Beta diversity and taxonomic sufficiency: Do higher‐level taxa reflect heterogeneity in species composition?

Aim Virtually all studies exploring the use of taxonomic surrogates in assessing patterns of diversity have focused on clear shifts in the location of samples in multivariate space. The potential use of coarser levels of taxonomic resolution to detect patterns of variability in multivariate space, corresponding to β‐diversity in the case of presence/absence data, remains unexplored. Here we considered five ecological data sets of highly diverse marine molluscan assemblages to test the hypothesis that patterns in compositional heterogeneity would be maintained at coarser levels of taxonomic resolution. Location Italy, Norway, New Zealand and the Arctic. Methods We used multivariate dispersion based on the Jaccard resemblance measure of presence/absence data as a measure of β‐diversity to test the null hypothesis that patterns of heterogeneity in species composition for molluscs would be maintained at coarser levels of taxonomic resolution. Tests to compare β‐diversities among groups (based on distances to centroids and using 9999 permutations) were carried out separately for each of five data sets at the species level and then for each of genus, family, order and class levels. Results Differences in multivariate dispersion at the species level (heterogeneity in the identities of species) were maintained for genera and for families, but not at coarser levels of taxonomic resolution (order or class). These results were consistent across all data sets, despite differences in their spatial scale and extent, geographical location, environmental and habitat features (benthic soft sediments, rocky reefs or kelp holdfasts). Main conclusions These results suggest that either genera or families may be used as effective taxonomic surrogates to detect spatial differences in β‐diversity for molluscs. The use of surrogates can provide considerable sampling efficiencies for biodiversity assessments. We consider, however, that a degree of caution and more work is needed, as heterogeneity at the species level may not be reflected by taxonomic surrogates at smaller spatial scales.     

Comparing biological classifications of freshwater phytoplankton: a case study from South China

The use of ecological classification systems is becoming more and more widely used when studying phytoplankton. Grouping phytoplankton species into ecologically coherent groups allow to reduce redundancy and in this way, to handle a minor number of biological variables when investigating the ecological status of aquatic ecosystems. Three ecological classifications are mostly used when freshwater phytoplankton is studied: functional groups or coda, morpho-functional groups (MFGs) and morphology-based functional groups (MBFGs). In this study, these three ecological classifications were comparatively used along with two taxonomic classifications based on species and genera to analyse phytoplankton response to environmental variability in three sub-tropical Chinese reservoirs. Canonical correspondence analysis was performed to compare the five mentioned biological classifications. When ecological classifications were used, the percentage of variance explained in the biological groups?Cenvironmental variables was higher than that explained by the taxonomic classifications. Coda and MFGs showed a very high degree of overlapping, but since coda are associated to very detailed environmental templates, this method was more helpful in explaining phytoplankton variability in relation to environmental factors.     

Taxonomic Precision of Different Hypervariable Regions of 16S rRNA Gene and Annotation Methods for Functional Bacterial Groups in Biological Wastewater Treatment

High throughput sequencing of 16S rRNA gene leads us into a deeper understanding on bacterial diversity for complex environmental samples, but introduces blurring due to the relatively low taxonomic capability of short read. For wastewater treatment plant, only those functional bacterial genera categorized as nutrient remediators, bulk/foaming species, and potential pathogens are significant to biological wastewater treatment and environmental impacts. Precise taxonomic assignment of these bacteria at least at genus level is important for microbial ecological research and routine wastewater treatment monitoring. Therefore, the focus of this study was to evaluate the taxonomic precisions of different ribosomal RNA (rRNA) gene hypervariable regions generated from a mix activated sludge sample. In addition, three commonly used classification methods including RDP Classifier, BLAST-based best-hit annotation, and the lowest common ancestor annotation by MEGAN were evaluated by comparing their consistency. Under an unsupervised way, analysis of consistency among different classification methods suggests there are no hypervariable regions with good taxonomic coverage for all genera. Taxonomic assignment based on certain regions of the 16S rRNA genes, e.g. the V1&V2 regions – provide fairly consistent taxonomic assignment for a relatively wide range of genera. Hence, it is recommended to use these regions for studying functional groups in activated sludge. Moreover, the inconsistency among methods also demonstrated that a specific method might not be suitable for identification of some bacterial genera using certain 16S rRNA gene regions. As a general rule, drawing conclusions based only on one sequencing region and one classification method should be avoided due to the potential false negative results.     

Species‐level image classification with convolutional neural network enables insect identification from habitus images

1. Changes in insect biomass, abundance, and diversity are challenging to track at sufficient spatial, temporal, and taxonomic resolution. Camera traps can capture habitus images of ground‐dwelling insects. However, currently sampling involves manually detecting and identifying specimens. Here, we test whether a convolutional neural network (CNN) can classify habitus images of ground beetles to species level, and estimate how correct classification relates to body size, number of species inside genera, and species identity.
2. We created an image database of 65,841 museum specimens comprising 361 carabid beetle species from the British Isles and fine‐tuned the parameters of a pretrained CNN from a training dataset. By summing up class confidence values within genus, tribe, and subfamily and setting a confidence threshold, we trade‐off between classification accuracy, precision, and recall and taxonomic resolution.
3. The CNN classified 51.9% of 19,164 test images correctly to species level and 74.9% to genus level. Average classification recall on species level was 50.7%. Applying a threshold of 0.5 increased the average classification recall to 74.6% at the expense of taxonomic resolution. Higher top value from the output layer and larger sized species were more often classified correctly, as were images of species in genera with few species.
4. Fine‐tuning enabled us to classify images with a high mean recall for the whole test dataset to species or higher taxonomic levels, however, with high variability. This indicates that some species are more difficult to identify because of properties such as their body size or the number of related species.
5. Together, species‐level image classification of arthropods from museum collections and ecological monitoring can substantially increase the amount of occurrence data that can feasibly be collected. These tools thus provide new opportunities in understanding and predicting ecological responses to environmental change.

     

More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data

Coral taxonomy and systematics continue to be plagued by a host of problems. Due to high phenotypic variability within species, morphological approaches have often failed to recognize natural taxa, and molecular techniques have yet to be applied to many groups. Here, we summarize the levels of paraphyly found for scleractinian corals and test, based on new data, whether paraphyly is also a significant problem in Faviidae, the second-most speciose hermatypic scleractinian family. Using both DNA sequence and morphological data we find that, regardless of analysis technique (maximum parsimony, maximum likelihood and Bayesian likelihood), many conventional taxonomic groups are not monophyletic. Based on two mitochondrial markers (COI and a noncoding region) that we amplified for 81 samples representing 41 faviid species and 13 genera, five genera that are represented by more than one species are paraphyletic, as is the family Faviidae. The morphological characters currently used to identify these corals similarly fail to recover many genera. Furthermore, trees based on both data types are incongruent, and total evidence analysis does little to salvage conventional taxonomic groupings. Morphological convergence, phenotypic variability in response to the environment, and recent speciation are likely causes for these conflicts, which suggest that the present classification of corals is in need of a major overhaul. We propose more detailed studies of problematic faviid taxa using standardized morphological, mitochondrial, and nuclear genetic markers to facilitate combining of data.     

A new classification of Cyperaceae (Poales) supported by phylogenomic data

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology due to their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C₄ photosynthesis and holocentric chromosomes. Goetghebeur′s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower, and embryo characters, plus anatomical and other information. Since then, several family-level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family-wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal, and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time, we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes, and 10 subtribes, and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, and Oreobolinae.     

The cellular slime mold guild and its bacterial prey: growth rate variation at the inter- and intraspecific levels

Summary A guild of cellular slime molds (CSM) consisting of two isolates from each of five species, representing two genera, and obtained from the same square meter of forest soil exhibited extensive growth rate variation when tested on a suite of 18 bacteria isolated from the same soil. Significant growth rate differences were found at each taxonomic level examined: among species of different genera, between genera, among species within genera, and between isolates (=clones) within species. The type of bacteria used as prey determined the relative rank of the growth rates in different CSM isolates, as well as the taxonomic level at which significant differences were found. We suggest a possible reconciliation between a previous hypothesis, based on competition, and contradictory experimental work on resource partitioning in this guild of bacterial predators. Our results raise a question about the efficacy of using single genotypes to represent a species when ecological ideas are developed through laboratory investigations.     

Species diversity and ecological range in relation to ploidy level in the flora of the Pyrenees

Polyploidy is a major process in plant evolution. Surprisingly, no study has examined its role in species diversification and ecological distribution in relation to other life history traits. In this study, we examine to what extent polyploidy and the other traditionally examined biological traits (pollination mode, dispersal mode and growth form) account for ecological and taxonomic diversity in the flora of the Pyrenees. Fifty genera (in 22 angiosperm families) were classified according to ploidy level, growth form, pollination mode and dispersal mode, and 451 species and/or subspecies in these 50 genera were classified according to ploidy level and growth form. We examined the contribution of ploidy level, pollination and dispersal modes and growth form to (i) the ecological range of species and genera, i.e., the number of natural habitats (defined by a combination of ecological characteristics) where they occur, and (ii) the taxonomic diversity of the 50 genera. Ploidy level and dispersal mode had significant effects on the taxonomic diversity of the 50 genera. Taxonomic diversity, but not polyploidy per se, was significantly correlated with ecological range of genera. For individual species, diploids had a larger ecological range than polyploids, and herbaceous growth forms had wider ecological distributions than other growth forms. Our results indicate that polyploidisation may be a source of ecological diversification of genera, not by increasing the ecological range of particular polyploid species compared to diploids, but rather by creating taxonomic diversity that leads in some genera to a diversification of the habitats occupied by different ploidy levels. This observation is consistent with previous observations of ecological divergence of chromosomal races in some species in the Alps and in the Pyrenees. As found in other studies, species diversification in the studied flora appears to be greatly influenced by the occurrence of multiple dispersal modes, while ecological range of species or subspecies is significantly increased by the presence of herbaceous species.     

The effect of taxonomic resolution on the assessment of ecological water quality classes

Within the ecological assessment of running waters based on benthic macroinvertebrates different levels of taxonomic resolution (species, genus, family and higher) are in use. Although assessment systems are often developed with detailed data on species level, water managers and other end-users could like to use data on higher taxonomic levels to assess the ecological quality of a water body because of limited human or money resources. The question that arises is, if an assessment system built with species level data is also applicable using data with a higher taxonomic resolution. Within the AQEM project a multimetric assessment system was developed to evaluate the ecological quality classes (from bad (1) to high (5) ecological quality) of different stream types throughout Europe. The present study focuses on the question whether the resulting water quality class changes using the AQEM Assessment Software (AAS) with different taxonomic resolutions and if yes, how large the deviations of ecological quality classes from the original classes are and if the deviations are unidirectional. For analyses data from four Austrian and two Dutch stream types were used. It is demonstrated that the assignment of a site to an ecological quality class may change if different taxonomic levels are used. Deviations in both directions (higher/lower ecological quality class) were observed. In most cases the divergence was only one ecological quality class, but also larger deviations occasionally occurred. The causes of changes in the assessment were investigated by separately looking into the underlying metrics of the multimetric system. Some of the evaluated metrics rely on autecological information on species level and are simply not applicable on higher taxonomic levels. Other metrics worked on higher taxonomic levels as well and showed more or less good distinctions between ecological quality classes. It is concluded that the AQEM Assessment Software is not applicable if data on higher taxonomic levels are used. As the deviations were not unidirectional and ranged from one to three ecological quality classes, it is not possible to include a correction factor for using the software with higher taxonomic resolution data.     

Influence of taxonomic and numerical resolution on the analysis of temporal changes in phytoplankton communities

From December 2003 to November 2005, we analyzed the phytoplankton community of four streams located in Central Brazil (Goiás State) to evaluate if the temporal changes in phytoplankton community structure were dependent on the taxonomic/numerical resolution used to represent the data. Classification based on functional criteria was also contrasted with taxonomic classification to assess whether these classification schemes produce different ordination patterns. Procrustean analyses indicated that ordination patterns generated with data based on the presence or absence of genera correlated significantly with the patterns generated by species density. Temporal trajectories of scores derived from functional groups significantly matched those derived from analyses based on quantitative data (density or biovolume) for genus or family. In general, the results indicated that some simplifications are justifiable, mainly when one takes into account the need for uninterrupted biomonitoring programs over large spatial scales in a continent-sized country with increasing environmental problems and with a relative paucity of scientists.     

The influence of species pools and local processes on the community structure: a test case with woody plant communities in China's mountains

Understanding how patterns of biodiversity vary among taxonomic levels can provide insights into the mechanisms that regulate the assembly of ecological communities. In this study, we examined the scale and environmental dependence of the relationship between number of species and number of genera/families in woody plant communities to investigate the influences of species pool and local ecological processes on the taxonomic structures of local communities. The data we used are based on a large number of forest plots collected across the eastern part of China and the globe. The results showed that the ratio of the number of genera/families:species and the taxonomic exponents, i.e. the exponents of the genus/family–species relationship, were generally lower than null expectations based on the regional species pool, suggesting that abiotic filtering (e.g. environmental filtering and dispersal limitation) is more important than interspecific competition in shaping local communities. The extent of species pool and the area sampled for local communities both influenced our ability to infer whether local ecological processes were important. In particular, the deviation of the taxonomic ratios and exponents between empirical and null patterns increased as the extent of species pool increased, and the taxonomic exponents declined as area of the local community increased, due partly to the reduced effect of interspecific competition. We conclude that regional species pools and local processes both influenced the taxonomic structure of local woody plant communities, but their effects vary substantially among spatial scales.     

Genomic relations among two non-mangrove and nine mangrove species of Indian Rhizophoraceae

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to study the genomic relationship among 11 members of Indian Rhizophoraceae represented by nine true mangroves and two non-mangrove species. The AFLP and RAPD bands were scored and analyzed for genetic similarities and cluster analysis was done which separated the 11 species studied into two main groups, the true mangroves and the non-mangroves. The polymorphism observed for these markers showed a high degree of genetic diversity among the constituent taxa of the family. The phylogenetic relationship inferred from molecular marker systems supported the traditional taxonomic classification of the family Rhizophoraceae based on morphological characters at the levels of tribe, phylogeny and delimitation of genera and species, except the intra-generic classification of the genus Bruguiera and the placement of Rhizophora in the family Rhizophoraceae.     

木灵藓科分类与系统学研究：历史、问题和展望

木灵藓科(Orthotrichaceae)是藓类植物中的第3大科。该科不仅种类多, 生态类型特殊, 而且是世界公认的多样化程度高、分类难度大、系统关系复杂的类群。当代木灵藓科植物分类系统学研究主要集中在该科的地区志编写和专属分类修订。目前, 除了热带美洲、热带非洲的变齿藓属(Zygodon)和火藓属(Schlotheimia)部分类群外, 木灵藓科主要类群的分类修订工作已基本完成, 但是有关亚科和属的划分和地位以及各属之间的关系等方面仍存在众多争议。木灵藓科分支系统学研究也不够系统全面, 有的仅应用了单个基因片段, 或者只涉及少数类群。因此, 需要基于更多的分子和形态学性状, 进一步开展世界木灵藓科植物的系统发育研究, 建立一个更趋自然的木灵藓科分类系统。     

Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois

The anuran tribe Paini, family Dicroglossidae, is known in this group only from Asia. The phylogenetic relationships and often the taxonomic recognition of species are controversial. In order to stabilize the classification, we used approximately 2100 bp of nuclear (rhodopsin, tyrosinase) and mitochondrial (12S, 16S rRNA) DNA sequence data to infer the phylogenetic relationships of these frogs. Phylogenetic trees reconstructed using Bayesian inference and maximum parsimony methods supported a monophyletic tribe Paini. Two distinct groups (I,II) were recovered with the mtDNA alone and the total concatenated data (mtDNA+nuDNA). The recognition of two genera, Quasipaa and Nanorana, was supported. Group I, Quasipaa, is widespread east of the Hengduan Mountain Ranges and consists of taxa from relatively low elevations in southern China, Vietnam and Laos. Group II, Nanorana, contains a mix of species occurring from high to low elevation predominantly in the Qinghai-Tibetan Plateau and Hengduan Mountain Ranges. The occurrence of frogs at high elevations appears to be a derived ecological condition. The composition of some major species groups based on morphological characteristics strongly conflicts with the molecular analysis. Some possible cryptic species are indicated by the molecular analyses. The incorporation of genetic data from type localities helped to resolve some of the taxonomic problems, although further combined analyses of morphological data from type specimens are required. The two nuDNA gene segments proved to be very informative for resolving higher phylogenetic relationships and more nuclear data should be explored to be more confident in the relationships.     

梧桐科分类学研究评述

梧桐科(Sterculiaceae)是锦葵目中的一个多型科,主要分布于热带和亚热带地区,只有少数种可分布到温带地区。由于该科植物的形态特征较为多样化,至今对于它的范围和所包含的属种数目在各国学者间仍没有达成共识。该文从梧桐科的分类地位和系统关系、属的分类地位和亲缘关系以及分类学新特征在梧桐科分类中的应用3个方面入手,分析了梧桐科分类学研究的历史、现状和存在的问题,特别是把来自分子资料的研究结果与传统分类进行了比较分析,试图为梧桐科的分类学研究提供更多的帮助。     

Which molecular markers for assessing which taxonomic level? The case study of the mite family Phytoseiidae (Acari: Mesostigmata)

The use of molecular markers for resolving systematics issues has improved our knowledge of life history. However, for the taxa studied herein—the predatory mite family Phytoseiidae—molecular phylogeny is impeded by a lack of suitable markers for deeper taxonomic levels. This study aims (i) to establish DNA amplification protocols for molecular markers known to resolve supraspecific nodes in other taxa, (ii) to determine their individual performance in assessing the clustering of species, genera, tribes and subfamilies, and (iii) to characterize the additional information provided when markers are concatenated. A new phylogenetic index is proposed based on ecological concepts, considering trees as a community of nodes. New and efficient protocols for DNA amplification of six molecular markers are provided. The concatenated tree globally provides more robust and reliable information, especially for deeper nodes. However, for assessing species identification and within‐genera phylogenies, the combined use of six markers does not seem necessary, underlining the need to resize experiments depending on their taxonomic objectives. Finally, this study lays the methodological foundations with which to test the present Phytoseiidae classification as the first phylogeny obtained shows incongruence with the present morphological classification.     

Reconciling taxonomy and phylogeny in the bristleworm family Eunicidae (polychaete,Annelida)

Eunicid annelids inhabit diverse marine habitats worldwide, have ecological and economic importance and have been pictured in the news as giant predator worms. They compose a traditional stable taxon recently supported as monophyletic but characterized by plesiomorphies. Most genera within the family have been recovered as paraphyletic in previous studies. We present a phylogenetic hypothesis for eunicid based on molecular (COI, 16S rDNA, 18S rDNA) and morphological data (213 characters), including an explicit attempt to account for serial homology. Eunicidae as well as monophyletic genera Marphysa sensu stricto and Lysidice is redefined based on synapomorphies. Nematonereis is synonymized to Lysidice. Leodice and Nicidion are resurrected to name monophyletic groups including species previously included in Eunice and Marphysa sensu lato. Traditional diagnostic characters such as the absence/presence of peristomial cirri, lateral antennae and branchiae are homoplasies and not informative at the generic level. Different coding of traditional characters (i.e. articulation of prostomial appendages) and novel characters of prostomial features and regionalization of the body support the monophyly of the family and genera level clades. Thus, the phylogenetic hypothesis presented here and the evolution of characters provided background information for taxonomic changes yielding evolutionary meaningful classification and diagnoses for the family and genera.     

Whole genome-based assessment of the taxonomic position of the arthropod pathogenic bacterium Rickettsiella grylli

Rickettsiella grylli is an intracellular bacterial pathogen of aquatic and terrestrial arthropods. Previous determination of its 16S rRNA-encoding sequence has led to the taxonomic classification of the genus Rickettsiella in the class Gammaproteobacteria, order Legionellales, family Coxiellaceae, i.e. in close vicinity to vertebrate pathogenic bacteria of the genera Coxiella and Legionella. Here we use the additional information available from the recently published first whole genome sequence from this genus to evaluate critically the taxonomic classification of R. grylli beyond the 16S rRNA gene level. Using phylogenetic reconstruction, together with significance testing on a data basis defined by a core set of 211 previously identified families of protein-encoding genes, together with a reanalysis of 16S rRNA gene data, the present study firmly corroborates the assignment of this species to both the class Gammaproteobacteria and the order Legionellales. However, the results obtained from concatenated and single protein, single protein-encoding gene, and 16S rRNA gene data demonstrate a similar phylogenetic distance of R. grylli to both the Coxiellaceae and the Legionellaceae and are, therefore, inconsistent with its current family-level classification. Consequently, a respective reorganization of the order Legionellales is proposed.