Application of Diversity Indices to Appraise Plant Availability in the Traditional Medicinal Markets of Johannesburg,South Africa

The lack of scientific rigour in analysing ethnobotanical surveys has prompted researchers to investigate ways of quantitatively describing their data, including the use of ecological diversity indices. There are numerous indices and measures available to describe sample diversity. Twenty-two measures of species richness, diversity and evenness were reviewed using six sets of ethnomedicinal data derived from 50 formal muti shop traders (of different ethnicities) and 100 informal street traders of traditional medicine in Johannesburg, South Africa, and a seventh data set from traders on the western boundary of the Kruger National Park, South Africa. The diversity measures were coupled with species accumulation curves to construct cumulative diversity curves used to determine the minimum viable sample size on which a diversity index should be based, and to better understand the differences in the relative diversities of the samples. Distinct differences in the relative abundance and diversity of plants sold by street traders and shop traders were evident. Species diversity and evenness was found to be higher in shops, thus resulting in a lower dominance in the sale of certain plant species compared to the street traders. A survey of an informal market should include no less than 35 research participants compared to no less than 20 for the muti shops. The use of selected indices of species richness (Margalef's), diversity (Shannon, Simpson's, Fisher's alpha, Hill's numbers) and evenness are recommended as a means of describing patterns exhibited within ethnobotanical data.     

A new relationship for rarefaction

All diversity indices are functions of the vector of the numbers of individuals in different species in a statistical population. So they are also functions of the number of species. It is well known, from the species-area curve and from collector's curves, that the number of species is a function of sampling effort. The rarefaction and Coleman functions are both functions that allow comparisons to be made at the same number of individuals, but have different mathematical forms. We show that the numerical difference between them, in the samples we have studied, is negligibly small. We show how to modify the Coleman function to allow for sampling without replacement, and show that the modified function is identical to the hypergeometric rarefaction function. Rarefaction should always be used, with any index, when comparing diversity in different size samples, but the number of species is the preferred index. Suggestions for comparing rarefaction curves from different samples are made.     

Multiplicity in palm uses by the Huaorani of Amazonian Ecuador

An ethnobotanical study of the palms used by the Huaorani in the Yasuní National Park and Huaorani Ethnic Reserve in Amazonian Ecuador was carried out. In this inventory, 37 palm species were found; all were used by the Huaoranis. One hundred and ninety-one different uses were recorded in eight ethnobotanical categories. Most species (64.9%) were used for house construction and human food. More than half of the species were used for domestic utensils (59.4%) and hunting and fishing implements (54%). A comparison is made between these data and past studies for the other six indigenous communities from Amazonian Ecuador. This paper shows the highest diversity of useful palm species and the highest number of different uses ever recorded for an indigenous group in Amazonian Ecuador. The data combine quantitative and qualitative approaches.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 149–159.     

Ethnobotanical Resources Management in the Arribes del Duero Natural Park (Central Western Iberian Peninsula): Relationships between Plant Use and Plant Diversity, Ecological Analysis, and Conservation

We analyze the floristic and ecological diversity of plants traditionally used in the Arribes del Duero Natural Park (Central Western Spain, Iberian Peninsula). We identified all plant species used by the local people and classified them in 10 general use-categories. All the ethnobotanical data used derive from global ethnobotanical research carried out from 2005 to 2009. The results are analyzed with respect to the total flora of the area and to the ecological diversity of the species in their habitats. The conservation and management of these taxa are also analyzed. We discuss the implications of their harvesting for the development and conservation of their natural populations and habitats.     

Functional rarefaction: estimating functional diversity from field data

Studies in biodiversity-ecosystem function and conservation biology have led to the development of diversity indices that take species' functional differences into account. We identify two broad classes of indices: those that monotonically increase with species richness (MSR indices) and those that weight the contribution of each species by abundance or occurrence (weighted indices). We argue that weighted indices are easier to estimate without bias but tend to ignore information provided by rare species. Conversely, MSR indices fully incorporate information provided by rare species but are nearly always underestimated when communities are not exhaustively surveyed. This is because of the well-studied fact that additional sampling of a community may reveal previously undiscovered species. We use the rarefaction technique from species richness studies to address sample-size-induced bias when estimating functional diversity indices. Rarefaction transforms any given MSR index into a family of unbiased weighted indices, each with a different level of sensitivity to rare species. Thus rarefaction simultaneously solves the problem of bias and the problem of sensitivity to rare species. We present formulae and algorithms for conducting a functional rarefaction analysis of the two most widely cited MSR indices: functional attribute diversity (FAD) and Petchey and Gaston's functional diversity (FD). These formulae also demonstrate a relationship between three seemingly unrelated functional diversity indices: FAD, FD and Rao's quadratic entropy. Statistical theory is also provided in order to prove that all desirable statistical properties of species richness rarefaction are preserved for functional rarefaction.     

Are diatom diversity indices reliable monitoring metrics?

A biological survey was carried out in 640 stations spread over the Loire-Bretagne National Network (France) between 1996 and 2000. Epilithic diatom inventories were obtained following standard methods. A total of 934 diatom taxa were identified. Common diversity indices (species richness, Shannon’s diversity, equitability, dominance, etc.) were calculated and compared against abiotic factors verify their reliability as biomonitoring metrics. Sampling stations were classified according to their trophic status (TP concentration). Several theoretical predictions about the relationship between community structural parameters and limnological variables were tested. In general, diversity indices exhibited poor linear correlations with environmental factors indicating ecological status. No clear patterns were found concerning species accumulation curves, occurrence-abundance, frequency-abundance and frequency distribution of diatom taxa between different trophic levels, although assemblages from stations with lower TP levels were characterized by relatively high dominances of certain taxa, mainly Achnanthidium minutissimum. In the light of these findings, the use of diatom diversity indices in biological quality surveillance protocols in continental waters is discouraged. Results are compared and discussed with similar studies.     

The use of incidence-based species richness estimators,species accumulation curves and similarity measures to appraise ethnobotanical inventories from South Africa

The incorporation of suitable quantitative methods into ethnobotanical studies enhances the value of the research and the interpretation of the results. Prediction of sample species richness and the use of species accumulation functions have been addressed little in applied ethnobotany. In this paper, incidence-based species richness estimators, species accumulation curves and similarity measures are used to compare and predict species richness, evaluate sampling effort and compare the similarity of species inventories for ethnobotanical data sets derived from the trade in traditional medicine in Johannesburg and Mpumalanga, South Africa. EstimateS was used to compute estimators of species richness (e.g. Jackknife), rarefaction curves, species accumulation curves and complimentarity. Results showed that while the Michaelis–Menten Means estimator appeared to be the best estimator because the curve approached a horizontal asymptote, it was not able to accurately predict species richness for one of the data sets when two of its subsamples were individually tested. Instead, the first-order Jackknife estimator best approximated the known richness.     

Community assessment techniques and the implications for rarefaction and extrapolation with Hill numbers

Diversity estimates play a key role in ecological assessments. Species richness and abundance are commonly used to generate complex diversity indices that are dependent on the quality of these estimates. As such, there is a long‐standing interest in the development of monitoring techniques, their ability to adequately assess species diversity, and the implications for generated indices. To determine the ability of substratum community assessment methods to capture species diversity, we evaluated four methods: photo quadrat, point intercept, random subsampling, and full quadrat assessments. Species density, abundance, richness, Shannon diversity, and Simpson diversity were then calculated for each method. We then conducted a method validation at a subset of locations to serve as an indication for how well each method captured the totality of the diversity present. Density, richness, Shannon diversity, and Simpson diversity estimates varied between methods, despite assessments occurring at the same locations, with photo quadrats detecting the lowest estimates and full quadrat assessments the highest. Abundance estimates were consistent among methods. Sample‐based rarefaction and extrapolation curves indicated that differences between Hill numbers (richness, Shannon diversity, and Simpson diversity) were significant in the majority of cases, and coverage‐based rarefaction and extrapolation curves confirmed that these dissimilarities were due to differences between the methods, not the sample completeness. Method validation highlighted the inability of the tested methods to capture the totality of the diversity present, while further supporting the notion of extrapolating abundances. Our results highlight the need for consistency across research methods, the advantages of utilizing multiple diversity indices, and potential concerns and considerations when comparing data from multiple sources.     

A non-phylogenetic alpha diversity approach on prokaryotic community structure in aquatic systems

Comparative analyses of accumulating phylotype-abundance data of prokaryotic communities are relatively scarce and mainly approached with phylogenetic methodologies. However, when a great fraction of phylotypes is captured within a sample, application of alpha diversity measures is also possible, enabling the exploration of structural changes in prokaryotic communities. In the present study, phylotype-abundance data of Archaea and Bacteria were compiled from previous works on freshwater, thermal springs, and submarine mud volcanoes in Eastern Mediterranean region. Samples within each environment were used as pseudo-replicates to enable comparisons between the two assemblages (Archaea and Bacteria) and among different environments whereas sampling effort was found similar among samples using rarefaction curves. Phylotypes were defined as 16S rRNA sequences with 98% similarity. The most common diversity indices were calculated and relative abundance distributions (RADs) were employed to provide a more detailed interpretation of observed diversity patterns. The freshwater and mud volcanoes environments were the most diverse with respect to Bacteria but the least diverse considering Archaea, whereas thermal springs yielded very similar diversity for both assemblages. Overall, bacterial diversity was higher than archaeal with respect to richness and evenness since Archaea were characterized by high dominance and phylotype-poor distributions. The present comparative analysis of alpha diversity may offer useful insights into ecological processes shaping prokaryotic community structure, however equal sampling effort among different environments must be verified prior to analysis.     

The effects of sample size on population genetic diversity estimates in song sparrows Melospiza melodia

To empirically determine the effects of sample size on commonly used measures of average genetic diversity, we genotyped 200 song sparrows Melospiza melodia from two populations, one genetically depauperate (n=100) and the other genetically diverse (n=100), using eight microsatellite loci. These genotypes were used to randomly create 10,000 datasets of differing sizes (5 to 50) for each population to determine what the effects of sample size might be on several estimates of genetic diversity (number of alleles per locus, average observed heterozygosity, and unbiased average expected heterozygosity) in natural populations of conservation concern. We found that at small sample sizes of 5 to 10 individuals, estimates of unbiased heterozygosity outperformed those based on observed heterozygosity or allelic diversity for both low- and high-diversity populations. We also found that when comparing across populations in which different numbers of individuals were sampled, rarefaction provided a useful way to compare estimates of allelic diversity. We recommend that standard errors should be reported for all diversity estimators, especially when sample sizes are small. We also recommend that at least 20 to 30 individuals be sampled in microsatellite studies that assess genetic diversity when working in a population that has an unknown level of diversity. However, research on critically endangered populations (where large sample sizes are impossible or extremely difficult to obtain) should include measures of genetic diversity even if sample sizes are less than ideal. These estimates can be useful in assessing the genetic diversity of the population.     

Genetic population structure in horse chestnut (Aesculus hippocastanum L.): effects of human‐mediated expansion across Europe

The geographical distribution of existing populations of horse chestnut (Aesculus hippocastanum L.) in Europe is determined by past demographic events during the Quaternary. In the present study we evaluate the imprints that northward expansions originated from common ancestry at southern Europe may have left on the present patterns of genetic variation for horse chestnut across the continent. Genetic diversity and levels of population structure in a European south–north gradient, ranging from the Balkans to the Scandinavian Peninsula, were determined with Amplified Fragment Length Polymorphism (AFLP) markers in 159 loci. A family of rarefaction techniques for the estimation of gene diversity was used to exclude potential confounding effects as a result of the unequal sample sizes. The results indicate that northern populations are not more genetically depleted than southern populations, thus suggesting that diversity for this species is not correlated with latitudinal distribution. Detailed hypotheses based on prediction models for different historical events associated with human‐mediated spread of cultivation are examined for a better understanding of the current genetic patterns of regional differentiation.     

The remedies of the folk medicine of the Croatians living in Cićarija, northern Istria

An ethnobotanical field study was conducted among the Croatians living in Ci?arija in northern Istria and a very restricted folk pharmacopoeia (of approximately only 30 remedies) was recorded. This finding suggests that a remarkable process of erosion of Traditional Knowledge (TK) may have taken place. The collected data were compared with the ethnobotanical findings of a field study previously conducted among the Istro-Romanians living in the nearby village of Zejane, who probably migrated there around the 14th Century. It was found that more than half of the botanical taxa were being used medicinally across the two communities, and that approximately one third of the actual medicinal plant uses were recorded in both communities. Correspondence analysis carried out comparing the same data with those of the ethnobotanical literature of Istria and Friuli-Venezia Giulia in North-Eastern Italy showed that the folk phytotherapy of the diverse ethnic populations living in multi-cultural Istria appears to be very similar.     

Fossil pollen as a record of past biodiversity

Quaternary pollen records may contribute uniquely to the understanding of present plant diversity. Pollen assemblages can reflect diversity at community and landscape scales but the time resolution of most studies does not match that of modern ecological studies. Because of the complicating effects of differential pollen productivity and dispersal, pollen records do not directly reflect equitability aspects of vegetation diversity. Vegetation diversity indices other than S (the total number of taxa) are therefore not appropriate for pollen assemblages. As a measure of the species richness palynological richness is biased by the lack of taxonomic precision, by a possible interference on pollen dispersal from vegetation structure and by pollen representation. The nonlinear relationship between species richness and pollen-taxa richness may be used in attempts to estimate past floristic richness from fossil pollen assemblages. Using a hypothetical example the strong effect of cover shifts in the vegetation affecting taxa with different representation (R_rel) values on observed palynological richness is demonstrated. It is suggested that estimates of relative pollen productivity should be used to guide the pollen sum on which pollen-type richness is estimated by rarefaction techniques and this approach is illustrated using a paired site study of late Holocene diversity dynamics. The need for a modern training set relating pollen-type richness to species richness, pollen productivity and vegetation structure is emphasized.     

Diversity of Interactions: A Metric for Studies of Biodiversity

Multitrophic interactions play key roles in the origin and maintenance of species diversity, and the study of these interactions has contributed to important theoretical advances in ecology and evolutionary biology. Nevertheless, most biodiversity inventories focus on static species lists, and prominent theories of diversity still ignore trophic interactions. The lack of a simple interaction metric that is analogous to species richness is one reason why diversity of interactions is not examined as a response or predictor variable in diversity studies. Using plant–herbivore–enemy trophic chains as an example, we develop a simple metric of diversity in which richness, diversity indices (e.g., Simpson's 1/D), and rarefaction diversity are calculated with links as the basic unit rather than species. Interactions include all two-link (herbivore–plant and enemy–herbivore) and three-link (enemy–herbivore–plant) chains found in a study unit. This metric is different from other indices, such as traditional diversity measures, connectivity and interaction diversity in food-web studies, and the diversity of interaction index in behavioral studies, and it is easier to compute. Using this approach to studying diversity provides novel insight into debates about neutrality and correlations between diversity, stability, productivity, and ecosystem services.     

Assessing the diversity pattern of cryophilous plant species in high elevation habitats

This study aimed to better document the diversity and distribution patterns of vascular cryophilous species across major habitat types in a high-elevation Mediterranean system in central Italy. The research addressed the following questions: (a) whether different habitats support similar levels of biodiversity in terms of total vascular plants richness and cryophilous species richness, and (b) how each habitat contributes to the total cryophilous species diversity. A random stratified sampling approach based on a habitat map was applied to construct rarefaction curves for overall cryophilous species richness and habitat type-specific cryophilous richness. Rarefaction curves were also constructed for all-species and exclusive species. To determine whether the targeted species represented a constant proportion of all species, the ratio between the rarefaction curves of the cryophilous species and all species was also calculated. The results highlight the importance of the different habitat types in overall and cryophilous species conservation because these different habitat types had progressively higher richness values. At the regional scale, steep slopes had the highest species diversity, the greatest exclusive species richness and a steep rarefaction curve. The diversity pattern of cryophilous taxa was not related to the general pattern of total species richness, with these species being more common in three habitat types with extreme environmental conditions: ridges, cliffs, and screes. For the establishment of successful biodiversity conservation programs, it is imperative to include species-poor habitats containing a high proportion of cryophilous species, which are considered to be threatened by climate warming.     

Patterns of genetic variability in central and peripheral populations of <Emphasis Type="Italic">Dipteryx alata</Emphasis> (Fabaceae) in the Brazilian Cerrado

This study tested whether genetic parameters in Dipteryx alata populations, estimated from genomic and chloroplastidial microsatellite markers, were distributed according to a central-peripheral model, inferring which factors drive this spatial distribution of genetic variability within populations. For each of the 23 populations sampled throughout the species’ range, the mean number of alleles per locus, expected heterozygosity and intrapopulation fixation indices were calculated using a rarefaction approach based on 54 alleles from 8 nuclear microsatellites. Explanatory variables were grouped into three subsets: the ecological suitability estimated by combining different techniques of ecological niche modeling, variables expressing human occupation, and a historical variable represented by the first eigenvector from the pairwise F _ST matrix based on cpDNA microsatellites. Each response variable was modeled using first (linear) and second (quadratic) order trend surface analysis (TSA). Multiple regressions were then used to evaluate the relative effects of the explanatory variables, based on AIC multi-model selection. In general, the genetic parameters did not follow a classical central-periphery model. Ecological suitability had a significance influence in all genetic parameters, so more suitable regions have higher genetic diversity and low endogamy. There was also a relationship between fixation indices and human impacts. The high genetic diversity in the southwestern region of Cerrado suggested that recent range expansion (after the Last Glacial Maximum) may also influenced the observed intrapopulation genetic patterns. Thus, complex combinations of both historical and ecological drivers, as well as contemporary human occupation, seem to drive current genetic composition within D. alata populations throughout its geographic range.     

A unified mathematical framework for the measurement of richness and evenness within and among multiple communities

Biodiversity can be divided into two aspects: richness (the number of species or other taxa in a community or sample) and evenness (a measure of the distribution of relative abundances of different taxa in a community or sample). Sample richness is typically evaluated using rarefaction, which normalizes for sample size. Evenness is typically summarized in a single value. It is shown here that Hurlbert's probability of interspecific encounter (Δ₁), a commonly used sample-size independent measure of evenness, equals the slope of the steepest part of the rising limb of a rarefaction curve. This means that rarefaction curves provide information on both aspects of diversity. In addition, regional diversity (gamma) can be broken down into the diversity within local communities (alpha) and differences in taxonomic composition among local communities (beta). Beta richness is expressed by the difference between the composite rarefaction curve of all samples in a region with the collector's curve for the same samples. The differences of the initial slopes of these two curves reflect the beta evenness thanks to the relationship between rarefaction and Δ₁. This relationship can be further extended to help interpret species-area curves (SAC's). As previous authors have described, rarefaction provides the null hypothesis of passive sampling for SAC's, which can be interpreted as regional collector's curves. This allows evaluation of richness and evenness at local and regional scales using a single family of well-established, mathematically related techniques.     

冀西北坝上地区的夜蛾科昆虫

系统调查研究冀西北坝上农牧交错带的鳞翅目Lepidoptera,夜蛾科Noctuidae蛾类,已知11亚科71属117种,并对其多样性做了分析。各月份蛾类组成及数量差异较大,从5月到9月蛾类多样性指数、物种丰富度和个体数基本呈上升趋势,多样性指数与均匀度(r=0.9943)、丰富度(r=0.8979)相一致。而不同月份间的蛾类相似程度差异较大。     

Identifying evolutionarily significant units for conservation of the endangered Malus sieversii using genome‐wide RADseq data

Malus sieversii, a wild progenitor of the domesticated apple, is an endangered species and is assigned second conservation priority by the China Plant Red Data Book. It is urgent to carry out in situ conservation of this species, but previous studies have not identified evolutionarily significant units (ESUs) for conservation management. In this study, we investigated the genetic diversity and relationships of six M. sieversii populations from China using integrated analysis of microsatellite (nSSR) data, genome‐wide SNPs and previous results in order to propose a reasonable conservation management. The results showed that levels of genetic diversity were inconsistently reflected by our nSSR and previous studies, suggesting that indices of genetic diversity are not effective to identify priority conservation areas for M. sieversii. Based on the selection criteria of ESUs for endangered species conservation, ESUs should reflect lineage divergence, geographical separation and different adaptive variation. Our phylogenetic tree based on genome‐wide SNPs yielded a clear relationship of divergent lineages among M. sieversii populations, leading to new different from those of previous studies. Three independent lineages, including the pairs of populations Huocheng‐Yining, Gongliu‐Xinyuan and Tuoli‐Emin, were identified. The geographic distances between populations among the different phylogenetic lineages were much greater than those within the same phylogenetic lineage. A cluster analysis on environmental variables showed that the three independent lineages inhabit different environmental conditions, suggesting that they may have adapted to different environments. Based on the results, we propose that three independent ESUs should be recognized as conservation units for M. sieversii in China.