Incidence-based Coverage Estimator Research Articles

Species-Enriched Grass-Clover Mixtures Can Promote Bumblebee Abundance Compared with Intensively Managed Conventional Pastures

(1) Land use intensification has led to serious declines in biodiversity, including in forage production systems for dairy cows. Agri-environmental schemes, such as enriching grasslands in floral species, were shown to be an effective tool to promote biodiversity in higher trophic levels. Here, we studied an innovative pasture-based dairy production system with floral-species-enhanced temporary grasslands, with respect to the effect on wild bee abundance and species richness. (2) We studied three grass-clover mixtures with perennial ryegrass and clover species with different levels of plant diversity for flower cover and wild bees. The grass-clover pastures were rotationally stocked with cattle and parts of the pastures were excluded from grazing. Intensively managed conventional permanent grasslands were studied as the common land use type. Wild bees were caught by sweep netting. Wild bee diversity was analysed with a general linear mixed model. For species richness, an incidence-based coverage estimator was calculated. (3) In total, 541 wild bees from 10 species were found. No wild bees were caught on the conventional grasslands. Wild bee abundance and species richness did not differ among the three grass-clover mixtures, but with increasing flower cover of white clover (Trifolium repens), wild bee abundance increased. Except for one solitary wild bee individual, the recorded community exclusively consisted of bumblebees. While generalist species that are commonly found on farmland dominated, rare long-tongued bumblebees made up 10% on the grazed sites of the multispecies mixture and made up 20% on the ungrazed strips of the binary mixture and multispecies mixture. (4) We conclude that multispecies mixtures can provide resources for generalist bumblebee species, especially when compared with conventional grasslands that offer no resources. Considering that the multispecies mixture has been also shown to reduce greenhouse gas emissions and nitrate leaching, while maintaining high forage yields, our findings add to the potential to promote a wide range of ecosystem services. Yet, should their full potential be enfolded, grazing should partially be excluded, and the mixture should be extended by plant species with more open flowers, suitable for solitary wild bees.

Effect of crop residue management on damage by Diatraea saccharalis (Lepidoptera: Crambidae), its egg parasitoids and the ants associated with sugarcane.

In the American continent, the sugarcane borer Diatraea saccharalis (F.) is the main pest in sugarcane producing areas. The objective of this study was to assess the effect of crop residue management on damage by D. saccharalis, its egg parasitoids and the ants associated with sugarcane. The study was carried out during 2011-2012, 2012-2013 and 2013-2014 crop cycles, in three commercial fields located in different regions of Tucumán state, Argentina. Two types of crop residue management (= treatments) were compared: conservation of trash at the soil surface (CT) and trash burning (TB). In 'trash conservation' treatment, crop residue was allowed to remain over the soil surface during the whole sugarcane growing season, while the second treatment consisted of complete burning of trash blanket approximately 2 weeks after harvest. The injury level was measured by recording the number of stalks bored and internodes bored. Parasitism was estimated by counting the total number of eggs and number of black eggs (which indicates the occurrence of egg parasitoids). Ants (Formicidae) richness was calculated by two estimators; abundance-based coverage estimator and incidence-based coverage estimator, using the non-parametric richness estimators: Chao 2 and Jackknife. Finally, the indicator value was estimated through the measurement of specificity and fidelity. In all the parameters studied no significant difference was found between TB and CT treatments.

Distribution and diversity of Tardigrada along altitudinal gradients in the Hornsund, Spitsbergen (Arctic)

Two transects were established and sampled along altitudinal gradients on the slopes of Ariekammen (77°01′N; 15°31′E) and Rotjesfjellet (77°00′N; 15°22′E) in Hornsund, Spitsbergen. In total 59 moss, lichen, liverwort and mixed moss–lichen samples were collected and 33 tardigrade species of Hetero- and Eutardigrada were found. The α diversity ranged from 1 to 8 per sample; the estimated number of species based on all analysed samples was 52±17 for the Chao 2 estimator and 41 for the incidence-based coverage estimator. According to the results of detrended canonical correspondence analysis, altitude and type of substratum were the most important factors influencing tardigrade communities in the investigated area. Macrobiotus crenulatus, M. hufelandi hufelandi and Hypsibius pallidus dominated in the lower elevations, whereas Echiniscus wendti and E. merokensis merokensis prevailed in samples from higher plots. Macrobiotus islandicus islandicus was collected most often from mosses collected from rock whereas Isohypsibius coulsoni from mosses collected from soil. Analyses of covariance were employed to test for differences in species richness between the transects in relation to altitude. Contrary to expectations, there were significant differences in species richness between the transects, but richness was not significantly related to altitude. Interestingly, significant effects of colonies of seabirds, little auk (Alle alle), on the tardigrades communities were detected. Additionally, in one of the samples first ever males of Milnesium asiaticum were found. Their measurements and microphotographs are provided herein.Keywords: Arctic; biodiversity; climate change; invertebrate ecology; Milnesium; Tardigrada.To access the supplementary material for this article, please see supplementary files in the column to the right (under Article Tools).(Published: 2 February 2015)Citation: Polar Research 2015, 34, 24168, http://dx.doi.org/10.3402/polar.v34.24168

Comparative performance of incidence-based estimators of species richness in temperate zone herpetofauna inventories

Species inventories provide the basic information for biodiversity studies. Designing cost-effective species inventories is important in estimating the species richness or the number of additional species expected in a study area. Complete species inventories are difficult to achieve and a variety of estimation methods are available to counter the underestimation of species richness associated with incomplete sampling. A main criterion of selecting an estimation method requires deciding on a sampling unit type. The sampling unit may vary across study and estimating species richness using different sample units may produce different results. We evaluated the ability of incidence-based estimators of species richness to provide reliable estimates of species richness of temperate herpetofauna (i.e. amphibian and reptile) communities using two different types of sampling units (i.e. numbers of sampling days and the number of sampling sites, respectively). Our results showed that incidence-based estimators varied in their performance according to the two sampling units used. The incidence-based coverage estimator performed best when sampling unit was the number of sampling days whereas second-order Jackknife was the best estimator using sites as sampling unit. We draw attention on the lack of robustness of incidence-based estimators to sampling unit and recommend using species richness estimators in inventories of herpetofauna depending on the sampling unit.

Associations Among Ground-Surface Spiders (Araneae) and Other Arthropods in Mesic Flatwoods

Mesic flatwoods in Florida are increasingly threatened by anthropogenic activities, and although they are known to be important for many species of macrofauna, little is known of the arthropod assemblages that inhabit them. As arthropods can be utilized as indicator taxa, we characterized the assemblages of ground-surface spiders (Araneae) and other arthropods at 2 mesic flatwood sites in Hillsborough County, Florida, and used the Chao 2, ICE (incidence-based coverage estimator), and Michaelis-Menten means species richness estimators to extrapolate the true species richness of ground-surface spiders. Sampling was conducted over a 4-month period at the sites using pitfall traps, with spiders being identified to the level of genus or species, and other arthropods to the level of order. We identified 31 spider species from 27 genera in 12 families, with Lycosidae being the dominant spider family at both sites. However, Collembola and Formicidae were the most abundant arthropod taxa. Ground-surface spiders were not strongly associated with any typical prey groups, indicating that environmental factors might also be important in structuring this community. Our results indicate that more intensive sampling of these habitats would be required to comprehensively sample and identify all of the species present, but from a management perspective, our results appear to be relatively consistent with previous surveys elsewhere.

A structured inventory of spiders (Arachnida, Araneae) in natural and artificial forest gaps at Porto Urucu, Western Brazilian Amazonia

A preliminary survey of the spider fauna in natural and artificial forest gap formations at “Porto Urucu”, a petroleum/natural gas production facility in the Urucu river basin, Coari, Amazonas, Brazil is presented. Sampling was conducted both occasionally and using a protocol composed of a suite of techniques: beating trays (32 samples), nocturnal manual samplings (48), sweeping nets (16), Winkler extractors (24), and pitfall traps (120). A total of 4201 spiders, belonging to 43 families and 393 morphospecies, were collected during the dry season, in July, 2003. Excluding the occasional samples, the observed richness was 357 species. In a performance test of seven species richness estimators, the Incidence Based Coverage Estimator (ICE) was the best fit estimator, with 639 estimated species. To evaluate differences in species richness associated with natural and artificial gaps, samples from between the center of the gaps up to 300 meters inside the adjacent forest matrix were compared through the inspection of the confidence intervals of individual-based rarefaction curves for each treatment. The observed species richness was significantly higher in natural gaps combined with adjacent forest than in the artificial gaps combined with adjacent forest. Moreover, a community similarity analysis between the fauna collected under both treatments demonstrated that there were considerable differences in species composition. The significantly higher abundance of Lycosidae in artificial gap forest is explained by the presence of herbaceous vegetation in the gaps themselves. Ctenidae was significantly more abundant in the natural gap forest, probable due to the increase of shelter availability provided by the fallen trees in the gaps themselves. Both families are identified as potential indicators of environmental change related to the establishment or recovery of artificial gaps in the study area.

Invertebrate Diversity Associated with Tropical Mistletoe in a Suburban Landscape from Northern Australia

The invertebrate fauna associated with the tropical mistletoe Decaisnina signata (Loranthaceae) parasitising a range of host trees was surveyed during the late dryseason (September-October) in suburban areas of Darwin, Northern Territory, a landscape which comprises extensive patches of natural vegetation within the urban matrix. A total of 113 species of insects and spiders representing 51 families and 12 orders was recovered from 38 samples. The estimated total species richness, however, suggests another 116 species are likely to occur on the mistletoe according to the incidence-based coverage estimator (ICE). Hymenoptera (especially Formicidae), Hemiptera (particularly Miridae), Araneae and Lepidoptera were the most dominant groups in our samples in terms of both species richness and relative abundance (measured as % site occupancy). Thysanoptera, Coleoptera and Psocoptera were also comparatively diverse but were substantially less abundant. Overall species and family richness were both positively correlated with mistletoe biomass, but the composition and taxonomic richness of invertebrates associated with mistletoes parasitising different host genera (Planchonia vs. Alstonia) or host species (Alstonia scholaris vs. A. actinophylla) were not significantly different. Our findings are in broad agreement with limited previous studies elsewhere that indicate mistletoes support a wide range of invertebrates, some of which are obligate specialists. We hypothesize that mistletoes support a unique assemblage of invertebrates that is independent of the host tree.

Use of species richness estimators improves evaluation of understory plant response to logging: a study of redwood forests

The recovery of native understory plant communities after timber harvest has received a great amount of attention worldwide. However, most of these studies have ignored the potentially significant effects that differences in habitat across forest development may have on the species–area relationship, even though sampling efficacy among forest developmental stages may differ markedly as a result of equal sampling within stages. We examined vascular plant community structure in coastal redwood forests of northern California (USA) in forest patches in each of four forest stages that develop with forest age: Initiation, Closure, Mature, and Old-growth. We also used a set of traditional and novel approaches to assess sampling efficacy and guide our sampling design. We initially sampled 75 circular plots (0.04 ha) in stands within each forest stage across a 1,347 km2 area. The species–area relationship suggested we had adequately sampled all stages after the first season of data collection, but non-parametric richness estimators (Incidence-based Coverage Estimator or ICE) and Michaelis–Menten means (MMMeans) rarefaction curves, indicated inadequate sampling of the older stages. Thus, we added four more samples within the Old-growth forest stage, establishing a more equitable sample of all stages. Our full data set demonstrated significant differences between plant communities in previously harvested forests (‘managed’ = Initiation, Closure, and Mature) and ‘unmanaged’ forests (Old-growth). Though several understory species were present in all stages, a suite of Old-growth indicator and restricted species suggest that recovery of some species may take long periods in managed forests. Interestingly, a separate suite of common understory species were lacking in Old-growth, and species richness in this stage was lower than in the mature managed forests. We discuss how this departure from the prediction of peak richness in Old-growth may relate to fire suppression in Old-growth forests. Lastly, analysis of our initial, smaller sampling of plots suggested that Old-growth plots were the least species rich. However, additional sampling of the Old-growth stage demonstrated that Old-growth plots were as rich as Closure plots. This has important implications for all studies concerned with measuring recovery after forest disturbances; stage-dependent habitat-mediated differences that affect sampling efficacy may not be captured by traditional sampling methods.

The Influence of Linear Elements on Plant Species Diversity of Mediterranean Rural Landscapes: Assessment of Different Indices and Statistical Approaches

This paper mainly aims to study the linear element influence on the estimation of vascular plant species diversity in five Mediterranean landscapes modeled as land cover patch mosaics. These landscapes have several core habitats and a different set of linear elements--habitat edges or ecotones, roads or railways, rivers, streams and hedgerows on farm land--whose plant composition were examined. Secondly, it aims to check plant diversity estimation in Mediterranean landscapes using parametric and non-parametric procedures, with two indices: Species richness and Shannon index. Land cover types and landscape linear elements were identified from aerial photographs. Their spatial information was processed using GIS techniques. Field plots were selected using a stratified sampling design according to relieve and tree density of each habitat type. A 50x20 m2 multi-scale sampling plot was designed for the core habitats and across the main landscape linear elements. Richness and diversity of plant species were estimated by comparing the observed field data to ICE (Incidence-based Coverage Estimator) and ACE (Abundance-based Coverage Estimator) non-parametric estimators. The species density, percentage of unique species, and alpha diversity per plot were significantly higher (p < 0.05) in linear elements than in core habitats. ICE estimate of number of species was 32% higher than of ACE estimate, which did not differ significantly from the observed values. Accumulated species richness in core habitats together with linear elements, were significantly higher than those recorded only in the core habitats in all the landscapes. Conversely, Shannon diversity index did not show significant differences.

Evaluation of Sampling Methods and Species Richness Estimators for Ants in Upland Ecosystems in Florida

The growing emphasis on including invertebrates in global biodiversity conservation efforts has prompted an increase in the study of invertebrate assemblages. Invertebrate sampling designs and the bias of individual methods, nevertheless, remain poorly understood for a variety of habitats. We used a structured inventory approach to sampling ants in Þve upland ecosystems in Florida. We evaluated the efÞciency of quantitative and nonquantitative methods for sampling ants. We also evaluated the performance of four species richness estimators. A total of 3,774 species occurrences were distributed among 1,732 samples that contained 94 species from 31 genera. Twenty unique species and 10 duplicate species were collected. Compared with a comprehensive species list for Florida, sampling captured 66% of the regional fauna and 70 Ð90% of species within the ecosystems studied. Combinations of sampling methods were much more effective for assessing species richness. Individual methods were complementary and sampled only part of the entire assemblage. Nonparametric estimators (an incidence-based coverage estimator (ICE) and a jackknife estimator (Jack2)) performed better than lognormal Þtting, and Michaelis-Menten curve extrapola- tion. However, none of the estimators was stable, and their estimates should be viewed with skepticism. The results of this study provide support for the use of the Ants of the Leaf Litter (ALL) protocol for thoroughly sampling ant assemblages in temperate and subtropical ecosystems. Furthermore, our results indicate that even in relatively species-poor (compared with the tropics) temperate and subtropical regions, a large sampling effort that includes multiple sampling methods is the most effective manner of thoroughly sampling an ant assemblage. Therefore, we suggest that structured inventory should be adopted for a wider variety of terrestrial invertebrate studies.

Estimación de la riqueza de especies de Asteraceae mediante extrapolación a partir de datos de presencia-ausencia

Se estimaron los patrones de riqueza en México de cuatro tribus de la familia Asteraceae del país que recientemente han sido revisadas (Mutisieae, Senecioneae, Tageteae y Vernonieae) mediante extrapolación, utilizando datos de las etiquetas de ejemplares de herbario. Se utilizó el método de estimación de riqueza no paramétrico ICE (“Incidence-based Coverage Estimator”), el cual se basa en datos de presencia-ausencia de las especies por área. Se evaluaron 553 especies, que representan 18.3% de la riqueza de Asteraceae presente en México, representadas por 24,304 registros de herbario recolectados en 14,714 diferentes localidades. La información fue analizada dividiendo al país en cuadrículas con celdas de 1° de latitud y longitud y con celdas de 0.5°. Se identificaron las celdas con alta riqueza conocida (hot spots), así como aquellas que la extrapolación sugiere que contienen una alta riqueza estimada. Se determinaron las que parecen ameritar mayor atención en futuros trabajos de exploración, utilizando las diferencias entre la riqueza estimada y la observada para cada celda, con base en el supuesto teórico de que el valor estimado es más cercano al valor real.

The net result: evaluating species richness extrapolation techniques for littoral pond invertebrates

Summary1. Total species richness for an assemblage or site is a valuable measure in conservation monitoring and assessment, but protocols for sampling and species richness determination in wetland habitats such as ponds, bogs or mires remain largely unrefined.2. Techniques for estimation of total richness of an assemblage based upon replicated sampling offer the opportunity to derive useful estimates of total richness based upon small numbers of samples, and limit sampling‐derived disturbance which can be particularly problematic in small aquatic habitats.3. We quantified the performance of eight of the most commonly encountered estimators of species richness for a variety of littoral zone macrofauna from ponds, comparing estimated richness to maximum richness derived from sampling.4. Estimates using non‐parametric techniques based on species incidence provided the most accurate and precise estimates. The estimators Chao 2 and incidence‐based coverage estimator (ICE) from this category were reliable and consistent slight over‐estimators; the abundance‐based estimator Chao1 also performed well.5. Species inventory based on relatively small numbers of samples might be significantly improved by use of non‐parametric estimators for quantification of species richness.6. Use of non‐parametric estimators of species richness can assist biodiversity inventory by preventing erroneous rankings of habitat richness based upon observed species numbers from limited sampling.

THE ANT FAUNA OF A TROPICAL RAIN FOREST: ESTIMATING SPECIES RICHNESS THREE DIFFERENT WAYS

Species richness is an important characteristic of ecological communities, but it is difficult to quantify. We report here a thorough inventory of a tropical rain forest ant fauna and use it to evaluate species richness estimators. The study was carried out in ;1500 ha of lowland rain forest at La Selva Biological Station, Costa Rica. Diverse methods were used, including canopy fogging, Malaise traps, Berlese samples, Winkler samples, baiting, and manual search. Workers of 437 ant species were encountered. The abundance distribution was clearly lognormal, and the distribution emerged from a veil line with each doubling of sampling effort. Three richness estimates were calculated: the area under the fitted lognormal distribution, the asymptote of the Michaelis-Menten equation fit to the species accumulation curve, and the Incidence-based Coverage Estimator (ICE). The per- formance of the estimators was evaluated with sample-based rarefaction plots. The inventory was nearly complete because the species accumulation curve approached an asymptote, the richness estimates were very close to the observed species richness, and the uniques and duplicates curves were both declining. None of the richness estimators was stable in sample- based rarefaction plots, but regions of stability of estimators occurred. The explanation of rarity is one key to understanding why richness estimates fail. Fifty-one species (12% of the total) were still uniques (known from only one sample) at the end of the inventory. The rarity of 20 of these species was explained by ''edge effects'': ''methodological edge species'' (possibly abundant at the site but difficult to sample because of their microhabitat), and ''geographic edge species,'' known to be common in habitats or regions outside of La Selva. Rarity of 31 species remained unexplained. Most of the 51 rare species were known from additional collections outside of La Selva, either in other parts of Costa Rica or in other countries. Only six species were ''global uniques,'' known to date from only one sample on Earth. The study demonstrates that patterns of species occurrence early in an inventory may be inadequate to estimate species richness, but that relatively complete inventories of species-rich arthropod communities are possible if multiple sampling methods and extensive effort are applied.

Realistic simulation of the effects of abundance distribution and spatial heterogeneity on non-parametric estimators of species richness

: Several non-parametric estimators have been proposed for estimating species richness from a spatial sample. While the label non-parametric may suggest that a method makes few assumptions, these estimators are known to rely on a homogeneous community with certain abundance distributions. In this paper we simulate the effect of different abundance distributions (geometric series, log-normal, and broken-stick models) and of different types of spatial heterogeneity (species-specific aggregation, gradients, and an edge effect) on the performance of four non-parametric estimators of species richness for presence-absence data (Jack1, Jack2, Chao2, and ICE). In order to focus on parameter settings likely to be encountered in real communities, we derived simulation parameters from real data from four agricultural habitat types in central Switzerland. Based on an ANOVA of relative bias, all estimators failed for communities simulated under the geometric model and were considerably affected by a simulated edge effect, but species-specific aggregation, an environmental gradient, and differences between community types had little effect on estimator performance. Species abundance distribution and spatial heterogeneity influence estimator performance by decreasing the proportion of species represented in the sample, which may be counteracted by adapting the sampling design. For reasonably complete samples, Chao2 was the least biased, but suffered from a large variance, as did Jack2. We recommend using the first order jackknife Jack1 or the incidence-based coverage estimator ICE, but only for samples that contain at least 80% of the species.

Diversity and distribution of herbaceous vascular epiphytes in a tropical evergreen forest at Varagalaiar, Western Ghats, India

Herbaceous vascular epiphytes were screened in a total sample of 13 445 trees (in 153 species) and 348 lianas (in 30 species) ≥30 cm girth at breast height in a 30 ha plot of tropical evergreen forest at Varagalaiar, Indian Western Ghats. Of these, 4.3% of trees and 3.7% of lianas were infested with epiphytes. Epiphyte diversity totaled 26 species in 19 genera and 10 families. Sixteen species were angiosperms in three families (Orchidaceae 54%; Piperaceae and Araceae 8%) and 10 species (38%) were pteridophytes in seven families. The orchid, Pholidota pallida was most abundant and occurred on 178 (29.6%) stems. Asplenium nidus occurred on the maximum of 62 host species. The species richness estimators employed for species accumulation curves after 100 times randomization of sample order have stabilized the curve at 18th and 19th hectares respectively for Incidence-based Coverage Estimator and Chao2. A total of 588 trees and 13 liana stems lodged epiphytes, 74% of which were evergreen species and 26% deciduous. Epiphyte density was greater (56%) in deciduous species (Bischofia javanica 30% and Vitex altissima 8%). A significant positive relationship was found between trunk size and epiphyte association. Larger epiphyte species occurred mostly on middle and larger stems and smaller epiphyte species occurred on smaller stems. The majority of epiphytes (92%) were of autochorous dispersal type, bearing capsule or dust diaspores, while the remaining species with berries and nutlets are dispersed by small vertebrates.