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Practical measures of marine biodiversity based on relatedness of species
Abstract
In contrast to terrestrial biodiversity, marine biodiversity has a number of distinctive features that suggest that a broader strategy for its conservation might be more appropriate than a local reserve-based one. Traditional diversity measures based on species richness and evenness often have disadvantages in the assessment of biodiversity change on wide spatial scales and long timescales. Alternative measures based on the degree of relatedness of species overcome these problems to varying degrees. They fall into two categories. Taxonomic distinctiveness measures are used as a means of preferentially selecting species from an inventory for conservation purposes: species that diverge close to the base of a phylogenetic or taxonomic tree and have few close relatives will preserve more evolutionary history than those that diverge further up and have more congeners. Complementary subsets of species can also be selected to provide representativeness of the widest range of evolutionary characters. Taxonomic distinctness measures, on the other hand, are a means of comparing patterns of relatedness in community samples in the field, and monitoring changes in these patterns over space or time. They measure either the average distance apart of all pairs of individuals or species in a sample, traced through a taxonomic tree, or the variability in structure across the tree. These measures are beginning to find application in broad scale geographical comparisons of biodiversity, in environmental impact assessment and in evaluation of surrogates for biodiversity estimation.
... It has been well established that in communities impacted by anthropogenic degradation, the taxonomic spread of taxa is reduced, and, in severe cases, may only contain closely related or sibling species within a genus (Tweedley et al. 2015). Conversely, unimpacted communities display a wider taxonomic spread, with taxa belonging to many different taxonomic ranks (Warwick & Clarke 2001, Tweedley et al. 2017). To investigate variation in taxonomic distinctness, the TAXDTEST routine was used. ...
... To investigate variation in taxonomic distinctness, the TAXDTEST routine was used. The measures selected for this were the average taxonomic distinctness (∆ + ), i.e., the average path length (taxonomic distance) between every taxa tracked through a taxonomic classification, and the variation in taxonomic distinctness (Ʌ + ), i.e., the variability in the path length between taxa (Warwick & Clarke 2001). The full taxa list for both decades was subjected to the routine to calculate the 'expected' value and 95% confidence intervals for ∆ + and Ʌ + , which was utilised to create funnel plots. ...
Coastal waters are biodiverse and highly productive ecosystems, supporting various habitats and providing refuge, nutrition, and favourable physical conditions for many species. These ecosystems are also valuable for commercial, industrial, and recreational purposes, and consequently, many have been negatively impacted by anthropogenic activities. Despite their importance, relatively little information is known about how these activities impact the biota coastal waters support, particularly the invertebrate communities. This study examined the long- and short-term temporal and spatial variation in the megabenthic invertebrate fauna of Cockburn Sound, a heavily utilised coastal embayment in temperate Western Australia, within which there is a proposal to construct a new container port. Firstly, a suite of interdecadal analyses were conducted by comparing trawl data from seven sites across Cockburn Sound sampled in two seasons in 2007/08 and 14 years later in 2021/22 to determine whether there had been a shift in the characteristics of the megabenthic invertebrate community. Secondly, a contemporary analysis focussing on seasonal, short-term interannual, and spatial variation was conducted using the data from 2021/22 and additional samples collected in 2022/23. From the interdecadal analyses, a total of 214 invertebrate taxa representing 17 classes and six phyla were recorded for the two surveys. There was a substantial decline in abundance, biomass, and diversity measures between decades, with a clear shift in community composition. The largest temporal declines in abundance were for arthropods and echinoderms, two pollution and disturbance-sensitive phyla. Abundance-biomass curves revealed a contrasting viewpoint of undisturbed ecosystem condition due to the dominance of large-bodied opportunistic crustaceans in both decades. A total of 175 taxa from 15 classes and six phyla were recorded in the contemporary sampling, with the community significantly differing in diversity measures, abundance, and biomass across sites and between seasons, highlighting finer-scale spatial and seasonal influences that act on the community. Fluctuating abundances of crustacean, mollusc, and echinoderm taxa were apparent, with greater abundances in autumn of 2022/23. A gradient of declining diversity measures moving southwards in the Sound was apparent, most clearly expressed by taxa richness. The findings of this study document concerning patterns in the invertebrate communities of Cockburn Sound across decades and likely display the cumulative detrimental effects of press (e.g. sediment eutrophication, increased industrialisation) and pulse (e.g. marine heatwave, hypoxia event) disturbances. This study showcases the value of historical data sets in forming a comprehensive view of contemporary invertebrate community trends and the data will be useful in the environmental impact assessment of the proposed container port development.
... To assess the differences in taxonomic distinctness (Δ + ) from expected Δ + values determined from the species list of polychaetes from the Gulf of Mexico, we used a randomization approach (as suggested by Clarke & Warwick [57,58] and by Warwick & Clarke [59]). A simulated distribution was created, leading to a theoretical mean (a horizontal line displaying the taxonomic distinctness for all polychaete species shown in the graph of Δ + or Λ + for all the sampling stations against richness in each station) and to a confidence funnel for each, Δ + , and Λ + , from random subsamples of the polychaete species as suggested by Bhat and Magurran [60]. ...
The spatial patterns of taxonomic diversity of annelid polychaete species from the continental shelf in the Southern Gulf of Mexico were examined in this study. We used taxonomic distinctness and its spatial variations to explore the diversity patterns and how they change between Southern Gulf of Mexico regions. In addition, using taxonomic distinctness as a dissimilarity measure and Ward’s Clustering, we characterized three distinct faunal assemblages. We also investigated patterns of richness, taxonomic distinctness, and distance decay of similarity between sampling stations as a ß-diversity measure. Finally, we examined
the spatial relationships between polychaete assemblages and environmental variables to test the relative importance of spatial and environmental components in annelid polychaete community structure from the Southern Gulf of Mexico. We used a combination of eigenvector-based multivariate analyses (dbMEMs) and distance-based redundancy analysis (dbRDA) to quantify the relative importance of these explanatory variables on the spatial variations of taxonomic distinctness. The significance level of spatial and environmental components to the distribution of polychaete species showed that the combined effect of spatial processes and sediment characteristics explained a higher percentage of the variance than those parameters could alone.
... Two of these metrics relied upon the taxonomic relationships of the species in a sample. These metrics are called Average Taxonomic Distinctness (AvTD) and Variation in Taxonomic Distinctness (VarTD) (Warwick & Clarke 2001). AvTD is a measure of the degree to which the species in a sample are related taxonomically to each other, and is the average path length between every pair of species traced through a taxonomic tree. ...
The study of taxonomy and systematics can enhance ecological and conservation science. However, understanding how taxonomy and systematics can bring about such enhancement is not always readily appreciated. This situation can lead to some ecologists ignoring or dismissing the benefits of working with taxonomists and systematists to achieve their goals. Here I provide examples, from collaborative research with marine bryozoologist Dennis Gordon, on how his understanding of taxonomy and systematics has enabled insights into the regeneration of biogenic reef habitat impacted by fishing, the factors that influence the distribution of bryozoan assemblages and thickets in the New Zealand region, and where they require protection.
... Therefore, when measuring the diversity index of 5 different species, the results of "5 species in the same genus" and "5 species in different genus" indicate that the latter result has high diversity. Therefore, an index that takes into account this taxonomy has been devised by Warwick [14]. A feature of this index is the use of taxonomic distances. ...
There is an initiative called GX (Green Transformation) started by the Japanese government against the climate change problem. The Japanese Patent Office has released the GXTI (Green Transformation Technologies Inventory), a technology classification for technologies related to GX. In this paper, trends in the number of patent applications for the Top 5 technologies related to GXTI were analyzed. In addition, the technology diversity of the Top 5 was analyzed. For diversity analysis, taxonomic indices applying the concept of biodiversity were discussed. As a result of introducing this index, it has become possible to grasp the ratio of research and development according to the level of technological integration.
Aggregation of species with similar ecological properties is one of the effective methods to simplify food web researches. However, species aggregation will affect not only the complexity of modeling process but also the accuracy of models’ outputs. Selection of aggregation methods and the number of trophospecies are the keys to study the simplification of food web. In this study, three aggregation methods, including taxonomic aggregation (TA), structural equivalence aggregation (SEA), and self-organizing maps (SOM), were analyzed and compared with the linear inverse model–Markov Chain Monte Carlo (LIM-MCMC) model. Impacts of aggregation methods and trophospecies number on food webs were evaluated based on the robustness and unitless of ecological network indices. Results showed that aggregation method of SEA performed better than the other two methods in estimating food web structure and function indices. The effects of aggregation methods were driven by the differences in species aggregation principles, which will alter food web structure and function through the redistribution of energy flow. According to the results of mean absolute percentage error (MAPE) which can be applied to evaluate the accuracy of the model, we found that MAPE in food web indices will increase with the reducing trophospecies number, and MAPE in food web function indices were smaller and more stable than those in food web structure indices. Therefore, trade-off between simplifying food webs and reflecting the status of ecosystem should be considered in food web studies. These findings highlight the importance of aggregation methods and trophospecies number in the analysis of food web simplification. This study provided a framework to explore the extent to which food web models are affected by different species aggregation, and will provide scientific basis for the construction of food webs.
In Mexico, shrimp is the most important fishing resource in terms of value, and second in production. Ten percent of the country's production comes from catches in the southern Gulf of Mexico. Several studies report the number of marine species recorded in this zone; however, few consider bycatch, and still fewer determine biodiversity indexes. This work identified the species captured in shrimp trawls from 22 commercial fishing trips from August 2016 to December 2017 in the south of the Gulf of Mexico. Four indexes of taxonomic diversity were determined: richness, evenness, average taxonomic distinctness, and variation. The indexes were calculated by season (dry, rainy, and northerly), spatial scale (terrigenous, carbonate, and Contoy zones), and depth interval: 1 (<10 m), 2 (10-20 m), 3 (20-40 m), and 4 (>40 m). The zones were separated according to the sedimentological characteristics described in the literature, and the depth ranges were arbitrarily defined considering the bathymetry of the zone. Nine classes, 51 orders, 121 families, 207 genera, and 334 species (152 terrigenous, 289 carbonates, and 76 Contoy) were recorded. Evenness index was highest in Contoy (0.75), followed by the terrigenous (0.54) and carbonate zones (0.35). Average taxonomic distinctness was greater in the carbonate (83.51) zone, followed by the Contoy (75.83) and terrigenous (74.55) zones. Contoy was identified as the most variable based on taxonomic distinctness (301.1). Also, the same index calculated by depth stratum and zone showed that the deeper zones generally have more phylogenetic relationships. The determinations of these indexes are proposed and can be used as points of reference to assess the variation and status of marine communities in the region.
The Sierra Gorda de Querétaro Biosphere Reserve (SGQBR) is one of the largest natural protected areas in Mexico; however, little is known about the richness and diversity of amphibians and reptiles. We present an updated list of species of both groups, the conservation status of these species, as well as an analysis of their diversity with respect to other protected natural areas (NPAs) in central Mexico. The SGQBR contains 132 herpetofauna species (35 amphibians and 97 reptiles). The richest and most diverse families for amphibians were Hylidae (anurans) and Plethodontidae (caudates), and for reptiles Phrynosomatidae (lizards), Colubridae and Dipsadidae (snakes). The values of taxonomic diversity of the SGQBR were similar to those for the regional pool considering others NPAs. However, it did not achieve the highest values compared to the adjacent Los Mármoles National Park or Sierra Gorda de Guanajuato Biosphere Reserve. There was a high complementarity in the species composition between El Chico National Park and SGQBR for both herpetofauna groups. Although a formal list is presented, it is necessary to carry out a greater number of studies focused on analyzing diversity, considering functional attributes of the species and the richness by vegetation types.
Species of the marine nematode genus Pontonema have been found to dominate the macrobenthos under abnormally high conditions of particulate organic enrichment. Populations from organically enriched habitats in six localities (Kiel fjord, Germany; the Garroch Head sewage-sludge dump ground in the Firth of Clyde, Scotland; Cornelian Bay, N.E. England; the Tyne estuary, N.E. England; Sete, N.W. Mediterranean, France; Blanes Bay, N.W. Mediterranean, Spain) have been compared. Multivariate analyses of 16 morphometric characters in males, and 13 in females, shows that each population is significantly different morphologically from every other population. However, there is morphological overlap between the populations, and it is considered pragmatic to recognize three species in this group, based on a few stable morphological characters: P. vulgare (Bastian, 1865) from the Baltic, P. alaeospicula Bett and Moore 1988 from the UK sites, and P. mediterranea sp. nov. from the Mediterranean. P. mediterranea sp. nov. is described. The species were not found to have established sympatry in this study, unlike many other opportunistic taxa from organically enriched habitats, and the significance of this is discussed.
In a previous note, Warwick & Clarke (1995; Mar Ecol Frog Ser 129:301-305) used 2 indices, Delta and Delta*, to demonstrate a continuous decrease in taxonomic distinctness of marine macrofaunal assemblages along a gradient of increasing environmental contamination, in a situation where species diversity remained constant, in the vicinity of 1 oilfield in the Norwegian sector of the North Sea. These indices are tested here using species abundance data from 3 other oilfields in the Norwegian sector, each sampled on 3 different occasions. No consistent pattern of decreasing taxonomic distinctness with increasing environmental contamination is evident.
Reductions in number of species and diversity and increased dominance of opportunistic species occurred late in the sequence of response to oil as a stress factor (within 500 to 1000 m of discharge sources). However, multivariate analyses, (classification analysis using the Bray-Curtis dissimilarity index) and ordination (multi-dimensional scaling) clearly distinguished site groupings related to oil activities at distances of up to 2 to 3 km from the Ekofisk pollution source and up to 1.5 km from the Eldfisk source. The first recorded changes in benthic communities in response to oil were increased abundance patterns of some species and changes in the presence and absence patterns of rare species, with species being mostly present in one site group and mostly absent in another site group. Only under severe pollution did the opportunistic species, which have often been suggested as universal indicators of pollution, dominate. The major site groupings could still be distinguished after aggregation to higher taxa (families and even phyla) when using multivariate analyses. If this finding proves to be a general one then great savings in time and effort, with little or no loss of precision, wdl be possible in environmental monitoring.
A new species of free living marine nematode, Pontonema alaeospicula sp. nov., is a dominant member of the fauna in three organically polluted sublittoral habitats off the Scottish coast. The species is described and the genus reviewed. A schematic pictorial key to the genus is provided. Some notes on the biology of P. alaeospicula sp. nov. are given, based on initial studies of the population in situ and in laboratory culture.
Taxonomic distinctness is a univariate (bio)diversity index which, in its simplest form, calculates the average 'distance' between all pairs of species in a community sample, where this distance is defined as the path length through a standard Linnean or phylogenetic tree connecting these species. It has some appealing properties: it attempts to capture phylogenetic diversity rather than simple richness of species and is more closely linked to functional diversity; it is robust to variation in sampling effort and there exists a statistical framework for assessing its departure from 'expectation'; it appears to decline monotonically in response to environmental degradation whilst being relatively insensitive to major habitat differences; and, in its simplest form, it utilises only simple species lists (presence/absence data). Many of its practical characteristics remain to he explored, however, and this paper concentrates on the assumptions made about the weighting of step lengths between successive taxonomic levels (species to genera, genera to families etc.), which when accumulated give the overall path lengths. Using data on free-living marine nematodes from 16 localities/habitat types in the UK, it is shown that the relative values of taxonomic distinctness for the 16 sets are robust to variation in the definition of step length. For example, there is a near perfect linear relationship between values calculated using a constant increment at each level and a natural alternative in which the step lengths are proportional to the number of species per genus, genera per family, family per suborder etc. These weightings are then manipulated in more extreme ways, to capture the structure of phylogenetic diversity in more detail, and a contrast is drawn between the biodiversity of island (the Isles of Scilly) and mainland (UK) locations and habitats. This paper concludes with a discussion of some of the strengths and weaknesses of taxonomic distinctness as a practical tool for assessing biodiversity.
Practical approaches to measuring biodiversity are reviewed in relation to the present debate on systematic approaches to conservation, to fulfil the goal of representativeness: to identify and include the broadest possible sample of components that make up the biota of a given region. Rather than adapting earlier measures that had been developed for other purposes, the most recent measures result from a fresh look at what exactly is of value to conservationists. Although debate will continue as to where precisely these values lie, more of the discussion has been devoted to ways of estimating values in the absence of ideal information. We discuss the current principles by assuming that the currency of biodiversity is characters, that models of character distribution among organisms are required for comparisons of character diversity, and that character diversity measures can be calculated using taxonomic and environmental surrogates.
Full text at:
www.vliz.be/imisdocs/publications/125660.pdf
Electrophoretic patterns for eight enzyme loci clearly distinguish six
sibling species in the well-known pollution indicator worm, Capitella
capitata. Unlike sibling species of Drosophila, the Capitella species
have virtually no alleles in common. Close examination has revealed only
slight morphological differences between species, while life histories
and reproductive modes are very distinct. The Capitella species are
ideally suited for genetic and evolutionary studies.
pointds out a series of precursors to Connell's paper, which all suggest implcitly or epxlicitly that stress or disturbance should promote diversity. The most clealry relevant is Horns 1975 paper in Cody et al about succession as a markov process. Makes the point that Connel should have cited him.
In a recent paper Warwick & Clarke (1995: Mar Ecol Prog Ser 129:301-305) introduced 2 new measures of community diversity, Delta and Delta*. These measures differ from more conventional diversity indices by incorporating the taxonomic relatedness of species into their calculation. In this paper we compare temporal trends in Delta and Delta* with more conventional diversity measures for the demersal fish community of the northern North Sea. We show that, contrary to the findings for benthic invertebrates, indices that incorporate taxonomic distinctness show identical time trends to conventional measures. This, perhaps, suggests that when perturbations are sufficiently large to affect conventional indices of diversity, taxonomic diversity indices may already have reached levels from which they march in step with conventional indices.
A definition of biodiversity is adopted that takes account not only of numbers of species, but also of the degrees of difference among them. The most appropriate measure of species differences is likely to be made in terms of genealogical relationships, as embodied in taxonomic classifications. Five new measures of taxonomic diversity are compared with existing measures of species richness and taxonomic root weighting for prioritising areas for the conservation of biodiversity, using as an example some data for 43 bumble bee species of the sibiricus-group. Although certain of the new measures can be shown to perform better than any existing methods, more extensive trials are needed, and further refinements can be anticipated. We conclude that combining species richness with taxonomic diversity to give a single measure inevitably involves compromise, as either component could be maximised in its own right. Nonetheless, the new prioritisation methods are already capable of giving practical results.