Diversity and taxonomic relatedness of species

 Indicator summary

 Summary of indicator structure and function

Examples of how the indicators is used for ecosystem management and ecosystem status and trends

Definition and/or background

The following is from Fulton et al (2004a) -

Community diversity has received a substantial amount of attention in ecological literature and the species diversity of certain groups (e.g. birds, mammals and benthos) have been selected as core monitoring variables in general ecological monitoring programs (Tegler et al. 2001). Diversity can be measured in various ways and can be used as an indicator of change in community composition. For example, Shannon’s H’ is widely used because it can detect reduction in less common and rare species, as was found by Kaiser and Spencer (1996) in a study of trawl impacts on North Sea infauna. Other ways of examining diversity include Bayesian-based Poisson modelling (MacNally and Fleishman 2002), which links diversity to the presence-absence of indicator species, and a diversity-spectra approach, where the diversity at size distribution of fishes (for example) are plotted and the slope of the spectra behaves in a similar way to size-spectra analysis (Murawski 2000). While the concept is still receiving considerable attention from groups evaluating potential indicators (e.g. SCOR-IOC Working Group 119 “Quantitative Ecosystem Indicators for Fisheries Management”, and the Canadian Ecological and Monitoring and Assessment Network, to name two), the concept of diversity has actually been questioned (Hulbert 1971). This is primarily because species diversity indices that measure only richness and evenness have limited application, as they can be misleading in many ways (Hill 1973, Rice 2000) and are susceptible to inadequate sampling (Soetaert and Heip 1990). They can be hard to estimate, may have little biological meaning and the relative weighting of richness and evenness used often remains poorly justified (Rochet and Trenkel 2003). As they are a mixture of evenness and richness, they cannot distinguish between rich communities dominated by a few common species or species poor communities where all species have about equal abundance. In contrast, they indicate large differences between communities with very similar suites of common species, but different numbers of rare species. As a result, diversity indices are susceptible to missing regime shifts or guild replacements and of giving “false alarms” when there are recruitment pulses (Rice pers. com.). Moreover, they cannot inform as to whether the community composition is of related species or unrelated species. It is assumed that a diverse community is comprised of a higher proportion of unrelated or distantly related species than related species. Traditional indices only measure richness (the number of species in a system) and evenness (the distribution of relative abundance among species), but are not sensitive to the relatedness between species (Hall 1999).

Taxonomic diversity indices

To address the issue of relatedness between species, additional measures of diversity were recently introduced by Warwick and Clarke (1995) and Izsak and Price (2001). The indices proposed by Warwick and Clarke (1995) measure taxonomic diversity (Δ), computed from species abundance data, and taxonomic distinctness (Δ*), calculated using presence-absence data or percentage cover. These are indices of taxonomic ‘relatedness’ as they consider taxonomic separation with (Δ) and without (Δ*) the contribution of species diversity. The biological basis for these indicators is that, generally, unperturbed communities have higher taxonomic separation of species, which is lost when a system is perturbed (there may be no change in simple species diversity, but the species present are now more closely related to each other) and the former system state is considered to be more diverse (Jennings et al. 2001). The indices are a measure of the taxonomic distance, or mean path along a taxonomic hierarchy between two randomly chosen individuals, though Δ* is conditional on the individuals being from different species (Jennings et al. 2001). As the path length between individuals is based on taxonomy and not genetic distance it is not true relatedness, but collecting genetic information for all species in a community is impracticable (Warwick and Clarke 1995). When this index was tested, by analysing the response of a small benthic community to pollution around an oilfield, a continuous decrease in taxonomic distinctness was detected along a gradient of increasing contamination, whereas traditional diversity indices did not detect the changes (Figure 5.1) as they are sensitive only to species diversity not the relatedness of the species and therefore cannot detect the shift in taxonomic separation mentioned above. It was also applied in an examination of the fishing effects on a North Sea fish assemblage (Hall and Greenstreet 1998), but results were less clear, even showing a slight correlation with traditional diversity indices. Nevertheless, it is believed that this indicator has potential as it is more robust (given usual data constraints and problems) than traditional diversity indices  (Clarke and Warwick 1999), though more testing on fisheries data sets is required. As Δ and Δ* are average measures they are relatively insensitive to disparities in sampling effort and taxonomic rigour (Izsak and Price 2001).

Figure 5.1: Plots comparing the sensitivity of macrobenthic communities to different diversity indices along a pollution gradient around the Ekofisk oil field in the North Sea. Taxonomic distinctness and diversity increase with (log) distance from the centre of oil drilling activity, whereas similar plots for the Shannon species diversity index (H’), species richness (Margalef’s D) and evenness (Pielou’s J) show little change (after Warwick and Clarke 1995).

The taxonomic similarity (Δ_S) uses presence-absence data and is derived from the average taxonomic relatedness of any two species from different sites. It is related to Δ*, but whereas that index measures α- (within habitat) and γ- (within region) diversity, Δ_S is a measure of b-diversity (turnover in species along a gradient) (Izsak and Price 2001). A taxonomic similarity matrix is constructed by calculating Δ_S values for each pairwise combination of species at two sites, using the taxonomic distance and the number of taxonomic levels (species, genus, family etc) used to classify the species of interest. β-diversity is then the median (or average) value of this matrix. Preliminary studies performed during the development of Δ_S indicate that it does capture β-diversity while being more robust to sampling effort and taxonomic rigour than the commonly used Jaccard coefficient (Izsak and Price 2001).

Réyni index (H_α)

The Réyni index is a diversity index used in diversity ordering procedures to rank communities in terms of their diversity.  The index has been used in studies of fishing effects on diversity in the North Sea (Figure 5.2) and is calculated using:

where P_i is the proportional abundance of the ith species and a determines the relative weighting towards species richness or dominance. The approach involves calculating H_a for a range of a values and then plotting H_a against a. If the trajectories for communities cross they are not comparable, but if one consistently falls below another (as demonstrated in Figure 5.2, which compares the diversity of fish communities in the North Sea) the community with the lower curve is considered to be less diverse (Jennings et al. 2001).

Figure 5.2: Réyni diversity profiles for fish communities in three regions of the North Sea. The southwestern sector is more diverse, because the profiles do not cross and the profile for the southwestern area is always highest (after Rogers et al. 1999 in Jennings et al. 2001).

Attribute

Community structure and heterogeneity

Purpose

fisheries, birds and mammals

Taxa

Data required

The following is from Fulton et al 2004a -

• Counts of individuals per species recorded
• If counts (and thus proportional abundance) are not available biomass or % cover can be used for the calculation of D*
• Taxonomic analysis of species sampled

Ecosystem applicability

The following if from Fulton et al (2004a) -

Should be suitable for all ecosystems, though these indices have only been tested for benthic communities in the North Sea and fish communities in the north-east Atlantic (Rogers et al. 1999 in Jennings et al. 2001).

Identified capability

Biological classification level

Response variable

Drivers

Is there any additional information that would be of interest in regards to ecological drivers?

If not can leave this section blank and just fill in the table instead.

Robustness

The following is from Fulton et al 2004a -

Standard diversity indices: Low, as they will easily miss biologically significant changes but highlight insignificant ones. Attempts to correct for these problems by selecting diversity indices with particular balances of richness, evenness and dominance allow prior expectations to strongly influence any results (Rice 2000). More importantly, diversity indices may be misleading in that the intensive harvesting of abundant species will enhance evenness and as a result many indices would suggest an increase in diversity resulting from fishing, a rather anomalous conclusion (Rice and Gislason 1996). This is quite apart from the data collection issues associated with diversity indices such as what quantitative scale is used for the measurements, how consistently the data is collected, whether or not the absence of a species is informative (Rice 2000). Use of any of the common diversity indices as an ecological indicator of the effects of fishing is not advised. However, if a standard diversity index is used the Simpson index or the Probability of Interspecific Encounter (PIE) perform as well as any and they have direct ecological interpretations (Rochet and Trenkel 2003).

Taxonomic indices: Medium, but require more testing on community data sets that include fish and invertebrates. Robustness would be improved if reference points can be constructed from diversity data from reference areas. Taxonomic diversity is potentially the weakest of the three indices, as it is limited by the requirement for sound species identification and it should be used in conjunction with community abundance analysis such as k-dominance curves.

Réyni index: Medium, it may be useful for comparing community diversity, but the approach may suffer from at least some of the problems mentioned above as dogging standard diversity indices.

Current status and trends

what was it like in an undisturbed/unexploited system?

how would it be expected to change?

which way is the indicator showing a population is going in?  decreasing or increasing ??

Management strategies and/or objectives

define a standard set of management objectives?? ie from Indiseas

• Conservations biodiversity
• Ecosystem stability and resistance to perturbations
• ecosystem structure and functioning
• resource potential

has it been used in a management strategy? if so how?

relationship to management strategies/ objectives

Stakeholder/public acceptability

Acceptability with stakeholders

• by all stakeholder
• by the public
• understandable to the stakeholders

Associated links

Hyperlinks to organisations, databases, webportals, and ID books, that are associated with this indicator, if appropriate.

References

Fulton, E.A., Smith, A.D.M., Webb, H., and Slater, J. (2004a) Ecological indicators for the impacts of fishing on non-target species, communities and ecosystems: Review of potential indicators. AFMA Final Research Report, report Number R99/1546.

References that Fulton et al uses for this indicator:

Clarke, K.R., and R.M. Warwick. 1999. The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels. Marine Ecology-Progress Series 184: 21-29.

Hall, S.J. 1999. The effects of fishing on marine ecosystems and communities. Blackwell Science Ltd, Oxford.

Hall, S. J., and S. P. R. Greenstreet. 1998. Taxonomic distinctness and diversity measures: responses in marine fish communities. Marine Ecology Progress Series 166: pp 227-29.

Hill, M. O. 1973. Diversity and evenness: a unifying notation and its consequences. Ecology 54, no. 2: pp 427-32.

Hurlbert, S. H. 1971. The nonconcept of species diversity: a critique and alternative parameters . Ecology 52, no. 4: pp 577-86.

Iszak, A., and A.R.G. Price. 2001. Measuring BETA-diversity using a taxonomic similarity index, and its relation to spatial scale. Marine Ecology Progress Series 215: pp 69-77.

Jennings, S., M.J. Kaiser, and J.D. Reynolds. 2001.  Marine fisheries ecology.,. 417 p . London: Blackwell Science .

Kaiser, M. J., and B. E. Spencer. 1996. The effects of beam-trawl disturbance on infaunal communities in different habitats. Journal of Animal Ecology 65: pp 348-58.

MacNally, R., and E. Fleishman. 2002. Using “indicator” species to model species richness: model development and predictions. Ecological Applications 12(1): pp79-92.

Murawski, S. A. 2000. Definitions of overfishing from an ecosystem perspective. ICES Journal of Marine Science 57: pp 649-58.

Rice, J.C. 2000. Evaluating fishery impacts using metrics of community structure. ICES Journal of Marine Science 57: pp 682-88.

Rice, J.C., and H. Gislason. 1996. Patterns of change in the size spectra of numbers and diversity of the North Sea fish assemblage, as reflected in surveys and models. ICES Journal of Marine Science 53: pp 1214-25.

Rochet, M.-J., and V. M. Trenkel. 2003. Which community indicators can measure the impact of fishing? a review and proposals. Canadian Journal of Fisheries and Aquatic Science 60: pp 86-99.

Soetaert, K., and C. Heip. 1990. Sample-size dependence of diversity indices and the determination of sufficient sample size in a high-diversity deep-sea environment. Marine Ecology Progress Series 59: pp 305-7.

Tegler, B., M. Sharp, and M.A. Johnson. 2001. Ecological monitoring and assessment network’s proposed core monitoring variables: an early warning of environmental change. Environmental monitoring and assessment 67: pp 29-56.

Warwick, R. M., and K. R. Clarke. 1995. New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress. Marine Ecology Progress Series 129: pp 301-5.

Background reading

Fulton, E.A., Fuller,M., Smith, A.D.M., and Punt, A. (2004) Ecological indicators of the ecosystem effects of fishing: Final report. AFMA Final Research Report, report Number R99/1546.

Possible references for updating this indicator

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