Seasonal variations in macrobenthic taxonomic diversity and the application of taxonomic distinctness indices in Bohai Bay,northern China

Taxonomic diversity indices have a number of desirable properties as indicators in the assessment of environmental quality, and have become an important measure in biodiversity studies. Macrobenthic taxonomic variations were studied in Bohai Bay, northern China, an area under threat from rapid human development. Four seasonal cruise datasets were collected between 2006 and 2007. Environmental conditions exhibited large fluctuations due to human development; nitrogen and phosphorus were the main environmental stressors. A total of 97 macrofauna taxa were identified belonging to 88 genera, 72 families, 36 orders, 14 classes, and nine phyla. Analysis of similarity indicated that there were significant assemblage differences across sampling stations as well as seasons. Four taxonomic indices, taxonomic diversity (Δ), taxonomic distinctness (Δ*), average taxonomic distinctness (Δ⁺), and variation in taxonomic distinctness (Λ⁺) were calculated using abundance data. Among the stations and seasons, there were greater variations in both Δ and Λ⁺ than in Δ* and Δ⁺. The funnel plot of Δ⁺ could identify disturbed stations to some extent, but was not always a strong indicator of disturbance. The Δ⁺ performance was better in autumn than in spring, but could not identify a disturbed station in autumn due to a low number of species. The efficiency of taxonomic distinctness may depend on taxa or the pollution indicators. Taxonomic distinctness indices can be effective at assessing environmental degradation when correctly applied; however, they are unsuitable for directly assessing environmental quality in a new area prior to efficiency testing.     

The use of indicator taxa as representatives of communities in bioassessment

1. Sampling and processing of benthic macroinvertebrate samples is time consuming and expensive. Although a number of cost‐cutting options exist, a frequently asked question is how representative a subset of data is of the whole community, in particular in areas where habitat diversity is high (like Dutch surface water habitats). 2. Weighted averaging was used to reassign 650 samples to a typology of 40 community types, testing the representativeness of different subsets of data: (i) four different types of data (presence/absence, raw, ²log‐ and ln‐transformed abundance), (ii) three subsets of ‘indicator’ taxa (taxa with indicator weights 4–12, 7–12, and 10–12) and (iii) single taxonomic groups (n = 14) by determining the classification error. 3. ²log‐ and ln‐transformed abundances resulted in the lowest classification error, whilst the use of qualitative data resulted in a reduction of 10% of the samples assigned to their original community type compared to the use of ln‐transformed abundance data. 4. Samples from community types with a high number of unique indicator taxa had the lowest classification error, and classification error increased as similarity among community types increased. Using a subset of indicator taxa resulted in a maximum increase of the classification error of 15% when only taxa with an indicator weight 10–12 were included (error = 49.1%). 5. Use of single taxonomic groups resulted in high classification error, the lowest classification error was found using Trichoptera (68%), and was related to the frequency of the taxonomic group among samples and the indicator weights of the taxa. 6. Our findings that the use of qualitative data, subsets of indicator taxa or single taxonomic groups resulted in high classification error implies low taxonomic redundancy, and supports the use of all taxa in characterising a macroinvertebrate community, in particular in areas where habitat diversity is high.     

Macroinvertebrate drift in the upper Wye catchment,Wales

Drift samples collected at five sites in the upper catchment of the River Wye yielded 99 taxa (excluding Chironomidae and Simuliidae). Significantly fewer taxa were collected from a site on the impounded River Elan (W4) compared with nearby River Wye sites. Mean daily density of drifting macroinvertebrates ranged from 6.3 × 10^-2 to 782.9 × 10^-2m^-3, with greatest densities during the summer months, and Ephemeroptera, Coleoptera and Diptera generally comprised the greatest proportion of animals collected. Chironomids formed a considerable proportion of collections at W4 and the relative abundance of ephemeropterans, coleopterans and trichopterans was generally significantly less at W4 than at other sites. Estimates of the total numbers of invertebrates drifting past each site varied from 8.3 × 10³ to 1 373.1 × 10³day^-1. Total numbers drifting were significantly related to estimates of total benthic density and similar relationships were established for some major taxonomic groups and some species.     

Stable carbon isotope variability associated with taxonomic composition of lotic benthic algae

We examined the relationship between the δ¹³C and taxonomic composition of benthic algae collected from a riffle (fast current habitat) of a non‐shaded mountain stream, which is a tributary of the Kiso River, Japan. The benthic algal δ¹³C ranged from ?20.6 to ?14.2‰ and tended to be ¹³C‐depleted with increasing relative abundance of upright filamentous cyanobacteria and ¹³C‐enriched with increasing relative abundance of prostrate filamentous cyanobacteria. Using isotopic mass balance equations, the relative abundance of the dominant taxa, upright and prostrate filamentous cyanobacteria, small diatoms and others, explained 74% of δ¹³C variability. This study shows a case where the difference in taxonomic composition is a possible source of the isotopic variability of benthic algae, which is a mixture of taxa with distinct isotopic signatures.     

The soil food web of two beech forests (<Emphasis Type="Italic">Fagus sylvatica</Emphasis>) of contrasting humus type: stable isotope analysis of a macro- and a mesofauna-dominated community

The structure of the soil food web in two beech (Fagus sylvatica) forests, the Göttinger Wald and the Solling forest (Northern Germany), was investigated using variations in tissue ¹⁵N concentrations of animal species or taxa. The Göttinger Wald is located on a limestone plateau and characterized by mull humus with high macrofauna activity, particularly of Lumbricidae, Diplopoda and Isopoda. In contrast, the Solling forest is located on a sandstone mountain range and characterized by moder humus. The soil fauna of this forest is dominated by mesofauna, particularly by Collembola, Enchytraeidae and Oribatida. In June 1995 soil fauna was sampled using heat extraction. Three soil layers were analysed at each of the sites. ¹⁵N/¹⁴N ratios of bulk material increased strongly with soil depth in both forests. This also applied to the water-soluble fraction at the Göttinger Wald, but not at the Solling. Generally, the water-soluble fraction was more enriched in ¹⁵N than the bulk materials. For most animals studied ¹⁵N/¹⁴N ratios varied little with soil depth. In both forests soil animals could be classified either as saprophages, including microphytophages, or predators. On average, the δ¹⁵N of predatory taxa (Chilopoda, Araneida, Gamasina, Staphylinidae) exceeded that of saprophagous or microphytophagous taxa (Lumbricidae, Isopoda, Diplopoda, Collembola, Oribatida, Enchytraeidae) by 4.4 and 3.9‰ for the Göttinger Wald and the Solling, respectively. We assume that most of the saprophagous or microphytophagous taxa studied consist of primary and secondary decomposers and hypothesize that predators prey more on secondary than primary decomposers. Generally, average δ¹⁵N values differed little between saprophagous (Lumbricidae, Diplopoda, Isopoda) and microphytophagous taxa (Collembola, Oribatida). The variations in δ¹⁵N values of species within these taxa consistently exceeded the variation between them, indicating that the species of each of these taxa form a continuum from primary to secondary decomposers. Also, variations in δ¹⁵N values within predatory taxa in most cases exceeded that between taxa excluding top predators like Sorex. We conclude that using higher taxonomic units in soil food web analysis is problematic and in general not consistent with nature. Higher taxonomic units may only be useful for depicting very general trophic groupings such as predators or microbi-detritivores.     

Relationships between length and weight of freshwater macroinvertebrates in Japan

Relationships between weight (W; dry weight) and length (L; head capsule width, total body length or head carapace length) were examined in 31 Japanese freshwater macroinvertebrate taxa, using the form W = aL ^b . The relationships were expressed as data of the lowest taxonomic level and data of higher taxonomic levels. The length–weight relationships obtained in this study were similar to those obtained in North America and Europe at the lowest taxonomic level, whereas they could be different from those obtained in North America and Europe at the higher taxonomic levels. We suggest that researchers should make their own regressions for a target taxon or use the regression for the same taxon as possible lower taxonomic level in the local area.     

Calcium content of littoral Cladocera in three softwater lakes of the Canadian Shield

Aqueous calcium (Ca) concentrations are declining in softwater lakes of the Canadian Shield largely because of decades of acid deposition and afforestation following timber harvesting. Populations of pelagic cladoceran taxa with high Ca requirements, especially Daphnia spp., are declining in response to reduced aqueous Ca availability. However, the Ca content, and thus the requirements of littoral cladoceran taxa are unknown; therefore, the potential vulnerability of this major component of lake ecosystems to ongoing regional Ca decline remains uncertain. Here, we identify the body Ca concentration of nine littoral cladoceran taxa collected from three lakes in the Muskoka-Haliburton region of Ontario, Canada. Ca content differed among taxonomic groups, ranging from 3.6 mg g⁻¹ for Acroperus harpae to 23.2 mg g⁻¹ for Disparalona spp. Perhaps surprisingly, some littoral microcrustacean taxa have Ca burdens comparable to the Ca-rich daphniids. Therefore, there may be differential responses to ongoing lake water Ca declines among taxa within littoral communities as has been observed among open-water taxa, with potential ecological repercussions for near-shore food webs.     

Ectomycorrhizal fungi are shared between seedlings and adults in a monodominant Gilbertiodendron dewevrei rain forest in Cameroon

Ectomycorrhizal networks may facilitate the establishment and survival of seedlings regenerating under the canopies of tropical forests and are often invoked as a potential contributor to monodominance. We identified ectomycorrhizal fungi in a monodominant Gilbertiodendron dewevrei (Fabaceae) rain forest in Cameroon, using sporocarps and ectomycorrhizae of three age categories (seedlings, intermediate trees, and large trees) and tentatively revealed nutrient transfer through ectomycorrhizal networks by measuring spontaneous isotopic (¹³C and ¹⁵N) abundances in seedlings. Sporocarp surveys revealed fewer ectomycorrhizal fungal taxa (59 species from 1030 sporocarps) than molecular barcoding of ectomycorrhizal roots (75 operational taxonomic units from 828 ectomycorrhizae). Our observations suggest that ectomycorrhizal fungal diversity is similar to that in other mixed tropical forests and provide the first report of the Tuber‐Helvella lineage in a tropical forest. Despite some differences, all age categories of G. dewevrei had overlapping ectomycorrhizal fungal communities, with families belonging to Thelephoraceae, Russulaceae, Sebacinaceae, Boletaceae, and Clavulinaceae. Of the 49 operational taxonomic units shared by the three age categories (65.3% of the ectomycorrhizal fungal community), 19 were the most abundant on root tips of all categories (38.7% of the shared taxa), supporting the likelihood of ectomycorrhizal networks. However, we obtained no evidence for nutrient transfer from trees to seedlings. We discuss the composition of the ectomycorrhizal fungal community among the G. dewevrei age categories and the possible role of common ectomycorrhizal networks in this rain forest.     

The first results of meiobenthos study in the Cái River (Central Vietnam)

The first data on the composition and quantitative development of meiobenthos in the small tropical Cái River (Central Vietnam) at the end of the “small rainy season” (early June) have been obtained. In the community composition, 101 taxa out of 15 systematic groups have been documented. Specimens which are new for science (Acari), new for the fauna of Vietnam (Nematoda, etc.), and rare representatives of surface waters (Syncarida) are found. The largest part of taxonomic diversity is formed by Nematoda (38 taxa), Annelida (18), and Chironomidae (22). The same groups dominated in abundance. The taxonomic richness, abundance, and biomass of the community varied within 4–45 taxa, 3.8–161.9 thousand ind/m², and 0.05–2.2 g/m². In general, the type of changes of all parameters along the river profile was classical: the values increased from the upper mountain sections to the lower plain parts. The revealed pattern testifies to the important role that hydrodynamics play in the macroscale distribution of meiobenthos in the river during the period under study. The dependence that the community characteristics have on the local features of biotopes (microdistribution) is not as definite and requires an additional study of more extensive material.     

Reorganising the order Bacillales through phylogenomics

Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome-based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of eight families (and six family incertae sedis taxa) within the order Bacillales. This showed several anomalies in the current family and order level classifications including the existence of four Bacillaceae and two Paenibacillaceae “family” clades. Furthermore, the families Staphylococcaceae and Listeriaceae belong to the sister order Lactobacillales. Finally, we propose a consensus phylogenomic approach which may diminish algorithmic biases associated with single approaches and facilitate more accurate classification of a broad range of taxa at the higher taxonomic levels.     

Effects of dissolved organic matter and ultraviolet radiation on the accrual, stoichiometry and algal taxonomy of stream periphyton

1. We investigated the effects of dissolved organic matter (DOM) and ultraviolet‐B (UVB) radiation on periphyton during a 30‐day experiment in grazer‐free, outdoor artificial streams. We established high [10–12 mg carbon (C) L⁻¹] and low (3–5 mg C L⁻¹) concentrations of DOM in artificial streams exposed to or shielded from ambient UVB radiation. Periphyton was sampled weekly for ash‐free dry mass (AFDM), chlorophyll (chl) a , algal biovolume, elemental composition [C, nitrogen (N) and phosphorus (P)], and algal taxonomic composition. 2. Regardless of the UVB environment, increased DOM concentration caused greater periphyton AFDM, chl a and total C content during the experiment. Increased DOM also significantly increased periphyton C : P and N : P (but not C : N) ratios throughout the experiment. Algal taxonomic composition was strongly affected by elevated stream DOM concentrations; some algal taxa increased and some decreased in biomass and prevalence in artificial streams receiving DOM additions. UVB removal, on the other hand, did not strongly affect periphyton biomass, elemental composition or algal taxonomic composition for most of the experiment. 3. Our results show strong effects of DOM concentration but few, if any, effects of UVB radiation on periphyton biomass, elemental composition and algal taxonomic composition. The effects of DOM may have resulted from its absorption of UVA radiation, or more likely, its provision of organic C and nutrients to microbial communities. The strong effects of DOM on periphyton biomass and elemental composition indicate that they potentially play a key role in food web dynamics and ecosystem processes in forested streams.     

Replicability of physicochemistry and macroinvertebrate assemblages in stream mesocosms: implications for experimental research

1. The replicability of mesocosms is assessed in a case study of artificial streams (4 m²) flanking a lowland chalk river in southern U.K. Among‐mesocosm comparisons of physicochemistry and macroinvertebrate assemblage composition (in drift and benthos) were made during a 2‐year survey of 12 outdoor once‐through linear channels. 2. Mesocosm physicochemistry was highly replicable, with statistically significant congruence in temporal variation across the mesocosm series, low spatial variation and no significant blocking or positional effects arising from mesocosm layout. Parallel physicochemistry was attributed to the outdoor stream‐side location and short water residence times. 3. Mesocosms were colonized by 127 macroinvertebrate taxa from 15 taxonomic orders. Both benthic and drifting assemblages were comparable among mesocosms, with no significant effect of mesocosm layout. Small differences in taxonomic composition were, however, evident among particular mesocosms, with higher (e.g. Tinodes, Limnius and Elmis) or lower (e.g. Pisidium and Valvata) abundances observed for a minority (5%) of taxa. We conclude that large (4 m²) outdoor flow – through mesocosms can be replicable when located near to the source system and allowed to establish naturally.     

The use of taxonomic distinctness to assess environmental disturbance of insect communities from running water

1. Taxonomic distinctness (or average taxonomic breadth) of a sample is a measure of diversity that has the great advantage of not being sensitive to variations in sampling effort, unlike measures of species richness. It can also be tested for departures from expectation and can thus be used to determine whether a site has suffered from a genuine loss of diversity. 2. Taxonomic distinctness or delta⁺ was measured using all insect species from three datasets obtained from running water habitats: reference or least disturbed sites from channel and bank habitats on rivers from the Australian state of Victoria; test sites distributed along a water quality gradient in Victoria and sites immediately below a series of dams in Victoria and New South Wales. The last two datasets comprised sites subject to a range of obvious disturbances. 3. At reference sites delta⁺ was generally within the range of expected values (95% confidence limits) for both habitats as would be anticipated for these essentially undisturbed sites. However, 13–14% of sites fell below the lower confidence limits. Sites in river basins with less cover of natural habitat had slightly but significantly lower delta⁺ values than those with more cover and these sites contributed to this anomaly. 4. Delta⁺ was inversely correlated with water quality (r = −0.54, P = 0.002) as measured by the first axis of a PCA of water quality variables. It was also inversely correlated with individual variables, such as turbidity and total phosphorous. 5. Delta⁺ was below expectation for 18 of the 19 dam sites and at 13 of these sites delta⁺ values were below the lower confidence limit. 6. Delta⁺ was a sensitive index of diversity that generally distinguished sites suffering from environmental disturbance. Only a few previous studies of river ecosystems have used delta⁺, which did not respond consistently to disturbance because either too few taxa at species or higher taxonomic levels were available or because longitudinal changes in species composition swamped the signal from delta⁺. Neither of these problems occurred with the current datasets. 7. Delta⁺ responded more readily to disturbance than number of species, perhaps because taxonomic distinctness reflects some of the multivariate nature of community samples, whereas number of species is blind to this aspect.     

Seasonal niche differentiation among closely related marine bacteria

Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.Subject terms: Microbial ecology, Microbial ecology     

Biodiversity surrogacy: indicator taxa as predictors of total species richness in Brazilian Atlantic forest and Caatinga

The use of indicator taxa as biodiversity surrogates has received widespread attention in conservation planning, but remains a highly contentious issue. Here we assess biodiversity surrogacy in the two most important biomes of tropical northeastern Brazil, Atlantic forest and Caatinga. We examine the extent to which species richness is correlated among taxonomic groups, and assess relationships between the richness of individual groups, and combinations of groups and total species richness. We introduce a new approach to dealing with autocorrelation between focal taxon richness and total species richness, using standardized data such that each taxon is given equal weight. Our Atlantic forest data covered seven taxa (bryophytes, pteridophytes, trees, ants, euglosine bees, birds, and mammals; total of 768 species) sampled from 12 sites; in Caatinga it was four taxa (trees, spiders, beetles and ants; total of 184 species) from 25 sites. Our results showed that: (1) in nearly all cases the species richnesses of individual taxa were significantly correlated with each other; (2) the species richnesses of most individual taxa were significantly correlated with total species richness in both biomes; (3) only two taxa were required for excellent (R ² > 80%) surrogacy of total species richness in both biomes; and (4) the same two taxa (trees and ants) can provide reasonable (R ² > 60%) surrogacy for total richness in these contrasting biomes. Our findings therefore suggest that the ‘shopping basket of taxa’ required for effective biodiversity surrogacy may not only need to be very small (two taxa), but may also be very limited in composition.     

Differential dispersal rates in an intertidal meiofauna assemblage

Meiofaunal nematodes and copepods disperse passively with sediment bedload, and copepods also display active emergence and reentry behavior. Epigrowth-feeders may be the nematode feeding group most susceptible to passive transport because they live closest to the sediment surface. We used bottom traps at a nematode-dominated intertidal mudflat in Maine, USA, to test the hypotheses that (1) meiofauna taxa disperse in relative proportions different from those of the ambient community; (2) copepods have the highest relative dispersal rate (number of individuals trap⁻¹ day⁻¹ ambient individual⁻¹) and are not as tightly linked as other taxa to sediment flux; and (3) epigrowth-feeders have the highest nematode relative dispersal rate. Results supported all three hypotheses. Nematodes accounted for 95.8% of the individuals in cores, but only 38.9% of the individuals in traps. Copepods accounted for 1.5% of the individuals in cores, but 56.7% of the individuals in traps. Less common taxa also had different relative proportions in cores and traps, as did nematode feeding groups and individual species. The relative dispersal rate was far higher for copepods than for any other taxonomic group, and the absolute (number of individuals trap⁻¹ day⁻¹) and bulk (number of individuals g sediment⁻¹ trap⁻¹ day⁻¹) dispersal rates for copepods were equal to those of the 65-fold more abundant nematodes and higher than those for all other taxa. The non-selective deposit-feeders were the most abundant nematode feeding group in the ambient community, but the epigrowth-feeders as a group and as individual species had the highest absolute, relative, and bulk dispersal rates. Non-metric multidimensional scaling (MDS) using analysis of similarity (ANOSIM) and species similarity percentages (SIMPER) reflected these differences between ambient and dispersing nematode assemblages. Significant positive regression relationships between sediment weight and the number of individuals captured in traps for nematodes and some other taxa indicated that they moved passively in the bedload. Lack of a significant regression relationship for copepods suggested an active behavioral component to dispersal. Meiofauna populations in this soft-bottom community were highly dynamic, demonstrating that the role of dispersal must be included in any consideration of the ecology of soft-bottom systems at local and regional spatial scales.     

Classification of weevils as a data-driven science: leaving opinion behind

Data and explicit taxonomic ranking criteria, which minimize taxonomic change, provide a scientific approach to modern taxonomy and classification. However, traditional practices of opinion-based taxonomy (i.e., mid-20^th century evolutionary systematics), which lack explicit ranking and naming criteria, are still in practice despite phylogenetic evidence. This paper discusses a recent proposed reclassification of weevils that elevates bark and ambrosia beetles (Scolytinae and Platypodinae) to the ranks of Family. We demonstrate that the proposed reclassification 1) is not supported by an evolutionary systematic justification because the apparently unique morphology of bark and ambrosia beetles is shared with other unrelated wood-boring weevil taxa; 2) introduces obvious paraphyly in weevil classification and hence violates good practices on maintaining an economy of taxonomic change; 3) is not supported by other taxonomic naming criteria, such as time banding. We recommend the abandonment of traditional practices of an opinion-based taxonomy, especially in light of available data and resulting phylogenies.     

Power law relationships among hierarchical taxonomic categories in algae reveal a new paradox of the plankton

Aim In this continental‐scale study, the biodiversity of benthic and planktonic algal communities was explored. A recent analysis of extinct and extant tree communities by Enquist et al. (2002) showed that richness of higher taxa was a power function of species richness, invariant across temporal and spatial scales. Here we examined whether the relationships between algal richness at hierarchical taxonomic levels conform to power laws as seen for trees, and if these relationships differ between benthic and planktonic habitats. Location Streams from more than 50 major watersheds in the United States. Method A total of 3698 samples were collected from 1277 locations by the National Water‐Quality Assessment Program. Three types of stream habitat were sampled: richest targeted habitats, depositional targeted habitats, and phytoplankton. The relationships between taxonomic richness at the species level vs. all higher categories from genus to phylum across the three habitats were examined by ordinary least squares (OLS) regressions after ln‐transformation of all variables. The slopes, b, of these regressions represent the exponents of the power functions that scaled the richness of higher taxonomic levels (T) to species richness (S) in the form: T∝S^b. Results Algal richness at hierarchical taxonomic categories (genus to phylum) is a power function of species richness. The scaling exponent of this function, which captures the diversification of higher taxa, i.e. the rate of increase of their richness with the increase of species richness, is significantly different across environments. Main conclusions The differential algal diversification in the three studied habitats emphasizes the fundamental role of the environment in structuring the communities of simple organisms such as algae. The finding that the diversification of higher taxa is greater in the seemingly homogeneous planktonic environment, when compared to benthic habitats, encompassing an array of ecological niches, poses a new paradox of the plankton.     

Sensitivity analysis of different methods of coding taxonomic polymorphism: an example from higher-level bat phylogeny

New information concerning strengths and weaknesses of different methods of coding taxonomic polymorphisms suggests that results of some previous studies may have been unintentionally biased by the methods employed. In this study, we demonstrate that a form of sensitivity analysis can be used to evaluate the effects of different methods of coding taxonomic polymorphisms on the outcome of phylogenetic analyses. Our earlier analysis of higher‐level relationships of bats (Mammalia: Chiroptera) employed superspecific taxa as terminals and scored taxonomic polymorphisms using ambiguity coding. Application of other methods of dealing with polymorphisms (excluding variable characters, inferring ancestral states, majority coding) to the same data yields phylogenetic results that differ somewhat from those originally reported based on ambiguity coding. Monophyly of some clades was supported in all analyses (e.g., Microchiroptera, Rhinopomatoidea, and Nataloidea), while other groups found to be monophyletic in the original study (e.g., neotropical Nataloidea) appeared unresolved or nonmonophyletic when other methods were used to code taxonomic polymorphisms. Several groupings that were apparently refuted in the initial study (e.g., Noctilionoidea including Mystacinidae) were supported in some analyses, reducing some of the apparent incongruence between the trees in our earlier analysis (which were based principally on morphology) and other trees based on molecular data. Perceived support for various groupings (branch support, bootstrap values) were in some cases significantly affected by the methods employed. These results indicate that sensitivity analysis provides a useful tool for evaluating effects of different methods of dealing with taxonomic polymorphism in superspecific terminal taxa. Variation in results obtained with different methods suggests that it is always preferable to sample at the species level when higher‐level taxa exhibit taxonomic polymorphism, thus avoiding methodological biases associated with different methods of dealing with taxonomic polymorphisms during data analysis.     

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing

Background

The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes’ phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities.

Results

We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community.

Conclusions

The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing.