Species richness is a fundamental measurement of community and regional diversity, and it underlies many ecological models and conservation strategies. In spite of its importance, ecologists have not always appreciated the effects of abundance and sampling effort on richness measures and comparisons. We survey a series of common pitfalls in quantifying and comparing taxon richness. These pitfalls can be largely avoided by using accumulation and rarefaction curves, which may be based on either individuals or samples. These taxon sampling curves contain the basic information for valid richness comparisons, including category‐subcategory ratios (species-to-genus and species-toindividual ratios). Rarefaction methods ‐ both sample-based and individual-based ‐ allow for meaningful standardization and comparison of datasets. Standardizing data sets by area or sampling effort may produce very different results compared to standardizing by number of individuals collected, and it is not always clear which measure of diversity is more appropriate. Asymptotic richness estimators provide lower-bound estimates for taxon-rich groups such as tropical arthropods, in which observed richness rarely reaches an asymptote, despite intensive sampling. Recent examples of diversity studies of tropical trees, stream invertebrates, and herbaceous plants emphasize the importance of carefully quantifying species richness using taxon sampling curves.

/pdf/quantifying-biodiversity-procedures-and-pitfalls-in-the-2ut2f3nw4g.pdf

Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Both the magnitude and the urgency of the task of assessing global biodiversity require that we make the most of what we know through the use of estimation and extrapolation. Likewise, future biodiversity inventories need to be designed around the use of effective sampling and estimation procedures, especially for 'hyperdiverse' groups of terrestrial organisms, such as arthropods, nematodes, fungi, and microorganisms. The challenge of estimating patterns of species richness from samples can be separated into (i) the problem of estimating local species richness, and (ii) the problem of estimating the distinctness, or complementarity, of species assemblages. These concepts apply on a wide range of spatial, temporal, and functional scales. Local richness can be estimated by extrapolating species accumulation curves, fitting parametric distributions of relative abundance, or using non-parametric techniques based on the distribution of individuals among species or of species among samples. We present several of these methods and examine their effectiveness for an example data set. We present a simple measure of complementarity, with some biogeographic examples, and outline the difficult problem of estimating complementarity from samples. Finally, we discuss the importance of using 'reference' sites (or sub-sites) to assess the true richness and composition of species assemblages, to measure ecologically significant ratios between unrelated taxa, to measure taxon/sub-taxon (hierarchical) ratios, and to 'calibrate' standardized sampling methods. This information can then be applied to the rapid, approximate assessment of species richness and faunal or floral composition at 'comparative' sites.

Estimating Terrestrial Biodiversity through Extrapolation

Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness. Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data. Here we extended previous rarefaction and extrapolation models for species richness (Hill number q D, where q ¼ 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number q D, q . 0) and present a unified approach for both individual-based (abundance) data and sample- based (incidence) data. Using this unified sampling framework, we derive both theoretical formulas and analytic estimators for seamless rarefaction and extrapolation based on Hill numbers. Detailed examples are provided for the first three Hill numbers: q ¼ 0 (species richness), q ¼ 1 (the exponential of Shannon's entropy index), and q ¼ 2 (the inverse of Simpson's concentration index). We developed a bootstrap method for constructing confidence intervals around Hill numbers, facilitating the comparison of multiple assemblages of both rarefied and extrapolated samples. The proposed estimators are accurate for both rarefaction and short-range extrapolation. For long-range extrapolation, the performance of the estimators depends on both the value of q and on the extrapolation range. We tested our methods on simulated data generated from species abundance models and on data from large species inventories. We also illustrate the formulas and estimators using empirical data sets from biodiversity surveys of temperate forest spiders and tropical ants.

/pdf/rarefaction-and-extrapolation-with-hill-numbers-a-framework-1m0gvt1mro.pdf

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

Summary
Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. The sample-size- and coverage-based integrations of rarefaction (interpolation) and extrapolation (prediction) of Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages.
We briefly review the conceptual background of Hill numbers along with two approaches to standardization. We present an R package iNEXT (iNterpolation/EXTrapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity). Two types of biodiversity data are allowed: individual-based abundance data and sampling-unit-based incidence data.
Several applications of the iNEXT packages are reviewed: (i) Non-asymptotic analysis: comparison of diversity estimates for equally large or equally complete samples. (ii) Asymptotic analysis: comparison of estimated asymptotic or true diversities. (iii) Assessment of sample completeness (sample coverage) across multiple samples. (iv) Comparison of estimated point diversities for a specified sample size or a specified level of sample coverage.
Two examples are demonstrated, using the data (one for abundance data and the other for incidence data) included in the package, to illustrate all R functions and graphical displays.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12613

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

Many Neotropical species whose range is restricted to tropical montane cloud forests (TMCF) are in danger of local or total extinction due to warming and drying as air warmed by climate change ascends these mountains. While the species richness of many arthropod higher taxa declines at high elevations, those species that do reside in TMCF are often highly specialised and endemic, rendering their natural history especially interesting. However, we know little about these TMCF arthropods. One genus of ants, Adelomyrmex Emery, 1897 (Hymenoptera: Formicidae), is characteristic of many TMCFs in Central America, and exemplifies this pattern. While workers of this genus are very common in leaf litter samples, winged males and winged queens have been unknown and nests have never been observed for most species. Here we report how a combination of affordable digital field microscopes and DNA barcoding has allowed nest discovery and documentation and linked male and worker Adelomyrmex. Based on this work, we have now learned that male Adelomyrmex can be quite abundant locally.

Observations of Adelomyrmex (Hymenoptera: Formicidae) reproductive biology facilitated by digital field microscopy and DNA barcoding

The ant genus Syscia Roger, 1861 is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work, the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be identified at many sites, but assignment of specimens to species spanning multiple sites was problematic. To improve species delimitation, Ultra-Conserved Element (UCE) phylogenomic data were sequenced for all forms, both within and among sites, and a phylogeny was inferred. Informed by phylogeny, species delimitation was based on monophyly, absence of within-clade sympatry, and a subjective degree of morphological uniformity. UCE phylogenomic results for 130 specimens were complemented by analysis of mitochondrial COI (DNA barcode) data for an expanded taxon set. The resulting taxonomy augments the number of known species in the New World from 3 to 57. We describe and name 31 new species, and 23 species are assigned morphospecies codes pending improved specimen coverage. Queens may be fully alate or brachypterous, and there is a wide variety of intercaste female forms. Identification based on morphology alone is very difficult due to continuous character variation and high similarity of phylogenetically distant species. An identification aid is provided in the form of a set of distribution maps and standard views, with species ordered by size.

/pdf/integrating-uce-phylogenomics-with-traditional-taxonomy-3j03ardpd3.pdf

Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Bothriomyrmex paradoxus Dubovikov and Longino sp. nov. is described from Costa Rica, based on two collections from widely separated localities. These are the first collections of the genus Bothriomyrmex in the Americas. The genus Bothriomyrmex can be divided into Palearctic species (Both- riomyrmex s.s.) and Oriental and Australian species, based on differences in palp formula and queen wing venation. Bothriomyrmex paradoxus shares palp and wing characters with the Palearctic species. It is probably native to Central America and long separated from its Old World relatives.

A new species of the genus Bothriomyrmex Emery, 1869 (Hymenoptera: Formicidae: Dolichoderinae) from Costa Rica

We conducted the first inventory of ants on the Islas Murcielago, Area de Conservacion Guanacaste (ACG) of Costa Rica. We conducted this study on a chain of seven islands and a nearby mainland site...

Ants of the Islas Murciélago: An Inventory of the Ants on Tropical Dry Forest Islands in Northwest Costa Rica

12. The Southern Pacific Lowland Evergreen Moist Forest of the Osa Region - Lawrence E. Gilbert, Catherine A. Christen, Mariana Altrichter, John T. Longino, Peter M. Sherman, Rob Plowes, Monica B. Swartz, Kirk O. Winemiller, Jennifer A. Weghorst, Andres V

John T. Longino

Papers

Observations of Adelomyrmex (Hymenoptera: Formicidae) reproductive biology facilitated by digital field microscopy and DNA barcoding

Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

A new species of the genus Bothriomyrmex Emery, 1869 (Hymenoptera: Formicidae: Dolichoderinae) from Costa Rica

Ants of the Islas Murciélago: An Inventory of the Ants on Tropical Dry Forest Islands in Northwest Costa Rica

12. The Southern Pacific Lowland Evergreen Moist Forest of the Osa Region - Lawrence E. Gilbert, Catherine A. Christen, Mariana Altrichter, John T. Longino, Peter M. Sherman, Rob Plowes, Monica B. Swartz, Kirk O. Winemiller, Jennifer A. Weghorst, Andres V