Sample-based Rarefaction Curves Research Articles

Woody Species Diversity and Biomass Carbon Sequestration in Private Residential Green Infrastructure of Dilla Town, Southern Ethiopia

Urban forests have an important role in biodiversity conservation, environmental improvement, and ecosystem services including climate change mitigation enhancement. The objectives of the current study were to: assess plant types and management strategies of the owners; woody species’ composition, structure, and diversity; and estimate aboveground biomass of trees and associated carbon stock in private residential green infrastructure (PRGI) at Dilla town. This study was conducted at three kebeles, the lowest administrative unit in Ethiopia. Ninety-four households were randomly selected from a proportional sample size for each kebele. A complete inventory of woody species was done after measuring the area occupied by plants at each household. At plot level, the aboveground biomass of sampled trees was calculated by using an allometric biomass equation developed for agroforestry species. Diversity was described by using different indices The free software EstimateS 9.1.0 was used to generate data for the construction of sample-based rarefaction curves and SPSS version 20 for descriptive statistics. Based on plant types and arrangement, the households manage their PRGI in 15 categories on area size, ranging from 10 m2 to 1229 m2, with an average holding size of 207.5 m2. A total of 66 plant species belonging to 45 families were identified. Overall, a total of 1220 stem ha−1 contributed to an aboveground carbon stock of 64.35 ton ha−1 of which 50.4% is from fruit trees and the rest from timber trees. The results suggest that PRGIs can serve as reservoirs of non-native and native plant species, including five native tree species currently facing conservation concerns.

Plot size matters: Toward comparable species richness estimates across plot-based inventories.

To understand the state and trends in biodiversity beyond the scope of monitoring programs, biodiversity indicators must be comparable across inventories. Species richness (SR) is one of the most widely used biodiversity indicators. However, as SR increases with the size of the area sampled, inventories using different plot sizes are hardly comparable. This study aims at producing a methodological framework that enables SR comparisons across plot‐based inventories with differing plot sizes. We used National Forest Inventory (NFI) data from Norway, Slovakia, Spain, and Switzerland to build sample‐based rarefaction curves by randomly incrementally aggregating plots, representing the relationship between SR and sampled area. As aggregated plots can be far apart and subject to different environmental conditions, we estimated the amount of environmental heterogeneity (EH) introduced in the aggregation process. By correcting for this EH, we produced adjusted rarefaction curves mimicking the sampling of environmentally homogeneous forest stands, thus reducing the effect of plot size and enabling reliable SR comparisons between inventories. Models were built using the Conway–Maxell–Poisson distribution to account for the underdispersed SR data. Our method successfully corrected for the EH introduced during the aggregation process in all countries, with better performances in Norway and Switzerland. We further found that SR comparisons across countries based on the country‐specific NFI plot sizes are misleading, and that our approach offers an opportunity to harmonize pan‐European SR monitoring. Our method provides reliable and comparable SR estimates for inventories that use different plot sizes. Our approach can be applied to any plot‐based inventory and count data other than SR, thus allowing a more comprehensive assessment of biodiversity across various scales and ecosystems.

Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests.

Innovative techniques, such as environmental DNA (eDNA) metabarcoding, are now promoting broader biodiversity monitoring at unprecedented scales, because of the reduction in time, presumably lower cost, and methodological efficiency. Our goal was to assess the efficiency of established inventory techniques (live-trapping grids, pitfall traps, camera trapping, mist netting) as well as eDNA for detecting Amazonian mammals. For terrestrial small mammals, we used 32 live-trapping grids based on Sherman and Tomahawk traps (total effort of 10,368 trap-nights); in addition to 16 pitfall traps (1,408 trap-nights). For bats, we used mist nets at 8 sites (4,800 net hours). For medium and large mammals, we used 72 camera trap stations (5,208 camera-days). We identified vertebrate and mammal taxa based on eDNA analysis (12S region, with V05 and Mamm01 markers) from water samples, including a total of 11 3-km transects for stagnant water sampling and seven small streams for running water sampling. A total of 106 mammal species were recorded. Building on sample-based rarefaction and extrapolation curves, both trapping grids and pitfall were successful, recording 91.16% and 82.1% of the expected species for these techniques (~22 and ~9 species), and 16.98% and 6.60% of the total recorded mammal species, respectively. Mist nets recorded 83.2% of the expected bat species (~48), and 34.91% of the total recorded species. Camera trapping recorded 99.2% of the predicted large- and medium-sized species (~31), and 33.02% of the total recorded species. eDNA recorded 75.4% of the expected mammal species for this technique (~68), and 47.0% of the total recorded species. eDNA resulted in a useful tool that saves on effort and reduces sampling costs. This study is among the first to show the large potential of eDNA metabarcoding for assessing Amazonian mammal communities, providing, in combination with conventional techniques, a rapid overview of mammal diversity with broad applications to monitoring, management and conservation. By including appropriate genetic markers and updated reference databases, eDNA metabarcoding method can be extended to the whole vertebrate community.

A socio-ecological system perspective on trade interactions within artisanal fisheries in coastal Kenya

Assessments of coastal artisanal fisheries are progressively adopting a social-ecological system (SES) approach as an effective means to accumulate knowledge and integrate findings on different aspects of the fisheries. Ostrom’s SES framework was used to guide assessment of interactions between and within the harvesting and supply-chain processes and the effect of external drivers, seasonal monsoons and tourism, on both processes in a coastal artisanal fishery system in Gazi Bay, Kenya. Specific analyses focused on seasonal catch composition, key resource user groups involved in the fish trade and the resource units traded by each user group. The snowball method was used to identify key resource user groups within the fishery sector, who were then interviewed using semi-structured questionnaires (n = 60). Additionally, existing annual shore-based catch assessment and monthly fish landings data for the years 2014 and 2015 were incorporated for analysis of artisanal catch properties (species composition and weight). Comparison of seasonal catch composition was carried out using sample-based rarefaction curves. Higher fish landings and higher species diversity were recorded during the North-East Monsoon season. Further, a simple fish harvesting-supply network comprising of six key resource user groups (i.e. hotels, fish processing companies, dealers, small-scale fish processors (mama karanga), fish mongers and fishers) was outlined. The tourism industry, through hotels, creates a high demand for fish coinciding with a higher catchability and supply during the calm North-East Monsoon season and consequently, dealers hire migrant fishermen to target pelagic fish. Evidence of interactions within and between different fishery sub-systems, as well as the effect of monsoon seasons and tourism on the exploitation and market dynamics of the multispecies fishery, highlight the need for comprehensive management plans to strengthen self-organization among resource users and to increase adaptive capacity within the fishery system.

Effects of buildings on plant composition and diversity in a Mediterranean protected area

In natural protected areas, buildings such as small villages, farms, shepherd's huts, camps, small hotels or visitor centres are common, usually at very low densities. Although buildings could play a role in modifying the biodiversity of natural protected areas, there has hardly been any attempt to describe the composition and characteristics of the vegetation associated with these buildings. Here, we analysed if there is specific vegetation associated with buildings in a set of six buildings within the Doñana National Park (SW Spain). We used Detrended Correspondence Analysis to identify trends of variation associated with buildings, and G-tests to examine if the species associated with buildings differed significantly in geographical distribution and functional characteristics from the species of the natural area. To compare species richness between the plots associated with the buildings and those associated with the natural area, sample-based rarefaction curves were created using incidence data. We found that buildings increased the richness of plant communities, mainly of species with a wide geographical distribution or which are adapted to heavy disturbance. This effect remained even 40 years after abandonment, which means that buildings act as a long-lasting refuge for ruderal and invasive plant species that remain around them, but not invading the surroundings unless there are disturbances. We conclude that the perturbation caused by isolated buildings seem to create localized plant diversity hotspots in the sands of the Doñana ecosystems that remain distinct from the surrounding natural area for decades.

Hand searching versus pitfall trapping: how to assess biodiversity of ground beetles (Coleoptera: Carabidae) in high altitude equatorial Andes?

The use of ground beetles (Coleoptera: Carabidae) as bioindicators of environmental change depends on the reliability and the effectiveness of the sampling methods. Those that have been tested in the temperate zone and in tropical forests still await experimentation in tropical high-altitude environments. For the first time, pitfall trapping and hand searching have been compared in Ecuadorian paramo above 4000 m a.s.l., in terms of practical effectiveness. The study was performed on six volcanoes and was based on the comparison of 28 sampling sessions (pitfall trapping and hand searching) performed along two different elevational belts [lower superparamo (LSP) and upper superparamo (USP)]. Analyses of sampling sessions showed that detected species richness is slightly higher with hand searching than with pitfall trapping, regardless of the elevation. Additionally, hand searching is more time-effective than pitfall trapping. The performance of the sampling method slightly varies when species assemblage composition is analysed in relation to elevational belts. In the LSP, hand searching and pitfall trapping should be simultaneously used to obtain exhaustive inventories of carabid biodiversity, since different species are likely to be collected by each method. In the USP, hand searching and pitfall trapping efficiency is very similar, but hand searching allows to collect a slightly larger number of species. Lastly, the sample-based rarefaction curves showed that four temporal replicates are mandatory to obtain a robust dataset and an exhaustive inventory of the true species richness and species assemblages composition. Our findings suggest a combined use of hand searching and pitfall trapping in the LSP, while both methods can be used alone for surveying carabids in the USP. Furthermore, hand searching is recommended if the aim is to obtain an inventory of species diversity, whereas pitfall trapping seems more convenient for fine grain ecological and comparative studies.

Long-term stability of the hawkmoth fauna (Lepidoptera, Sphingidae) in a protected area of Brazilian Atlantic Rain Forest

Hawkmoths are an important component of tropical ecosystems, with significant roles as herbivores and pollinators. These moths can be used as indicators in biodiversity assessments because they can be easily sampled and identified. However, hawkmoths have seldom been surveyed over the long term for this purpose, especially in the Neotropical region. Considering that long-term datasets are of indisputable importance for understanding and monitoring temporal changes in biodiversity, this study assessed long-term changes in the hawkmoth fauna in a protected Atlantic Rain Forest area over a period of 64 years. We used historical and recent empirical datasets to ask whether faunal-diversity patterns and species composition have changed over time. We used individual- and sample-based rarefaction and extrapolation curves based on Hill number (diversity order of q = 0) to compare species richness, and the probability version of the abundance-based Chao-Jaccard index to assess beta diversity over time. To assess changes in faunal composition, we conducted a nonmetric multidimensional scaling analysis and performed an analysis of similarities to test whether the community composition has changed. Our results clearly showed long-term stability of the hawkmoth community over the 64 years, despite the growing human-induced landscape changes that occurred in the region surrounding the study area during the last 6 decades. This study emphasizes the importance of large remnants of Atlantic Forest for long-term maintenance of both functional diversity and ecosystem functioning.

Experiments with dead wood reveal the importance of dead branches in the canopy for saproxylic beetle conservation

Abstract Vertical gradients of habitats are a typical characteristic of forest ecosystems. Sun-exposed dead wood in the upper canopy, for instance, provides a habitat for saproxylic beetles distinct from that in the more shaded dead wood below the canopy. Canopy research, however, is challenging due to both the limited accessibility and potential confounding effects of temperature on trapping probability when activity traps are used. We studied saproxylic beetle assemblages along a complete vertical gradient without bias caused by temperature effects on activity. Using crane-like constructions attached to the top of large Silver Fir trees (Abies alba), we exposed bundles of freshly cut branches of European Beech (Fagus sylvatica), Silver Fir and Norway Spruce (Picea abies) in three different vertical strata (upper canopy, mid-canopy and near the ground). The bundles in the upper canopy were fully exposed to the sun and the bundles in the mid-canopy and near the ground were in the shade. We allowed beetles to colonize the bundles of branches for one growing period and then reared beetles from each bundle over three years. The species composition of saproxylic beetle assemblages differed between bundles in the upper canopy and near the ground; bundles in the mid-canopy had an intermediate assemblage composition. The abundance of saproxylic beetles was higher near the ground than in the upper canopy, whereas the number of species showed the opposite pattern. Overlapping confidence intervals of sample-based rarefaction and extrapolation curves for species diversity indicate that estimated gamma diversity per stratum is similar across the three strata. Our results support earlier studies that revealed the importance of habitat heterogeneity as a driver of the biodiversity of taxa associated with dead wood. As we controlled for wood diameter and tree species diversity, our study suggests that the microclimatic variability within dead wood – and thus habitat heterogeneity for saproxylic beetles – is higher in the upper canopy than near the ground. For biodiversity conservation in forests, our results support a strategy of enhancing the number of trees with microhabitats, particularly those with dead branches in the upper tree crown. Dead branches and standing dead trees should only be removed, e.g. for safety reasons, if no other option is available.

Analysis of spatial patterns informs community assembly and sampling requirements for Collembola in forest soils

The relative importance of niche separation, non-equilibrial and neutral models of community assembly has been a theme in community ecology for many decades with none appearing to be applicable under all circumstances. In this study, Collembola species abundances were recorded over eleven consecutive years in a spatially explicit grid and used to examine (i) whether observed beta diversity differed from that expected under conditions of neutrality, (ii) whether sampling points differed in their relative contributions to overall beta diversity, and (iii) the number of samples required to provide comparable estimates of species richness across three forest sites. Neutrality could not be rejected for 26 of the forest by year combinations. However, there is a trend toward greater structure in the oldest forest, where beta diversity was greater than predicted by neutrality on five of the eleven sampling dates. The lack of difference in individual- and sample-based rarefaction curves also suggests randomness in the system at this particular scale of investigation. It seems that Collembola communities are not spatially aggregated and assembly is driven primarily by neutral processes particularly in the younger two sites. Whether this finding is due to small sample size or unaccounted for environmental variables cannot be determined. Variability between dates and sites illustrates the potential of drawing incorrect conclusions if data are collected at a single site and a single point in time.

Fungal partner shifts during the evolution of mycoheterotrophy in Neottia.

Few previous studies have examined how mycobionts change during the evolution from autotrophy to mycoheterotrophy based on phylogenetic hypotheses. Neottia (Orchidaceae) comprises leafy species that are autotrophic and related leafless mycoheterotrophic species, and the phylogenetic relationships among them have been clarified. Accordingly, Neottia is a suitable taxon for investigating the question above. Here we clarified the diversity of mycobionts in Neottia plants and elucidated changes in the character of symbiotic associations during the evolution of mycoheterotrophy. We sequenced the internal transcribed spacer (ITS) regions of nuclear ribosomal (nr) DNA for mycobionts of Neottia plants. Furthermore, we selected one representative DNA sample from each fungal operational taxonomic unit (OTU) and used it to amplify the large subunit (LSU) nrDNA sequences. Phylogenetic analyses of Sebacinales (basidiomycetes), the dominant mycobiont of Neottia, were conducted and sample-based rarefaction curves generated for the observed mycobiont richness on each OTU. Leafy and leafless species in Neottia were associated with Sebacinales Group B and Sebacinales Group A, respectively. The composition and specificity level of fungal partners varied among Neottia species. Fungal partner composition and specificity level changed with speciation in both leafy and leafless Neottia species. In particular, mycorrhizal associations likely shifted from Sebacinales Group B to Group A during the evolution from autotrophy to mycoheterotrophy. Partner shifts to Sebacinales Group A have also been reported in the evolution of mycoheterotrophy of other plant groups, suggesting that convergence to this fungal group occurs in association with the evolution of mycoheterotrophy.

In and out: Effects of shoot- vs. rooted-presence sampling methods on plant diversity measures in mountain grasslands

Plant diversity measures (e.g., alpha- and beta-diversity) provide the basis for a number of ecological indication and monitoring methods. These measures are based on species counts in sampling units (plots or quadrats). However, there are two alternative conventions for defining a vascular plant species as “present” in a plot, i.e. “shoot presence” (a species is recorded if the vertical projection of any above-ground part falls within the plot) and “rooted presence” (a species is recorded only when an individual is rooted inside the plot). Very few studies addressed the effects of the two sampling conventions on species richness and diversity indices. We sampled mountain dry grasslands in Italy across different plot sizes and vegetation types to assess how large is the difference in alpha- and beta-diversity values and in sample-based rarefaction curves between the two methods. We found that the difference is greatly dependent on plot size, being more relevant, both in absolute and percentage values, at smaller grain; it is also dependent on habitat type, being larger in shallow-soil communities, as they have a sparser vegetation structure and host life-form types with a larger lateral spread. At fine spatial scales (<1m2) the difference is large enough to bias statistical inference, and we conclude that at such scales one should not attempt to compare plant diversity indices if they were not obtained with the same sampling convention.

Cliff outcrops used as condor communal roosts are local hotspots of occupancy and intense use by other bird species

Cliff outcrops are structural components of the environment that can maintain a large variety of wildlife; however, they are still rather overlooked in conservation planning. We evaluate whether cliffs used by the Andean condor (Vultur gryphus) for communal roosting are associated with local aggregations of other bird species, and if their presence in combination with other local (vegetation cover, plant species richness, topographic heterogeneity) and regional (distance to water) environmental variables play a significant role in the structuring of local bird diversity. We selected twenty-four localities in north-western Patagonia (Argentina) to compare the abundance and richness of birds across four habitat types: a cliff used as condor roost (CC), closest cliffs to CC not used for roosting with the same (SC) or different (DC) aspect and the vegetation matrix surrounding the cliffs (MA). This led to 264 fixed 100m-radius points spread over 96 sampling sites. We recorded more individuals and species on cliffs than on MA; however, sample-based rarefaction curves showed that the high species richness observed on cliffs was actually the consequence of the high number of individuals recorded. Habitat type, vegetation cover and the richness of dominant vascular plants were the most important variables accounting the richness and abundance of birds. We concluded that condor roosts represent suitable habitats for the aggregation of individuals of other bird species thus leading to hotspots of occupancy and high species richness. Those cliffs should be reconsidered in the mapping of important conservation areas and for the proposal of mesofilter conservation strategies.

Contrasting copepod community dynamics related to sampling strategies in the unsaturated zone of a karst aquifer

The sampling effect may reflect artifactual trends in species richness and distribution across various spatiotemporal scales. The paper aims to examine how sampling frequency impacts the observed community dynamics in groundwater habitats of the unsaturated zone of the Ciur Izbuc cave (northwestern Romania) and addresses data interpretation biases that can arise when different sampling strategies are applied. The patterns obtained by monthly sampling over a year were compared with the patterns from the seasonal samplings over 4 years and with those from sampling conducted at an interval of 2 days over 1 week. Sample-based rarefaction curves were computed to compare estimated species richness between datasets with different sampling frequencies. Self-organizing maps were used to explore the impact of sampling frequency on depicted patterns over various temporal frames. Sampling frequency contributed to contrasting species richness, abundances and spatiotemporal dynamics of copepods in the studied groundwater habitats across scales. Monthly sampling and seasonal sampling revealed maximum number of species (seven) and led to stable species estimates after 11 sampling occasions and 12 sampling occasions, respectively, while 1 week of every-other-day sampling was not enough to capture the highest number of species. Spatial heterogeneity of species distribution increased over 4 years of seasonal sampling. Our results demonstrated the importance of sampling rate and temporal frames in understanding depicted aquatic community dynamics a must before drawing conclusions. We advocate cautious data interpretation and pattern generalization in groundwater ecology to avoid hasty assessments of community changes across spatial and temporal scales.

Characterizing catches taken by different gears as a step towards evaluating fishing pressure on fish communities

To implement an ecosystem approach to fisheries management, there is a need to characterize the total pressure exerted by fisheries at the community level. French onboard observer data were used to derive catch metrics and compare fishing distribution across community components between two sites in the Southern Bay of Biscay. Sample-based rarefaction curves were used to standardize metrics across different active and passive gears, and correct for sample size differences. Six metrics for species, length and functional catch composition were tested. Length and functional metrics were found the most relevant metrics to highlight differences in catches between gears, sites, and gear-site interactions. Significant differences were found between gears, mainly in mean length and proportion of piscivores. None of the gears had the most diverse catch across all metrics. Small differences were found between sites, mainly in length range and species richness.

Butterflies of Sundarban Biosphere Reserve, West Bengal, eastern India: a preliminary survey of their taxonomic diversity, ecology and their conservation

The Indian Sundarbans, part of the globally famous deltaic eco-region, is little-studied for butterfly diversity and ecology. The present study reports 76 butterfly species belonging to five families, which is a culmination of 73 species obtained from surveys conducted over a period of three years (2009-2011) in reclaimed and mangrove forested areas and three species obtained from an earlier report. Six of these species are legally protected under the Indian Wildlife (Protection) Act, 1972. Random surveys were employed for both the study areas, supplemented by systematic sampling in reclaimed areas. The reclaimed and forested areas differed largely in butterfly richness (Whittaker’s measure of ß diversity = 0.55). For sample-based rarefaction curves, butterfly genera showed a tendency to reach an asymptote sooner than the species. Numerous monospecific genera (77.19% of the taxa) resulted in a very gentle but non-linear positive slope for the species-genus ratio curve. A species-genus ratio of 1.33 indicated strong intra-generic competition for the butterflies of the Indian Sundarbans. Mangrove areas were species poor, with rare species like Euploea crameri, Colotis amata and Idea agamarshchana being recorded in the mangrove area; while Danaus genutia was found to be the most frequent butterfly. Butterfly abundance was very poor, with no endemic species and the majority (53.9% of the taxa; n=41) were found locally rare. The changing composition of butterflies in the once species-poor mangrove zone of the fragile Sundarbans may interfere with their normal ecosystem functioning.

Sampling intensity in biodiversity assessment: malacofauna of selected floodplain water bodies

The assessment of completeness of mollusc species lists in selected permanent and temporary floodplain water bodies located within the lower Bug River valley, as well as estimation of the minimum number of samples required to obtain an acceptable efficiency of inventory in individual water bodies, was carried out using sample-based rarefaction curves and non-parametric estimator Chao2. The effect of sampling effort on different measures of species diversity (species richness, Shannon diversity exp(H’)) was examined. Dependence of sampling effort, inventories completeness and diversity measures on habitat stability was analysed by comparing permanent and temporary water bodies. Mollusc assemblages of the investigated water bodies showed high temporal and spatial variability, as well as inter-habitat differences (relatively low Jaccard’s similarity coefficient, J). Significant differences in diversity and composition of mollusc assemblages were found between permanent and temporary habitats, whereas species richness was similar in both permanence groups. In general, both species richness and diversity increased similarly with growing sampling effort. Total richness accuracy reached at least 90% of the predicted value (calculated with Chao2) with 5 to 14 random samples, depending on the water body (10–14 samples in permanent habitats and 5–10 samples in temporary ones). kEy words: aquatic molluscs, species richness, diversity, sampling effort, data set completeness

The luxury of vegetation and the legacy of tree biodiversity in Los Angeles, CA

Urban vegetation cover and biodiversity provide ecosystem services to city residents, though the mechanisms affecting managed vegetation cover and biodiversity across varying urban land uses are not well understood. To evaluate competing mechanisms influencing urban vegetation cover and tree biodiversity, we collected data from 350 plots in the City of Los Angeles, CA. Alpha (α) and beta (β) tree biodiversity were quantified using sample based rarefaction curves. Hypotheses of independent climate, land use, luxury and legacy effects were evaluated with residual regression analysis and best models were chosen using AIC. Residential land use had the highest α biodiversity at all sampling scales, but the lowest β diversity, possibly indicating a limited plant pool for managers. Increased median household income was independently related to each type of vegetation cover, supporting a luxury effect. Regression models explaining the most variation in cover also included population density. In contrast, tree species richness was only positively related to housing age, supporting the legacy effect. Median income had no independent effect on tree biodiversity, which contrasts with patterns in other arid cities. However, age and income had an interactive effect. The highest α and β tree diversity were found in old, high-income locations. Managing for ecosystem services provided by vegetation should prioritize low income neighborhoods for increasing cover, while managing for biodiversity should maintain existing diversity in older neighborhoods and encourage new species in newer neighborhoods.

Species richness of motile cryptofauna across a gradient of reef framework erosion

Coral reef ecosystems contain exceptionally high concentrations of marine biodiversity, potentially encompassing millions of species. Similar to tropical rainforests and their insects, the majority of reef animal species are small and cryptic, living in the cracks and crevices of structural taxa (trees and corals). Although the cryptofauna make up the majority of a reef’s metazoan biodiversity, we know little about their basic ecology. We sampled motile cryptofaunal communities from both live corals and dead carbonate reef framework across a gradient of increasing erosion on a reef in Pacific Panama. A total of 289 Operational Taxonomic Units (OTUs) from six phyla were identified. We used species-accumulation models fitted to individual- and sample-based rarefaction curves, as well as seven nonparametric richness estimators to estimate species richness among the different framework types. All procedures predicted the same trends in species richness across the differing framework types. Estimated species richness was higher in dead framework (261–370 OTUs) than in live coral substrates (112–219 OTUs). Surprisingly, richness increased as framework structure was eroded: coral rubble contained the greatest number of species (227–320 OTUs) and the lowest estimated richness of 47–115 OTUs was found in the zone where the reef framework had the greatest vertical relief. This contradicts the paradigm that abundant live coral indicates the apex of reef diversity.

Diversity Partitioning Using Shannon's Entropy and its Relationship to Rarefaction

Diversity (the variety of different types of organisms) of an ecological or paleoecological system reflects processes and history operating across a range of hierarchically related scales. For example, the diversity of a biofacies is the sum of the diversity in all the local patches composing the biofacies, the diversity of a depositional system is composed of all the biofacies composing the depositional system, and the diversity of a biotic province is composed of all the landscapes composing the province. Diversity at a larger scale (γ-diversity) incorporates both the average inventory diversity of units of the next smaller scale (α-diversity) and the compositional differences, or differentiation diversity, among the smaller units (β-diversity). Many familiar means of measuring diversity can be mathematically partitioned to determine the relative contribution of different diversity components at any hierarchical level. When using richness (the number of taxa in an ecological system) as a measurement of diversity, it is necessary to use rarefaction to correct for differences in sample size. The divergence between sample-based and individual-based rarefaction curves of a composite collection (γ-diversity) incorporating all the samples (α-diversity) contributing to a given hierarchical level reflects the degree of non-random compositional difference among the smaller scale units (β-diversity). Alternatively, Shannon's entropy can be partitioned additively: β-entropy equals γ-entropy (based on a composite sample) minus average α-entropy of the constituent samples. A useful property of entropy is that it can be converted to effective richness, the number of taxa that would result in the same entropy value if all were equally abundant. Effective richness can be thought of as a unit conversion from non-intuitive entropy units to more easily understood richness units. Effective richness derived from Shannon's entropy partitions diversity multiplicatively – i.e., β-diversity is the number of compositionally distinct smaller units that contribute to the total diversity at the higher level. Diversity partitioning is rapidly becoming adopted as a tool for directly addressing how the structure of higher-level ecological and paleoecological systems reflects interactions among lower-level units in response to environmental and evolutionary changes.

Evaluación de estimadores no paramétricos de la riqueza de especies. Un ejemplo con aves en áreas verdes de la ciudad de Puebla, México

Assessing non-parametric estimators of species richness. A case study with birds in green areas of the city of Puebla, Mexico Our objective was to evaluate the performance of non-parametric estimators of spe-cies richness with real data. During the 2003 breeding season, bird communities were sampled in two green areas in the city of Puebla (Mexico), and the corresponding sample-based rarefaction curves were obtained. Mean data were adjusted to two non-asymptotic and seven asymptotic accumulation functions, and the best model was selected by means of reliability criteria in information theory. The cumulative Weibull and the beta-P functions were the best-fit models. Bias, precision and accuracy of five non-parametric estimators of species richness (ICE, Chao2, Jackknife 1, Jackknife 2, and Bootstrap) were then assessed for increasing sampling efforts (1-53 sampling units) against the asymptote of the selected accumulation functions. All the non-parametric estimators here evaluated underestimated true richness most of the time, specially in one of the sites. However, after combining data from the two assemblages, only ICE, and Jackknife 1 and 2 exhibited bias below 10% with different sampling efforts, and only Jackknife 1 was globally accurate (scaled mean squared error x 100 &lt; 5%, even with low sampling efforts, ca. 20% of the total). Therefore, we propose using the Jackknife 1 non-parametric estimator as a lower limit to measure bird species richness in urban sites similar to those in the present study.