use of biomass or productivity data as the most appropriate variable because it can best represent per capita resource use and resource partitioning among organisms in competitive situations.     

Incorporating spatial autocorrelation in rarefaction methods: Implications for ecologists and conservation biologists

Recently, methods for constructing Spatially Explicit Rarefaction (SER) curves have been introduced in the scientific literature to describe the relation between the recorded species richness and sampling effort and taking into account for the spatial autocorrelation in the data. Despite these methodological advances, the use of SERs has not become routine and ecologists continue to use rarefaction methods that are not spatially explicit. Using two study cases from Italian vegetation surveys, we demonstrate that classic rarefaction methods that do not account for spatial structure can produce inaccurate results. Furthermore, our goal in this paper is to demonstrate how SERs can overcome the problem of spatial autocorrelation in the analysis of plant or animal communities. Our analyses demonstrate that using a spatially-explicit method for constructing rarefaction curves can substantially alter estimates of relative species richness. For both analyzed data sets, we found that the rank ordering of standardized species richness estimates was reversed between the two methods. We strongly advise the use of Spatially Explicit Rarefaction methods when analyzing biodiversity: the inclusion of spatial autocorrelation into rarefaction analyses can substantially alter conclusions and change the way we might prioritize or manage nature reserves.     

Predicting future community composition from random soil seed bank sampling – evidence from a drained lake bottom

Questions: What is the accuracy and reliability of the commonly used random soil sampling methodology for predicting seedling density, species richness and composition of the emerging seedling community? Location: Lake Kraenepoel, western Belgium. Methods: We compared density, species composition and observed and rarefactioned species richness of the seedling community emerging on a soft water lake bed exposed after drainage with the seedling community germinating in the laboratory from random soil samples in the same plots. Results: Seedling density did not differ between the two methods and there was a significant correlation between seedling density on the exposed lake bed and in the soil samples. This indicates that future seedling density can be reliably predicted based on soil sampling, in particular for the most abundant species. The most frequently occurring and abundant species among the seedlings in the soil samples were also the most frequent and abundant species germinating on the exposed lake bed. In contrast, species richness was much higher on the exposed lake bed than in the soil samples, and this difference was still significant for annual species after correction for differences in sampling intensity by rarefaction. We found no correlation between the number of species retrieved by the two methods. Although seedlings of rare and target species emerged on the lake bed, random soil sampling clearly failed to detect seeds of most of these species. Conclusions: Random soil sampling at a commonly used intensity and using the standard germination conditions can accurately predict future total seedling density and the density of the most abundant species. However, the method is not reliable for predicting the probability of establishment of populations of uncommon species. When executing a seed bank study, sampling intensity and germination conditions need to be adapted to the nature and the level of detail of the research question to be answered.     

Importance of assemblage‐level thinning: A field experiment in an alpine meadow on the Tibet plateau

Question: Which fraction of the decrease in species richness under fertilization can be explained by assemblage‐level thinning? Location: An alpine meadow on the eastern Tibet plateau. Methods: 60‐m² plots were randomly assigned to a control or one of four levels of ammonium phosphate fertilizer. Treatments were repeated for three years. The effect of as semblage‐level thinning was decided based on similarity in quadrats within and between fertilizing levels, bootstrap simulation based on random thinning of the high density (low production, low fertility) quadrats and correlation of species’ biomass in low fertility and high fertility. Results: Fertilization increased production, reduced species richness and reduced density of individuals. Heavily fertilized quadrats are more similar in species composition in 2000 but less similar in 2001 and 2002. Rarefaction showed that a decrease in density can account for 32.3‐42.9% decrease of species richness, but the simulated species richness is always significantly higher than the observed one. When production and species richness are similar at two levels of fertilization, species biomass in the higher fertility treatment is positively correlated with biomass at lower fertility. When the two fertilizer levels differed in production and species richness, there was no evidence of correlation in species biomass, suggesting that assemblage level thinning cannot explain all the loss of species. Conclusion: Although a decrease in density could explain much of the decrease (up to 42.9%) in species richness when this alpine meadow was fertilized, other important mechanisms such as interspecific competition cannot be ignored. Future studies should investigate the effect of assemblage level thinning on species diversity, and search for mechanisms responsible for a decrease in diversity.     

Tree species richness and composition 15 years after strip clear-cutting in the Peruvian Amazon

Although strip clear-cutting has a long history of use in the temperate zone, it was only recently introduced for timber extraction in tropical rain forests, where it is known as the Palcazú Forest Management System. In this system heterogeneous tropical forests are managed for native gap-dependent timber species by simulating gap dynamics through clear-cutting long, narrow strips every 40 years. As part of an assessment of the sustainability of this system, we evaluated the recovery of tree basal area, species richness, and composition after 15 years of regeneration on two strips (30 × 150 m) clear-cut in 1989 in Jenaro Herrera, Peru. Timber stocking and the effects of silvicultural thinning were assessed in both strips. The strips recovered 58–73% of their original basal area and 45–68% of their original tree species richness. Although both strips recovered more than 50% of their original composition, commercial species had lower basal areas and lower densities than in the forest before the clearing. Pioneer species with high basal areas remained dominant 15 years after the cutting. Silvicultural thinning in 1996 reduced the abundance of pioneer species in both strips, and increased the abundance of commercial species in one of the strips. Half of one strip was harvested by deferment-cut (only commercial trees >30 cm dbh and “other” species >5 cm dbh were cut); regeneration here had greater abundance of commercial species and lower abundance of pioneer species. The low stocking of commercial trees challenges the sustainability claims for this forest management system.     

Efficiency of a Rapid Assessment of the Diversity of Ground Beetles and Ants, in Natural and Disturbed Habitats of the Nahuel Huapi Region (NW Patagonia, Argentina)

We use sample-based rarefaction curves to evaluate the efficiency of a rapid species richness assay of ground beetles and ants captured in pitfall traps in the Nahuel Huapi National Park (NW Patagonia, Argentina). We ask whether ant species richness patterns show some concordance with those of beetles, and use several extrapolation indices for estimating the expected number of species at a regional scale. A total of 342 pitfall traps were spread in groups, at an intensity of 9 traps/100 m², with two collection stations, at each of 19 sites representative of burned and unburned habitats in the forest, scrub and steppe, along a west-to-east transect of 63 km long. The high regional habitat heterogeneity along the west-to-east gradient is paralleled by a turnover of beetle and ant species, although different families of Coleoptera show idiosyncratic responses across habitat types. Spatial stratification of sampling over three major habitats along with the inclusion of burned and unburned environments may improve sampling efficiency. The observed and extrapolated species richness suggests that we captured a high proportion of the total number of species of beetles and ants known for the region. However, trends in species richness of ants may not indicate similar trends in beetles. Ants and beetles cannot be used as surrogate taxa for the analysis of species richness patterns. Instead, both taxa should be considered as focal as they may offer complementary information for the analysis of the effect of disturbance and regional habitat heterogeneity on species diversity patterns at a regional scale.     

High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco

Genetic diversity at nine isozyme loci was surveyed in an endangered tree species, the argan tree, endemic to south-western Morocco. The species is highly diverse (3.6 alleles/locus) with populations strongly differentiated from each other (F _ST=0.25). This example is used to illustrate a method for standardizing measures of allelic richness in samples of unequal sample sizes, which was developed for the estimation of the number of species and relies on the technique of rarefaction. In addition, it is shown that the measure of subdivision, _ST, obtained when allelic richness is used in place ofh (Nei's index of diversity), is much larger than the F _ST [e.g. _ST(40)=0.52, where (40) indicates the specified sample used to estimate the allelic richness]. This suggests that rare alleles (which strongly influence measures of allelic richness) have a more scattered distribution than more frequent ones, a result which raises special conservation issues for the argan tree.     

Local diversity and ecological distribution of arboreal Psocoptera (Insecta) in Sumatra, Indonesia, and implications for conservation

Collections of arboreal Psocoptera from the four major national parks of Sumatra and from a range of habitats outside the parks (including many of the predominant perennial crops) are appraised for diversity and species overlap between habitats. The most speciose family (Psocidae, 72 morphospecies) is investigated to determine possible surrogacy values in relation to the more taxonomically intractable Other Psocoptera (17 families, 190 morphospecies), in its incidence in 16 different habitats and four main altitudinal zones. Considerable psocid richness persists in disturbed areas, and the values of protected areas and kebun gardening systems in their conservation are noted.     

Response of ground-dwelling beetle (Coleoptera) assemblages to giant knotweed (<Emphasis Type="Italic">Reynoutria</Emphasis> spp.) invasion

Giant knotweeds (Reynoutria spp.) are highly productive and aggressive invaders in riparian wetlands of Europe and North America. We sampled ground-dwelling beetles by pitfall traps from six sites comparing monotypic Reynoutria stands with the invaded native Urtica-dominated stands. Three sites were located in a semi-natural softwood forest and three sites were on a ruderal embankment. The analyses are based on a total of 13,244 individuals from 218 species. Location and site significantly influenced beetle assemblages. Moreover, there were pronounced differences between vegetation stands. The monotypic Reynoutria stands exhibited lower beetle abundance, species richness and rarefaction diversity irrespective of location. However, the negative effect on species richness, abundance and assemblage similarities were stronger on the transformed ruderal embankment than in the semi-natural softwood forest. Reynoutria invasion seems to influence microclimatic conditions. We found a higher abundance of silvicolous and a lower abundance of xerophilous ground beetles in the Reyountria stands than in the Urtica-dominated stands. Feeding guilds reacted differently to Reynoutria invasion that reduced the abundance of predators and herbivores but enhanced that of detritivores. Detritivores assumingly profit from the perennial presence of the large quantities of Reynoutria litter. We conclude that highly productive invaders pauperise the arthropod fauna and alter link strengths in trophic cascades shifting primary producer-based food webs to detritus-based food webs.