Measuring biological diversity

The diversity of a set of species refers to the joint dissimilarity of the species in the set. This paper discusses the measurement of diversity from the set of pairwise distances between the species in the set. A measure called the effective number of species is developed from a non-parametric probability inequality and is shown to have a simple interpretation in terms of comparing linear experiments.     

Quadratic diversity: Its maximization can reduce the richness of species

In recent decades numerous diversity indices have been introduced. Among them the quadratic entropy index Q expresses the mean difference between two individuals chosen from the community at random. Differing from diversity indices habitually employed, Q does not satisfy a property postulated earlier for those measures. Namely, the uniform distribution of species does not necessarily yield the maximal index value. Q is based on the difference matrix of species. For a given matrix one can seek for the vector yielding the maximum quadratic entropy. This task leads to a quadratic programming problem. Using the appropriate program of a program package, we determined the maximum vector for a genetic difference matrix of crane species, as published in the literature. We discovered that some components (frequencies) in the maximum vector are equal to zero. That is, by maximizing the quadratic diversity some species can be eliminated. We discuss briefly the possible implications of this observation. Moreover, even if all elements in the maximum vector are positive, the elements can differ.     

Measuring biological diversity using Euclidean metrics

We study the complementary use of Rao's theory of diversity (1986) and Euclidean metrics. The first outcome is a Euclidean diversity coefficient. This index allows to measure the diversity in a set of species beyond their relative abundances using biological information about the dissimilarity between the species. It also involves geometrical interpretations and graphical representations. Moreover, several populations (e.g., different sites) can be compared using a Euclidean dissimilarity coefficient derived from the Euclidean diversity coefficient. These proposals are used to compare breeding bird communities living in comparable habitat gradients in different parts of the world.     

Genetic similarity between two morphologically similar species of polychaetes

Glycera dibranchiata Ehlers and G. americana Leidy are two closely related and similar species of polychaetes. Electrophoretic studies of 11 enzyme systems encoded by 15 loci reveal that both species are polymorphic at about 50% of their enzyme loci, but that G. dibranchiata is the more variable as judged by heterozygosity per individual, genetic diversity, and effective number of alleles per locus. Both species show marked heterozygote deficiencies at nearly all polymorphic loci, possibly as the result of life-history features. Genetic similarity between the Glycera species suggests divergence at a level between species and sibling species compared to the Drosophila willistoni complex.     

Production of tropical copepods in Kingston Harbour, Jamaica: the importance of small species

The copepod community observed during an 18-month period at the mouth of eutrophic Kingston Harbour, Jamaica, was dominated by small species of Parvocalanus, Temora, Oithona, and Corycaeus. Mean copepod biomass was 22.1 mg AFDW m⁻³ (331 mg m⁻²). Annual production was 1679 kJ m⁻², partitioned as 174 kJ m⁻² naupliar, 936 kJ m⁻² copepodite, 475 kJ m⁻² egg and 93 kJ m⁻² exuvial production. All nauplii, most copepodites and many adults, equivalent to half of the biomass and production, were missed by a standard 200-μm plankton net, emphasizing the importance of nauplii and small species in secondary production estimates. The evidence suggests that growth rates and production are generally not food limited, and we speculate that size-selective predation shapes the structure of the harbour community. Biomass and production are higher than previous estimates for tropical coastal waters, but comparable to other eutrophic tropical embayments and many productive temperate ecosystems. Far from being regions of low productivity, tropical zooplankton communities may have significant production and deserve greater research attention than they currently receive. Received: 19 September 1997 / Accepted: 21 October 1997     

The importance of considering multiple interacting species for conservation of species at risk

Conservation of species at risk of extinction is complex and multifaceted. However, mitigation strategies are typically narrow in scope, an artifact of conservation research that is often limited to a single species or stressor. Knowledge of an entire community of strongly interacting species would greatly enhance the comprehensiveness and effectiveness of conservation decisions. We investigated how camera trapping and spatial count models, an extension of spatial-recapture models for unmarked populations, can accomplish this through a case study of threatened boreal woodland caribou (Rangifer tarandus caribou). Population declines in caribou are precipitous and well documented, but recovery strategies focus heavily on control of wolves (Canis lupus) and pay less attention to other known predators and apparent competitors. Obtaining necessary data on multispecies densities has been difficult. We used spatial count models to concurrently estimate densities of caribou, their predators (wolf, black bear [Ursus americanus], and coyote [Canis latrans]), and alternative prey (moose [Alces alces] and white-tailed deer [Odocoileus virginianus]) from a camera-trap array in a highly disturbed landscape within northern Alberta's Oil Sands Region. Median densities were 0.22 caribous (95% Bayesian credible interval [BCI] = 0.08–0.65), 0.77 wolves (95% BCI = 0.26–2.67), 2.39 moose (95% BCI = 0.56–7.00), 2.64 coyotes (95% BCI = 0.45–6.68), and 3.63 black bears (95% BCI = 1.25–8.52) per 100 km². (The white-tailed deer model did not converge.) Although wolf densities were higher than densities recommended for caribou conservation, we suggest the markedly higher black bear and coyote densities may be of greater concern, especially if government wolf control further releases these species. Caribou conservation with a singular focus on wolf control may leave caribou vulnerable to other predators. We recommend a broader focus on the interacting species within a community when conserving species.     

The relative importance of host-plant genetic diversity in structuring the associated herbivore community

Recent studies suggest that intraspecific genetic diversity in one species may leave a substantial imprint on the surrounding community and ecosystem. Here, we test the hypothesis that genetic diversity within host-plant patches translates into consistent and ecologically important changes in the associated herbivore community. More specifically, we use potted, grafted oak saplings to construct 41 patches of four saplings each, with one, two, or four tree genotypes represented among the host plants. These patches were divided among two common gardens. Focusing first at the level of individual trees, we assess how tree-specific genotypic identity, patch-level genetic diversity, garden-level environmental variation, and their interactions affect the structure of the herbivore community. At the level of host-plant patches, we analyze whether the joint responses of herbivore species to environmental variation and genetic diversity result in differences in species diversity among tree quartets. Strikingly, both species-specific abundances and species diversity varied substantially among host-tree genotypes, among common gardens, and among specific locations within individual gardens. In contrast, the genetic diversity of the patch left a detectable imprint on local abundances of only two herbivore taxa. In both cases, the effect of genetic diversity was inconsistent among gardens and among host-plant genotypes. While the insect community differed significantly among individual host-plant genotypes, there were no interactive effects of the number of different genotypes within the patch. Overall, additive effects of intraspecific genetic diversity of the host plant explained a similar or lower proportion (7-10%) of variation in herbivore species diversity than did variation among common gardens. Combined with the few previous studies published to date, our study suggests that the impact of host-plant genetic diversity on the herbivore community can range from none to nonadditive, is generally low, and reaches its most pronounced impact at small spatial scales. Overall, our findings strengthen the emerging view that the impacts of genetic diversity are system, scale, and context dependent. As the next step in community genetics, we should then start asking not only whether genetic diversity matters, but under what circumstances its imprint is accentuated.     

Accuracy of species and abundance minimal areas determined by similarity area curves

A new method for estimating the accuracy of a representative ecological sample (species minimal area and abundance minimal area determined by similarity area curves) is presented. Formulas are derived to calculate the adequate similarity level (I_S, respectively I_K) in relation to the desired accuracy of the sample: I_S=2 w/1+w for qualitative similarity and _K=2 x/(1+x)(1+y) for quantitative similarity, where w=desired qualitative accuracy of the sample, x=desired quantitative accuracy of the sample, y=abundance proportion of rare species. Based on samples from a low diversity environment in the supralittoral fringe of rocky shores (black zone), the new approach was tested and led to the following results: (1) Similarity area curves are an objective method to calculate the minimal area and to test the accuracy of the sample size chosen. (2) A large presample is necessary to calculate the minimal area. (3) The size of minimal area is subject to seasonal and regional variations. (4) Incidental species lead to an overestimation of the species minimal area. (5) Highly dominant species lead to an underestimation of the abundance minimal area.     

Environmental diversity as a surrogate for species representation

Because many species have not been described and most species ranges have not been mapped, conservation planners often use surrogates for conservation planning, but evidence for surrogate effectiveness is weak. Surrogates are well‐mapped features such as soil types, landforms, occurrences of an easily observed taxon (discrete surrogates), and well‐mapped environmental conditions (continuous surrogate). In the context of reserve selection, the idea is that a set of sites selected to span diversity in the surrogate will efficiently represent most species. Environmental diversity (ED) is a rarely used surrogate that selects sites to efficiently span multivariate ordination space. Because it selects across continuous environmental space, ED should perform better than discrete surrogates (which necessarily ignore within‐bin and between‐bin heterogeneity). Despite this theoretical advantage, ED appears to have performed poorly in previous tests of its ability to identify 50 × 50 km cells that represented vertebrates in Western Europe. Using an improved implementation of ED, we retested ED on Western European birds, mammals, reptiles, amphibians, and combined terrestrial vertebrates. We also tested ED on data sets for plants of Zimbabwe, birds of Spain, and birds of Arizona (United States). Sites selected using ED represented European mammals no better than randomly selected cells, but they represented species in the other 7 data sets with 20% to 84% effectiveness. This far exceeds the performance in previous tests of ED, and exceeds the performance of most discrete surrogates. We believe ED performed poorly in previous tests because those tests considered only a few candidate explanatory variables and used suboptimal forms of ED's selection algorithm. We suggest future work on ED focus on analyses at finer grain sizes more relevant to conservation decisions, explore the effect of selecting the explanatory variables most associated with species turnover, and investigate whether nonclimate abiotic variables can provide useful surrogates in an ED framework.     

DMSP-lyase activity in five marine phytoplankton species: its potential importance in DMS production

Activity of DMSP-lyase, which cleaves dissolved DMSP (henceforth DMSP_d-lyase), was examined in five axenically cultured phytoplankton species, including both DMSP-producing and non-DMSP-producing species. High DMSP_d-lyase activity was found in two DMSP producers, Heterocapsa triquetra strain NIES-7 and Scrippsiella trochoidea strain NIES-369 (Dinophyceae). The DMS production rates at 100 nM DMSP_d were 0.5 fmol cell⁻¹ min⁻¹ for H. triquetra and 0.3 fmol cell⁻¹ min⁻¹ for S. trochoidea. In a non-DMSP producer, Heterosigma akashiwo strain NIES-6 (Raphidophyceae), the DMSP_d-lyase activity was not found. Two DMSP-producing Prymnesiophyceae species, Isochrysis galbana strain CCMP-1323 and Gephyrocapsa oceanica strain NIES-353, did not show any obvious activity either, in contrary to other authors' findings on Phaeocystis sp., another DMSP-producing Prymnesiophyceae species. The comparison of the DMSP_d-lyase activity of the two Dinophyceae species with bacterial DMSP consumption and DMS production activity in Tokyo Bay showed that the DMSP_d-lyase activity of H. triquetra and S. trochoidea could be an important mechanism for DMS production during their blooms. Received: 9 April 1999 / Accepted: 10 December 1999     

Using abiotic variables to predict importance of sites for species representation

In systematic conservation planning, species distribution data for all sites in a planning area are used to prioritize each site in terms of the site's importance toward meeting the goal of species representation. But comprehensive species data are not available in most planning areas and would be expensive to acquire. As a shortcut, ecologists use surrogates, such as occurrences of birds or another well‐surveyed taxon, or land types defined from remotely sensed data, in the hope that sites that represent the surrogates also represent biodiversity. Unfortunately, surrogates have not performed reliably. We propose a new type of surrogate, predicted importance, that can be developed from species data for a q% subset of sites. With species data from this subset of sites, importance can be modeled as a function of abiotic variables available at no charge for all terrestrial areas on Earth. Predicted importance can then be used as a surrogate to prioritize all sites. We tested this surrogate with 8 sets of species data. For each data set, we used a q% subset of sites to model importance as a function of abiotic variables, used the resulting function to predict importance for all sites, and evaluated the number of species in the sites with highest predicted importance. Sites with the highest predicted importance represented species efficiently for all data sets when q = 25% and for 7 of 8 data sets when q = 20%. Predicted importance requires less survey effort than direct selection for species representation and meets representation goals well compared with other surrogates currently in use. This less expensive surrogate may be useful in those areas of the world that need it most, namely tropical regions with the highest biodiversity, greatest biodiversity loss, most severe lack of inventory data, and poorly developed protected area networks.     

Hidden genetic diversity in a key model species of coral

A total of 43 colonies of the scleractinian coral Pocillopora damicornis from lagoonal and reef slope sites in the western Indian Ocean (WIO) region were genetically characterised at one nuclear and two mitochondrial sequence markers and six microsatellite loci. Both mitochondrial and microsatellite data support the existence of two reciprocally monophyletic clusters (F- and NF-types) and provide evidence of the existence of two cryptic species of P. damicornis on reefs in WIO region and put current morphological delineation and geographical boundaries of P. damicornis and Pocillopora molokensis into question. The results add to ongoing studies on the phylogeny and phylogeography within the genus Pocillopora, which all point towards a range of unresolved morphological and molecular species boundaries. Nuclear phylogenies derived from the present and previously published sequences show evidence for incomplete lineage sorting and/or introgressive hybridisation between Pocillopora morphospecies. However, the two WIO types largely remain in separate clusters, further supporting the theory that these represent two different species.     

Spatial scale and species identity influence the indigenous-alien diversity relationship in springtails

Although theory underlying the invasion paradox, or the change in the relationship between the richness of alien and indigenous species from negative to positive with increasing spatial scale, is well developed and much empirical work on the subject has been undertaken, most of the latter has concerned plants and to a lesser extent marine invertebrates. Here we therefore examine the extent to which the relationships between indigenous and alien species richness change from the local metacommunity to the interaction neighborhood scales, and the influences of abundance, species identity, and environmental favorability thereon, in springtails, a significant component of the soil fauna. Using a suite of modeling techniques, including generalized least squares and geographically weighted regressions to account for spatial autocorrelation or nonstationarity of the data, we show that the abundance and species richness of both indigenous and alien species at the metacommunity scale respond strongly to declining environmental favorability, represented here by altitude. Consequently, alien and indigenous diversity covary positively at this scale. By contrast, relationships are more complex at the interaction neighborhood scale, with the relationship among alien species richness and/or density and the density of indigenous species varying between habitats, being negative in some, but positive in others. Additional analyses demonstrated a strong influence of species identity, with negative relationships identified at the interaction neighborhood scale involving alien hypogastrurid springtails, a group known from elsewhere to have negative effects on indigenous species in areas where they have been introduced. By contrast, diversity relationships were positive with the other alien species. These results are consistent with both theory and previous empirical findings for other taxa, that interactions among indigenous and alien species change substantially with spatial scale and that environmental favorability may play a key role in explaining the larger scale patterns. However, they also suggest that the interactions may be affected by the identity of the species concerned, especially at the interaction neighborhood scale.     

Influence of a dominant consumer species reverses at increased diversity

Theory and experiments indicate that changes in consumer diversity affect benthic community structure and ecosystem functioning. Although the effects of consumer diversity have been tested in the laboratory and the field, little is known about effects of consumer diversity in the subtidal zone, one of the largest marine habitats. We investigated the grazing effects of sea urchins on algal abundance and benthic community structure in a natural subtidal habitat of the Galápagos Islands. Three species of urchins (Eucidaris, Lytechinus, and Tripneustes) were manipulated in inclusion cages following a replacement design with three levels of species richness (one, two, and three species) with all possible two-species urchin combinations. Identity was the main factor accounting for changes in the percentage of substrate grazed and benthic community structure. Two out of the three two-species assemblages grazed more than expected, suggesting a richness effect, but analyses revealed that this increased grazing was due to a sampling effect of the largest and commercially valued urchin species, Tripneustes. Benthic community structure in treatments with Eucidaris, Lytechinus, and Tripneustes alone was significantly different at the end of the experiment, suggesting that resource use differentiation occurred. Communities in Tripneustes enclosures were characterized by abundant crustose coralline algae and grazed substrate, while those without it contained abundant green foliose algae (Ulva sp.). An unexpected emergent property of the system was that the most species-rich urchin assemblage underyielded, grazing less than any other assemblage with Tripneustes, effectively reversing its dominant influence observed in the two-species treatments. While further experiments are needed to discern the mechanisms of underyielding, it may be related to changing interspecific interactions as richness increases from two to three species or to density-dependent Tripneustes grazing. This study highlights the general importance of evaluating consumer richness effects across the entire range of species richness considered, as the performance of the most species-rich consumer assemblage could not be predicted by manipulations of intermediate levels of consumer species richness.     

Native fish diversity alters the effects of an invasive species on food webs

Aquatic communities have been altered by invasive species, with impacts on native biodiversity and ecosystem function. At the same time, native biodiversity may mitigate the effects of an invader. Common carp (Cyprinus carpio) is a ubiquitous, invasive fish species that strongly influences community and ecosystem processes. We used common carp to test whether the potential effects of an invasive species are altered across a range of species diversity in native communities. In mesocosms, treatments of zero, one, three, and six native fish species were used to represent the nested subset patterns observed in fish communities of lakes in Illinois, USA. The effect of the invader was tested across fish richness treatments by adding common carp to the native community and substituting native biomass with common carp. Native species and intraspecific effects reduced invader growth. The invader reduced native fish growth; however, the negative effect was minimized with increasing native richness. The zooplankton grazer community was modified by a top-down effect from the invader that increased the amount of phytoplankton. Neither the invader nor richness treatments influenced total phosphorus or community metabolism. Overall, the invader reduced resources for native species; and the effect scaled with how the invader was incorporated into the community. Higher native diversity mitigated the impact of the invader, confirming the need to consider biodiversity when predicting the impacts of invasive species.     

Effects of species diversity on community biomass production change over the course of succession

Over the past decade an increasing number of studies have experimentally manipulated the number of species in a community and examined how this alters the aggregate production of species biomass. Many of these studies have shown that the effects of richness on biomass change through time, but we have limited understanding of the mechanisms that produce these dynamic trends. Here we report the results of an experiment in which we manipulated the richness of freshwater algae in laboratory microcosms. We used two experimental designs (additive and substitutive) that make different assumptions about how patches are initially colonized, and then tracked the development of community biomass from the point of initial colonization through a period of 6-12 generations of the focal species. We found that the effect of initial species richness on biomass production qualitatively shifted twice over the course of the experiment. The first shift occurred as species transitioned from density-independent to dependent phases of population growth. At this time, intraspecific competition caused monocultures to approach their respective carrying capacities more slowly than polycultures. As a consequence, species tended to over-yield for a brief time, generating a positive, but transient effect of diversity on community biomass. The second shift occurred as communities approached carrying capacity. At this time, strong interspecific interactions caused biomass to be dominated by the competitively superior species in polycultures. As this species had the lowest carrying capacity, a negative effect of diversity on biomass resulted in late succession. Although these two shifts produced dynamics that appeared complex, we show that the patterns can be fit to a simple Lotka-Volterra model of competition. Our results suggest that the effects of algal diversity on primary production change in a predictable sequence through successional time.