Estimates Of Species Diversity Research Articles

Assessing sampling adequacy of mussel diversity surveys in wadeable Illinois streams

Freshwater mussels are one of the most imperiled groups of animals in North America. Effective resource management and conservation efforts require reliable estimates of species diversity and their distributions. However, sampling protocols for qualitative mussel surveys have not been well established and tested. Furthermore, the sampling effort required for a given data-quality goal (90% of species captured) often varies substantially among sites, and application of a standard effort probably would introduce bias into assemblage comparisons. We tested the sampling adequacy of time-based hand searches. We conducted 16-man-hour (mh) searches at each of 18 wadeable stream sites in Illinois that differed widely in environmental factors and historical species diversity and collected 27 to 942 individuals and 5 to 18 species per site. We accounted for imperfect species detectability by using the Chao-1 richness estimator and measured sampling adequacy as the % of the estimated number of species sampled. Four-mh searches, a frequently used effort, captured 15 to 100% of all species with an average of 61%, and yielded estimates of richness that were not significantly correlated with the estimated total richness (Pearson’s r = 0.39, p > 0.05). Ten-mh searches captured >70% of all species at >70% of sites and resulted in a significant correlation between observed and estimated richness (Pearson’s r ≥ 0.78, p < 0.01). A Random Forests (RF) model based on watershed and habitat characteristics (e.g., stream size and dominant substrate types) accounted for 45% of the variance in sampling adequacy of 4-mh searches. Sampling adequacy decreased with increasing stream size and substrate size but increased with % forest in the riparian zone and logs in the stream. A 2nd RF model was developed to predict the number of man-hours required to capture 70 ± 3% of all species, and it accounted for 37% of the variance. Our findings should serve as a guide for setting standard sampling efforts for mussel surveys in Illinois and probably other midwestern states and should provide a baseline for setting site-specific efforts. Our modeling approach is of general applicability for addressing sampling-adequacy issues in studies of any assemblage.

Quantitative estimation of insect diversity inhabitingCalotropis procerain industrial and nonindustrial areas of West Bengal, India

AbstractThis paper compares the species richnesses, Bray–Curtis similarities, species diversities, evennesses, and the results of various analyses (multivariate, logarithmic series, and lognormal distribution analyses) of insects from four orders (viz., Hemiptera, Orthoptera, aculeate Hymenoptera, and Coleoptera) inhabiting a medicinal plant,Calotropis proceraamong eight sites within industrial and nonindustrial zones in the Purba Medinipur district (erstwhile Midnapore), West Bengal, India. Both cluster analysis and principal component analysis indicate an effect of industrialization on the diversity of the four insect orders. The species community at each site exhibits an almost pure lognormal distribution. Bootstrap estimation of species diversity also points to the effect of industrialization. A comparison of the values ofxandN/Sof the logarithmic series indicates a typical relationship between the species community and its diversity. The number of unique species among the eight study sites is 6 according to jackknife estimation. Beta‐diversity analysis of the samples shows the impact of industrialization on the abundances and species richness of the insects. Altogether, 16 types of analytical procedure are applied for this purpose, and their suitabilities for this kind of data set are assessed. Disturbance, probably due to industrial emissions, has changed the compositions and structures of the insect communities out to a distance of at least 6 km from the core industrial area.

Underestimated spider diversity in a temperate beech forest

We used canopy fogging to study the high (20–26 m), intermediate (13–19 m) and low (5–6 m) strata in three European beech patches (Fagus sylvatica) in nine months (2005–2007) and estimate species richness and diversity of arboreal spiders. Eight species (10%) were previously unseen in European beech trees, and one of these is likely a new species. Moreover, two species are on the Bavarian red list. Our results revealed that the high stratum of the old-growth trees provided unique resources and possessed the greatest diversity and evenness, whereas intermediate and low strata had high similarity in respect to diversity, dominance, species, and family composition. Since the majority of beech forests consists of mature and young trees in Central Europe, and old-growth forests are rarely preserved, we recommend young beech be used in a sampling protocol for rapid biodiversity assessment. However, adding samples from the two higher strata to the lowest stratum (55 species), almost doubled the estimated species richness (102 species). This suggests that the lower stratum alone does not represent a true image of the total canopy fauna inventory in this, and likely other, beech stands. To complete this comprehensive inventory in European beeches, the Chao1 predicted that additional sampling would be needed in the highest stratum, where there is a high probability to find previously undetected species in a next survey. Our study clearly shows that neglecting the crowns of the largest, tallest trees risks underestimating the overall spider diversity in Central European forests.

Discovery of cryptic species among North American pine-feedingChionaspisscale insects (Hemiptera: Diaspididae)

Cryptic species are present in many animal groups and they may be best detected through large sample sizes collected over broad geographic ranges. Fine-scale local adaptation has been hypothesized to occur in armoured scale insects (Hemiptera: Diaspididae) and a consequence of this process may be multiple cryptic species. We estimate species diversity of pine-feeding Chionaspis scale insects across North America by inferring species boundaries using genealogical concordance across allele genealogies of two nuclear loci and one mitochondrial locus. Our ingroup sample includes 366 individual insects from 320 localities and 51 host species within the Pinaceae. We also conducted a morphological survey of all insect specimens and assigned them as either one of the two currently recognized pine-feeding species, Ch. heterophyllae, Ch. Pinifoliae, or with undescribed morphology. Using maximum likelihood allele genealogies in a majority-rule consensus to assess congruence, we conservatively detect ten species in this group. Most of these species are robust to alternative methods of genealogical inference (Bayesian inference, maximum parsimony) and a few are robust to the use of strict consensus to assess congruence. Species show both narrow and more widespread ranges where almost half of the individuals sampled belong to a single very widespread polyphagous species.

Taxonomic Structure of the Fossil Record is Shaped by Sampling Bias

Understanding biases that affect how species are partitioned into higher taxa is critical for much of paleobiology, as higher taxa are commonly used to estimate species diversity through time. We test the validity of using higher taxa as a proxy for species diversity for the first time by examining one of the best fossil records we have, that of deep-sea microfossils. Using a new, taxonomically standardized, data set of coccolithophorid species and genera recorded from 143 deep-sea drilling sites in the North Atlantic, Caribbean, and Mediterranean, we show that there is a two-stepped change in the ratio of species to genera over the last 150 myr. This change is highly unexpected and correlates strongly with changes in both the number of deep-sea sites yielding coccolithophorids that have been studied and with the number of taxonomists who have published on those sections. The same pattern is present in both structurally complex heterococcoliths and the simpler nannoliths, suggesting that increasing complexity is not the driving factor. As a stepped species-to-genus ratio exists even after subsampling to standardize either the numbers of sites or numbers of papers, both factors must be contributing substantially to the observed pattern. Although some limited biological signature from major extinction events can be recognized from changes in the species-to-genus ratio, the numbers of sites and the numbers of taxonomists combined explain some 82% of the observed variation over long periods of geological time. Such a strong correlation argues against using raw species-to-genus ratios to infer biological processes without taking sampling into account and suggests that higher taxa cannot be taken as unbiased proxies for species diversity.

Assessing microbial diversity using recent lake sediments and estimations of spatio-temporal diversity

Aim Recent papers have used large palaeolimnological datasets to reveal the biodiversity patterns of aquatic microorganisms. However, scant attention has been paid to the influence of time on these patterns. Where lake surficial sediment samples are used as integrals of diversity, the time interval of each sample varies according to differences in sediment accumulation rates. This paper aims to test the reliability of using lake surface sediments to measure and to compare microbial diversity when the potential influences of the species‐time relationships are taken into account. Location Alpine lakes in Europe. Methods We analysed microorganism (siliceous microalgae) assemblages in three European Alpine lakes using short sediment cores ( 210 Pb-dated) and annual sediment trap samples from 12 UK lakes. The same number of individuals was pooled for each sample 500 times to avoid sampling effort effects and to standardize species diversity estimation. The influence of time on the diversity score was assessed by simulating an increase of time span for surface sediment samples by cumulatively adding in successive sediment core samples (from the most recent to the oldest). We used species richness (S) and the exponential of the bias-corrected Shannon entropy index (exp(Hb-c)) to estimate diversity. Results Increasing the time interval represented by a surficial sediment sample did not affect the diversity results. The estimation of diversity was similar for cumulative and non-cumulative samples. Diversity estimation was only altered in lakes experiencing high community turnover due to strong environmental forcing during the time period spanned by the cumulative sample. Main conclusions The use of surface lake sediments is suitable for estimating the average site diversity of free-living microorganisms. Diversity is integrated in a single sample and species assemblage composition is derived from microbial communities living in distinct lake microhabitats. Species remains, accumulated in a single sample over several years of environmental variability, represent a diversity integral that captures a spatio-temporal component equivalent to the c-diversity measure.

Estimating tree species diversity across geographic scales

The relationship between number of species and area observed has been described using numerous approaches and has been discussed for more than a century. The general objectives of our study were fourfold: (1) to evaluate the behaviour of species–area curves across geographic scales, (2) to determine sample sizes necessary to produce acceptably precise estimates of tree species diversity, (3) to evaluate relationships among estimates of tree species diversity for local to large geographic scales, and (4) to determine whether the proportion of native tree species may be precisely estimated using sample sizes smaller than those necessary to estimate total tree species diversity. Such investigations are necessary to improve biodiversity monitoring at large scales. The analytical approaches included Monte Carlo bootstrap simulations and two geospatial methods and relied on a database populated with data for more than 12,000 national forest inventory plots (NFI) from 16 regional units, 13 European countries and three ecoprovinces of the United States of America (USA). Four primary results were obtained. First, tree species diversity may be precisely estimated using observations for a random subsample of 2,000–4,000 NFI plots. Second, large sample sizes are necessary to estimate tree species diversity for regional units or forest categories, except possibly for boreal forests for which the number of tree species is small. Third, estimates of the proportion of native tree species may be precisely estimated using tree species information for a random sample of approximately 30 NFI plots. Finally, our estimated species–area curves show that the curve shapes and relationships among estimates of tree species diversity at large scales clearly depend on the relative geographic location of the anchor regional unit (a European country or ecoprovince of the USA) relative to the other regional units. None of the well-known models for species–area curves adequately describes our results. The conclusion was that the uncertainties of the estimates reflect the unfavourable state of global biodiversity monitoring of species groups. The total numbers of tree species in our regional units, which cannot be adequately estimated, are small relative to other tree species-rich regions. Consequently, monitoring of tree species diversity is currently a highly uncertain enterprise at large scales.

Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences

The estimation of species diversity in fungal endophyte communities is based either on species counts or on the assignment of operational taxonomic units (OTUs). Consequently, the application of different species recognition criteria affects not only diversity estimates but also the ecological hypotheses that arise from those observations. The main objective of the study was to examine how the choice and number of genetic markers and species delimitation criteria influence biodiversity estimates. Here, we compare approaches to defining species boundaries in three dominant species complexes of tropical endophytes, specially Colletotrichum gloeosporioides agg., Pestalotiopsis microspora agg. and Trichoderma harzianum agg., from two Amazonian trees: Hevea brasiliensis and H. guianensis. Molecular tools were used to describe and compare the diversity of the different assemblages. Multilocus phylogenetic analyses [gpd, internal transcribed spacer (ITS) and tef1] and modern techniques for phylogenetic species delimitation were overlaid with ecological data to recognize putative species or OTUs. The results demonstrate that ITS alone generally underestimates the number of species predicted by other nuclear loci. These results question the use of ITS and arbitrary divergence thresholds for species delimitation.

Microbial diversity in saliva of oral squamous cell carcinoma

In the oral cavity, chronic inflammation has been observed at various stages of oral squamous cell carcinomas (OSCC). Such inflammation could result from persistent mucosal or epithelial cell colonization by microorganisms. There is increasing evidence of the involvement of oral bacteria in inflammation, warranting further studies on the association of bacteria with the progression of OSCC. The objective of this study was to evaluate the diversity and relative abundance of bacteria in the saliva of subjects with OSCC. Using 454 parallel DNA sequencing, ∼58,000 PCR amplicons that span the V4-V5 hypervariable region of rRNAs from five subjects were sequenced. Members of eight phyla (divisions) of bacteria were detected. The majority of classified sequences belonged to the phyla Firmicutes (45%) and Bacteroidetes (25%). Further, 52 different genera containing approximately 860 (16.51%) known species were identified and 1077 (67%) sequences belonging to various uncultured bacteria or unclassified groups. The species diversity estimates obtained with abundance-based coverage estimators and Chao1 were greater than published analyses of other microbial profiles from the oral cavity. Fifteen unique phylotypes were present in all three OSCC subjects.

Underestimated endemic species diversity in the dry inter‐Andean valley of the Río Marañón, northern Peru: An example from Mimosa (Leguminosae, Mimosoideae)

AbstractMolecular phylogenies which include multiple accessions of species and near complete taxon sampling can be an important tool for estimating species diversity when used in combination with traditional morphology‐based taxonomy. Here we use a densely sampled plastid gene tree for a morphologically complex group within the legume genus Mimosa (sect. Batocaulon ser. Andinae) to improve estimates of species limits and diversity in the poorly known dry inter‐Andean valley of the Río Marañón, northern Peru. Based on the plastid gene tree, Mimosa ser. Andinae, which previously comprised four species, is re‐circumscribed to include six Andean dry‐forest species from northern Peru, Ecuador and southern Colombia, including the new species, M. jaenensis, described here. A further three candidate species are identified within the section based on high levels of sequence variation among accessions. With the additional species, the Marañón valley is now known to harbour nine narrowly restricted endemic species of Mimosa, a pattern of multiple congeneric endemics mirrored in many other plant genera as well as several animal groups. Our results, in combination with other published studies, suggest that overall species diversity in the Marañón has been significantly under‐estimated. Further work is needed to identify conservation priority areas in the Marañón in order to protect its unique flora.

Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples

Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results. An average of 7,944 pyrosequences, spanning the V1 and V2 region of 16S rRNA genes, was obtained per sample. Although primer choice in barcoded pyrosequencing did not affect species richness and diversity estimates, detection of Actinobacteria strongly depended on the selected primer. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis (HITChip) correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. Quantitative PCR was employed to investigate the deviations in profiling between pyrosequencing and HITChip analysis. Since cloning and sequencing of random 16S rRNA genes from ileostomy effluent confirmed the presence of novel intestinal phylotypes detected by pyrosequencing, especially those belonging to the Veillonella group, the divergence between pyrosequencing and the HITChip is likely due to the relatively low number of available 16S rRNA gene sequences of small intestinal origin in the DNA databases that were used for HITChip probe design. Overall, this study demonstrated that equivalent biological conclusions are obtained by high-throughput profiling of microbial communities, independent of technology or primer choice.

SPECIES: AnRPackage for Species Richness Estimation

We introduce an R package <b>SPECIES</b> for species richness or diversity estimation. This package provides simple R functions to compute point and confidence interval estimates of species number from a few nonparametric and semi-parametric methods. For the methods based on nonparametric maximum likelihood estimation, the R functions are wrappers for Fortran codes for better efficiency. All functions in this package are illustrated using real data sets.

茶園におけるゴミムシ群集の多様性評価

環境保全型のチャ栽培体系がゴミムシ群集の種多様性に及ぼす影響を評価するため，ピットフォールトラップで茶園に生息するゴミムシ類を捕獲し，解析した。また，ゴミムシ類の多様性の効率的評価法を模索するため，種数および種多様度に対するピットフォールトラップの設置数と設置期間の効果を検討した。その結果，農薬散布程度の異なる栽培体系がゴミムシ群集の密度および発生種に及ぼす明確な影響は検出されず，種多様度に影響のないことが確認された。また，ゴミムシの種数に対するトラップ設置数の効果は有意であったが，種多様度に対するそれは有意でなかった。一方，設置期間は長くなるほど，種多様度が安定的な値をとることが確認された。つまり，少なくとも3個のピットフォールトラップを設置して，6ヶ月以上調査することにより，茶園のゴミムシ群集の多様度を推定することができる。

Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.

BackgroundThe demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification (“DNA barcoding”). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured.Methodology/Principal FindingsWe sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). Sørensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance.Conclusion/Significance Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and β-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.

On a Generalized Chu–Vandermonde Identity

In the present paper we introduce a generalization of the well–known Chu–Vandermonde identity. In particular, by inductive reasoning, the identity is extended to a multivariate setup in terms of the fourth Lauricella function. The main interest in such generalizations derives from the species diversity estimation and, in particular, prediction problems in Genomics and Ecology within a Bayesian nonparametric framework.

Phylogenetic relationships in the genus Astropecten Gray (Paxillosida: Astropectinidae) on a global scale: molecular evidence for morphological convergence, species-complexes and possible cryptic speciation

With over 150 described species, Astropecten Gray (Paxillosida:Astropectinidae) is one of the most species-rich genera among sea stars. This diversity is remarkable, because most species of Astropecten have a long-lived planktotrophic larval stage, which would be expected to lead to a low speciation rate. The taxonomy of this genus is complex and not well resolved, and phylogenetic relationships have only been addressed in the beginning of the last century. In order to resolve general taxonomic issues, identify speciation patterns and estimate species diversity within the genus Astropecten, we inferred a molecular phylogeny of 117 specimens of Astropecten belonging to 40 species from around the world using mitochondrial DNA (mtDNA) sequences of 12S rRNA, 16S rRNA and cytochrome oxidase subunit I (COI). We compared the resulting molecular phylogeny to a previously published morphological one by Döderlein and investigated the possibility of morphological convergence in species from different geographic regions. Finally, we also aimed at identifying potentially problematic descriptions and/or signs of cryptic speciation in Astropecten. The global molecular phylogeny exhibited three main clades, each containing specimens of the same geographic region: 1. the IndoPacific; 2. the Neotropics; and 3. the eastern Atlantic and Mediterranean. Phylogenetic inferences based on mtDNA indicate that morphological and ecological convergence has taken place in Astropecten, resulting in allopatric non-sister taxa with similar morphologies and habitat preferences. The comparison to Döderlein’s morphological phylogeny reveals congruence on the whole but many discrepancies on a local scale, indicating that meaningful morphological characters are not easily identified and categorized in Astropecten. Our results also reveal that A. polyacanthus Müller &amp; Tröschel and A. indicus Döderlein are species-complexes; cryptic speciation may have occurred within each of these morphospecies. Furthermore, several variants, previously presumed to be conspecific, exhibit genetic distances large enough to justify recognizing them as separate species.

Remotely sensed spectral heterogeneity as a proxy of species diversity: Recent advances and open challenges

Environmental heterogeneity is considered to be one of the main factors associated with biodiversity given that areas with highly heterogeneous environments can host more species due to their higher number of available niches. In this view, spatial variability extracted from remotely sensed images has been used as a proxy of species diversity, as these data provide an inexpensive means of deriving environmental information for large areas in a consistent and regular manner. The aim of this review is to provide an overview of the state of the art in the use of spectral heterogeneity for estimating species diversity. We will examine a number of issues related to this theme, dealing with: i) the main sensors used for biodiversity monitoring, ii) scale matching problems between remotely sensed and field diversity data, iii) spectral heterogeneity measurement techniques, iv) types of species taxonomic diversity measures and how they influence the relationship between spectral and species diversity, v) spectral versus genetic diversity, and vi) modeling procedures for relating spectral and species diversity. Our review suggests that remotely sensed spectral heterogeneity information provides a crucial baseline for rapid estimation or prediction of biodiversity attributes and hotspots in space and time.

Measure and mis-measure of species diversity in deep-sea chemosynthetic communities

Our knowledge of species diversity in deep-sea chemosynthetic communities has come a long way since their discovery in the late 1970s, However, their study poses serious challenges that are linked to their remoteness, the variable selectivity and effectiveness of sampling tools in different conditions, a lack of consensus on the size compartments and sieve size used in practice, and the persistent discovery of species that are previously unknown to science. Still, with increasing accessibility and new sampling tools, quantitative data are becoming both more frequent and extensive, reducing limitations in the estimation and comparison of species diversity. Here, we review the literature for common difficulties encountered in the measurement and comparison of species diversity within and among deep-sea chemosynthetic communities. We lay out recommendations for future and ongoing work that should lead to more accurate evaluations and more robust comparisons. We advocate: (1) complete transparency in the taxonomic levels used to compute reported diversity measures and public access to data tables after publication; (2) an effort to standardize size compartments and sieves used within the research community; (3) the use of families of species diversity measures that allow for differential weighting of abundant and rare species; (4) the evaluation of the completeness of inventories and the stability of all diversity measures for all groups of samples under comparison; and (5) caution in the use and interpretation of statistical tests on species diversity. Only through appropriate tools can we hope to gain the knowledge and understanding necessary for the management and protection of the often endemic fauna found in deep-sea chemosynthetic communities.

Diversity of macrobenthos in lowland streams: ecological determinants and taxonomic specificity

The present study contains the results of an investigation of the relationships between the environmental variables and the taxonomic diversity of common and important groups of benthic macrofauna: Chironomidae, Ephemeroptera, Odonata, Hirudinea and Gastropoda, collected from various types of bottom substrate in seven lowland streams of north-eastern Poland. Four metrics were used to express the diversity of the studied taxa in each sample as the examples of its four different aspects: species richness, rarity, Shannon-Weaver's diversity index and Pielou evenness index. The values of total species richness and Shannon-Weaver index were rarified by functional extrapolation with Michaelis-Menten asymptotic function chosen as a richness estimator. There are high differences in taxonomic diversity of benthic animals between the studied streams. The results of estimation of total species richness and total species diversity are mainly affected by the diversity of the taxon richest in species – larval Chironomidae and, to a lesser extent, Hirudinea. The total taxonomic diversity significantly correlates with the status of riparian vegetation and with the isolation of the sampling site, while the relationship with other environmental parameters, i.e. pollution and seasonality, is not significant. The diversity of Gastropoda and Hirudinea is significantly affected by pollution (positively), water depth and seasonality; whereas the diversity of Ephemeroptera and Chironomidae by the state of riparian vegetation, and that of Odonata by stream width and isolation of the site. The study presents and discusses reduced diversity of certain higher taxa as a result of a reduction in pollution loading to a stream with simultaneous unchanged values of the total diversity.

Metagenomics: Facts and Artifacts, and Computational Challenges

Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing (NGS) techniques.