Taxonomic Ambiguity Research Articles

Distribution and (palaeo)ecological affinities of the main Spiniferites taxa in the mid-high latitudes of the Northern Hemisphere

abstractIn marine sediments of late Cenozoic age, Spiniferites is a very common genus of dinoflagellate cysts (dinocysts). Despite some taxonomical ambiguities due to large range of morphological variations within given species and convergent morphologies between different species, the establishment of an operational taxonomy permitted to develop a standardized modern database of dinocysts for the mid-high latitudes of the Northern Hemisphere. In the database that includes 1490 surface sediment samples, Spiniferites mirabilis-hyperacanthus, Spiniferites ramosus and Spiniferites elongatus were counted in addition to Spiniferites belerius, Spiniferites bentorii, Spiniferites bulloideus, Spiniferites delicatus, Spiniferites lazus and Spiniferites membranaceus. Among these taxa, Spiniferites mirabilis-hyperacanthus, Spiniferites ramosus, and Spiniferites elongatus are easy to identify and are particularly common. Spiniferites bentorii and Spiniferites delicatus also are morphologically distinct and occur in relatively high percentages in many samples. Spiniferites lazus and Spiniferites membranaceus also bear distinctive features, but occur only in a few samples. The identification of other taxa (Spiniferites belerius, Spiniferites bulloideus, notably) may be equivocal and their reported distribution has to be used with caution. The spatial distribution of Spiniferites species, with emphasis on the five most common taxa, is documented here with reference to hydrography (salinity and temperature in winter and summer, sea ice cover), primary productivity and geographical setting (bathymetry, distance to the coastline). The results demonstrate distinct ecological affinities for Spiniferites elongatus, which has an Arctic-subarctic distribution and appears abundant in low productivity environments characterized by winter sea ice and large temperature contrast between winter and summer. Spiniferites mirabilis-hyperacanthus, which occurs in warm temperate water sites, is more abundant in high salinity environments. It shares its environmental domain with Spiniferites bentorii, which appears to have a narrower distribution towards the warm and high salinity end of the Spiniferites mirabilis-hyperacanthus distribution. In contrast, Spiniferites delicatus, which occurs in warm-temperate to tropical environments, shows preference for relatively low salinity and low seasonal contrasts of temperature. Spiniferites ramosus exhibits a particularly wide distribution that overlaps both cold and warm Spiniferites taxa. Its cosmopolitan occurrence and its long-ranging biostratigraphical distribution suggest a high plasticity of the species and/or co-occurrence of several cryptic species. Hence, whereas Spiniferites elongatus and Spiniferites mirabilis-hyperacanthus are useful palaeoecological indicators despite their large morphological variability, Spiniferites ramosus is a taxon with an unconstrained ecological significance.

Resolving taxonomic ambiguities: Effects on rarity, projected richness, and indices in macroinvertebrate datasets

Biodiversity information is an important basis for ecological research and environmental assessment, and can be impacted by choices made in the manipulation and analysis of taxonomic data. Such choices include methods for resolving multiple redundant levels of taxonomic resolution, as typically arise with morphological identification of damaged or immature aquatic macro-invertebrates. In particular, the effects of these processing choices on number of rare taxa are poorly understood yet potentially significant to the estimation of projected taxa richness and related evaluations such as biodiversity conservation value and survey sufficiency. Using aquatic macroinvertebrate data collected for two nearshore areas of Lake Superior, we determined how multiple methods of resolving taxonomic redundancies influence two commonly-used estimates of projected richness, Chao1 and Chao2, which hinge on the ratio of taxa that are singletons to doubletons (i.e., just one versus two individuals found) or uniques versus duplicates (i.e., just one versus two occurrences). We also determined how choice of ambiguous taxa method, including some modified specifically to retain rare taxa and others taken from the literature, influenced effort to reach 95% of projected richness, site-level richness and abundance, and representative invertebrate IBI scores. We found that Chao1 was more sensitive to method choice than Chao2, because singleton and doubleton status was more frequently affected when taxa were deleted, merged, or re-assigned in the process of resolving taxonomic redundancies than was unique and duplicate status. Methods that eliminated redundant taxa at the site scale but not the study-area scale tended to overinflate study area and projected richness, and resulted in a significant loss of abundance. The method that aggregated or deleted redundant taxa depending on abundance resulted in a decrease in site and study area richness, abundance, and an underestimation of projected richness. Methods which re-assigned parents to common children retained a majority of richness and abundance information and a more realistic estimate of projected taxa richness; however, the identity of poorly-identified parents was imputed. All methods resulted in little effect to typical IBI scores. Overall, no one method is fully capable of removing spurious richness at the study-area scale while preserving all taxa occurrence, abundance and rarity patterns. Therefore, the most appropriate method for making comparisons among sites may be different than the most appropriate method for comparing among surveys or among study areas, or if a goal is to estimate projected taxa richness or retain rare taxa information.

Redescription of the Amazonian tiny tree toad Amazophrynella minuta (Melin, 1941) (Anura: Bufonidae) from its type locality.

The description of Amazophrynella minuta was published in 1941 by the Swedish naturalist Douglas Melin based on material from Taracuá (Amazonas state, Brazil). This description was very brief and based on the morphology of few specimens with diagnostic characters and color variation not well defined. Moreover, the type series is currently in poor state of conservation. Consequently, taxonomic ambiguity surrounds the nominal taxon A. minuta, which hampers the description of many unnamed congeneric species. Herein, we redescribe A. minuta based on recently collected specimens from the type locality, designate a lectotype, formulate a new diagnosis, provide patterns of morphological variation, measurements and body proportions.

The toad fly Lucilia bufonivora: its evolutionary status and molecular identification.

The blow fly genus Lucilia is composed largely of saprophages and facultative myasis agents, including the economically important species Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae) and Lucilia sericata (Meigen). Only one species is generally recognized as an obligate agent of myiasis, Lucilia bufonivora Moniez, and this is an obligate parasite of toads. Lucilia silvarum (Meigen), a sister species, behaves mainly as a carrion breeder; however, it has also been reported as a facultative parasite of amphibians. Morphologically, these species are almost identical, and historically this has led to misidentification, taxonomic ambiguity and a paucity of studies of L. bufonivora. In this study, dipterous larvae were analysed from toad myiasis cases from the U.K., The Netherlands and Switzerland, together with adult specimens of fly species implicated in amphibian parasitism: L. bufonivora, L. silvarum and Lucilia elongata Shannon (from North America). Partial sequences of two genes, cox1 and ef1α, were amplified. Seven additional blow fly species were analysed as outgroups. Bayesian inference trees of cox1, ef1α and a combined-gene dataset were constructed. All larvae isolated from toads were identified as L. bufonivora and no specimens of L. silvarum were implicated in amphibian myiasis. This study confirms L. silvarum and L. bufonivora as distinct sister species and provides unambiguous molecular identification of L. bufonivora.

Molecular identification and phylogenetic assessment of species under genus Parapenaeopsis Alcock, 1901, from Indian waters

Genus Parapenaeopsis constitute an important fishery resource in Indian waters. Parapenaeopsis stylifera, being morphologically very similar to Parapenaeopsis coromandelica, mainly differentiated using telsonic armature and it is subject of controversy regarding the number of armature for the species. The present study was aimed to resolve the taxonomic ambiguity between P. stylifera and P. coromandelica and to study phylogenetic relationship among five species under the genus Parapenaeopsis using partial sequences of mitochondrial 16S ribosomal DNA (rDNA) and cytochrome c oxidase subunit I (COI) genes. Sequence analysis revealed an average genetic divergence value ranging from 7.65 to 20.3% for COI gene and 2.4 to 12.0% for 16S rDNA gene between five species under study. The result shows that P. stylifera and P. coromandelica Alcock, 1906 are genetically a distinct species with average divergence value of 7.6% based on COI sequence and 2.4% based on the 16S rDNA. However, systematic relationship between the P. stylifera and P. coromandelica were closer than other species, thus formed separate clade in phylogenetic tree. The species specific molecular signatures developed in the present study will be helpful in effective fisheries management of the species in Indian waters.

Tracing Genomic Divergence of Vibrio Bacteria in the Harveyi Clade.

The mechanism of bacterial speciation remains a topic of tremendous interest. To understand the ecological and evolutionary mechanisms of speciation in Vibrio bacteria, we analyzed the genomic dissimilarities between three closely related species in the so-called Harveyi clade of the genus Vibrio, V. campbellii, V. jasicida, and V. hyugaensis The analysis focused on strains isolated from diverse geographic locations over a long period of time. The results of phylogenetic analyses and calculations of average nucleotide identity (ANI) supported the classification of V. jasicida and V. hyugaensis into two species. These analyses also identified two well-supported clades in V. campbellii; however, strains from both clades were classified as members of the same species. Comparative analyses of the complete genome sequences of representative strains from the three species identified higher syntenic coverage between genomes of V. jasicida and V. hyugaensis than that between the genomes from the two V. campbellii clades. The results from comparative analyses of gene content between bacteria from the three species did not support the hypothesis that gene gain and/or loss contributed to their speciation. We also did not find support for the hypothesis that ecological diversification toward associations with marine animals contributed to the speciation of V. jasicida and V. hyugaensis Overall, based on the results obtained in this study, we propose that speciation in Harveyi clade species is a result of stochastic diversification of local populations, which was influenced by multiple evolutionary processes, followed by extinction events.IMPORTANCE To investigate the mechanisms underlying speciation in the genus Vibrio, we provided a well-assembled reference of genomes and performed systematic genomic comparisons among three evolutionarily closely related species. We resolved taxonomic ambiguities and identified genomic features separating the three species. Based on the study results, we propose a hypothesis explaining how species in the Harveyi clade of Vibrio bacteria diversified.

Molecular and morphological evidences resolve taxonomic ambiguity between Systomus sarana sarana (Hamilton, 1822) and S. sarana subnasutus (Valenciennes) and suggest elevating them into distinct species

Taxonomic ambiguity exists in genus Systomus and recently many new species were described under this genus. Systomus sarana subnasutus is considered a valid subspecies of S. sarana sarana although revisions have been done by some researchers. We employed a combination of morpho-meristics and molecular tools (Cytochrome c oxidase I, 16S and Cytochrome b genes of mitochondrial genome) to resolve the two species. Three morpho-meristic characters, head length/maxillary barbel length (HL/MxBL), Lateral Line Scales (LLSs) as well as two truss-based characters, had discernible variation between the two taxa. The sequence analysis (2353 nucleotides) depicted a separate clad of S. sarana subnasutus with high bootstrap support. The findings from combined use of morphology, meristics and mitogenes were concordant. The corroborative results suggest the possibility of two different species. The results suggest to adopt suitable management measures, accordingly.

Leaf cuticle and wax ultrastructure of genus Alnus Mill. in Hyrcanian forests of Iran

The genus Alnus had three taxa in the old floral resources of Iran. Recently, five new taxa were added to the flora based on morphological studies. Individual samples were collected from 25 sites throughout three provinces covering Hyrcanian forests of Iran and classified into the eight mentioned taxa and then prepared for micro-morphological studies. Four groups of taxa including A. subcordata var. subcordata, A. subcordata var. villosa, A. orientalis, and A. glutinosa subsp. antitaurica had a specific structure. Similar structure was also found between two new species of A. djavanshirii and A. dolichocarpa, which were distinguished from the other groups. Simple trichomes with variation in size and density were observed among the taxa. Alnus subcordata var. villosa and A. glutinosa subsp. antitaurica had the densest trichomes on dorsal and ventral leaf surfaces. The results of this study show the suitability of ultrastructure features as a micro-morphological marker for solving the taxonomical ambiguities of the genus Alnus in Hyrcanian forests.

Oak morphological traits: Between taxa and environmental variability

The seven oak species present in Lebanon show taxonomic ambiguity partly due to their great morphological variability among and within species. Very few investigations were conducted on oaks in Lebanon despite the presence of endemic species, and none tried to discriminate these according to their morphology, nor to determine subspecies or identify eventual hybrids. In this study 1328 leaves and 550 fruits were collected covering the whole range of oak species over the Lebanese territory; 24 leaf and 6 fruit traits were recorded and analyzed in order to differentiate among species, to define missing gaps for certain subspecies and to discriminate eventual hybrids and their possible parents. Environmental conditions were attributed in each sampling location to study the effect of selected environmental factors on leaf traits. PCA results showed that several leaf and fruit traits differ significantly among species, and that species leaf characteristics override the environmental influence. The interval between central nerve and apical leaf nerve, interval between apical and basal lobes, scale length and cupule diameter are the main contributors to differentiation among taxa. Oak species were grouped according to the 3 subgenus sections and species and subspecies were discriminated mainly according to fruit traits variance. Three potential hybrids were identified, with intermediate morphology or closer to one of their parents. Variation of morphological traits were discerned according to biogeographical gradients, and varied from one species to another.

Resolving taxonomic ambiguity and cryptic speciation of Hypotrigona species through morphometrics and DNA barcoding

Stingless bees are important pollinators of cultivated and wild plants, contributing significantly to biodiversity and food security. Conserving pollinator plant interactions is essential to secure these ecosystems services. The use of morphological features in the identification of stingless bees in the genus Hypotrigona is extremely difficult, due to many similarities among species resulting in taxonomic ambiguity. Here, we apply both traditional morphometrics and DNA barcoding as complementary tools for the identification of three Hypotrigona species from Kenya: Hypotrigona gribodoi, H. ruspolii and H. araujoi. Our results show that morphometrics separates H. gribodoi and H. ruspolii from H. araujoi; however there is an overlap between H. gribodoi and H. ruspolii. On the other hand, DNA barcoding separates the three species. There was lower genetic distance between H. araujoi and H. gribodoi from Kakamega (1.4%) than between H. gribodoi collected from Kakamega and H. gribodoi from Mwingi (4.3%). The high genetic distance or intraspecific distance within H. gribodoi strongly suggests cryptic speciation within this species, and that the H. gribodoi collected from Mwingi is a putative new species. Thus the use of morphometrics and molecular taxonomic approaches (DNA barcoding) provide a convenient, robust and reliable way to identify Hypotrigona species. It also indicates the need for a thorough revision of H. gribodoi species.

Population status of the Antarctic shag Phalacrocorax (atriceps) bransfieldensis

AbstractAntarctic shags Phalacrocorax (atriceps) bransfieldensis are the southernmost cormorants in the world and assessment of their conservation status has been complicated by the logistical challenges of obtaining regular estimates of population size, as well as by taxonomic ambiguity of the blue-eyed shag complex. The available information on the taxonomy, distribution and population size of Antarctic shags are reviewed and a refined estimate of the global population is presented: 11 366 breeding pairs, plus an additional 1984 pairs of uncertain taxonomic status in the South Orkney Islands. This analysis suggests a possible spatial shift in the distribution of Antarctic shags similar to that reported for other Antarctic seabirds, which probably reflects a gradient in environmental changes along the western Antarctic Peninsula. This review should aid future conservation and management assessments.

Unmasking a cryptic ethnotaxon: a case study on the identity of Dermonema virens (Nemaliales, Rhodophyta) in the Philippines

Indigenous knowledge on seaweed utilisation in the Philippines is common; with the coastal natives of the country’s northern region regarded as the most knowledgeable. Dependence on use of vernacular seaweed names valorises traditional wisdom, however, this is prone to taxonomic ambiguities. Such is the case for cryptic seaweed ethnotaxa whose accurate taxonomic recognition largely falls short. Known in the northern Philippines as an edible seaweed, the taxonomy of Salingongo or Kaññungu remains ambiguous. Molecular analysis based on plastid rbcL gene sequences revealed the identity of Salingongo/Kaññungu as Dermonema virens. Due to lack of any available mitochondrial DNA sequences for D. virens in GenBank, the COI-5P and cox2-3 spacer sequences generated from this study did not permit species recognition. The newly sequenced mtDNA accessions therefore served, otherwise, as the database representing the first mtDNA sequence reference for D. virens. The use of D. virens as an edible seaweed in the Philippines further reinforces the extensive overlap of traditional knowledge with regard to seaweed utilisation between the indigenous people from Taiwan and the northern Philippines. The case study presented here underpins the utility of molecular analysis, along with morphological evaluation, as a key combinatory tool for unmasking the diversity of seaweed ethnotaxa.

The complete mitochondrial genome and phylogeny of Indian oil sardine, Sardinella longiceps and Goldstripe Sardinella, Sardinella gibbosa from the Indian Ocean

The Indian oil Sardine, Sardinella longiceps and Goldstripe Sardinella, Sardinella gibbosa are the two commercially important, small pelagic fishes from Indian waters belonging to the family Clupeidae. Characterization of the complete mitogenome is very helpful in resolving taxonomic ambiguities and hence we characterized the complete mitogenome of S. longiceps and S. gibbosa from Indian waters. The assembled mitogenomes of S. longiceps and S. gibbosa are 16,613 and 16658 bp circles respectively, contained the 37 mitochondrial structural genes (2 rRNA, 22 tRNA, 13 protein-coding genes) with the gene order identical to that of typical vertebrates. In the phylogenetic tree, S. longiceps and S. gibbosa clustered with species belonging to the family Clupeidae. This study is the first report of the complete mitogenome of two commercially important clupeids from Indian waters which form the baseline for further studies on molecular systematics, population genetics, historic demography, adaptive variation and conservation of these species.

Peptide Nucleic Acid Based Molecular Authentication for Identification of Four Medicinal Paeonia Species Using Melting Array Analysis of the Internal Transcribed Spacer 2 Region.

Accurate taxonomic identification of plant materials in herbal medicines is important for product quality control. The genus Paeonia (Saxifragales) is the source of the herbal preparations Paeoniae Radix (Paeoniae Radix Alba and Paeoniae Radix Rubra) and Moutan Radicis Cotex. However, confusion has arisen regarding their contents due to linguistic and taxonomic ambiguities, similar morphologies and different definitions of Paeoniae Radix in the Korean and Chinese national pharmacopoeias, leading to the distribution of adulterated products. To develop a method for identifying the four Paeonia species used in these medicines, three fluorescently-labeled peptide nucleic acid (PNA) probes were designed against ITS2 sequences containing single nucleotide polymorphisms (SNPs) and used in a real-time PCR melting curve assay. Each of the four Paeonia species was accurately identified using this analysis. The accuracy and analytical stability of the PNA melting curve assay was confirmed using commercially available samples of the four Paeonia species. This assay is a reliable genetic tool to distinguish between different Paeonia-derived herbal medicines and identify the botanical origins of Paeoniae Radix and Moutan Radicis Cortex. This technique may also contribute to quality control and standardization of herbal medicines by providing a reliable authentication tool and preventing the distribution of inauthentic adulterants.

Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia

Abdullah ML, Nor SAM, Naim DMd. 2017. Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia. Biodiversitas 18: 1358-1366. The genus Ariidae contains many valuable fish species threatened by overfishing, but knowledge on distribution and threats is still limited due to taxonomic ambiguities. The aim of this study was to apply DNA barcoding techniques to establish a resource of DNA for identification of Ariidae species in Malaysia. A 621 bp of mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to resolve phylogenetic relationships and molecular taxonomy of eight presumed Malaysian Ariid species. We found the monophyly of most species was well established with a mean Kimura-2 parameter (K2P) interspecies distance of 9.6% except for two species, Arius venosus, and Nemapteryx caelata that have very low interspecies genetic distance. The BLAST result shows only two species matched the presumably eight identified fish species. Such discrepancies could arise as a result of misidentifications or errors in GenBank database input, hybridization or incomplete lineage sorting. We suggest the use of DNA barcoding is integrated into the workflow during taxonomic studies as it could significantly increase knowledge about species distributions.

Validation of DNA barcoding markers in common Mucuna species of India for taxonomy and pharmacognosy applications

Members of genus Mucuna are economically important due to their pharmaceutical and nutritional properties. The genus in India is represented by 10 species including perennial and annual life form. The genus represents considerable taxonomical ambiguities which is a major challenge in breeding and authentication purposes for taxonomy and pharmacognosy applications. Here we report efficacy of the DNA barcodes viz. a nuclear (nrITS2) and three chloroplast (matK, rbcl and trnH-psbA) regions in understanding the phylogenetic relationships among the four common species of Mucuna in India. Comparative analysis on the species discriminatory ability of these four genes was done on a group of 46 accessions of Mucuna representing 4 species. We found nrITS2 was effective in resolving all species with a mean intraspecific distance of 0.006 and mean interspecific distance of 0.104. Molecular investigations of the all the four regions revealed M. bracteata as the immediate perennial ancestor of annual M. pruriens. It is also observed in the present study none of the four barcode markers were unable to distinctly resolve two botanical varieties of M. pruriens viz., var. pruriens and var. utilis. Based on these outcomes we propose nrITS2 could be a suitable DNA barcode to resolve taxonomic boundaries of closely related Mucuna species, which share close phenotypic features and could also be used to authenticate the ingredients in the raw Mucuna products used in herbal preparations.

New combinations in Sino–Himalayan genusShivparvatia(Caryophyllaceae)

Three new combinations under the genus Shivparvatia are proposed here to solve taxonomic ambiguity in the genus Arenaria sensu lato. The species Arenaria melandryiformis, Arenaria monantha and Arenaria melandryoides were previously transferred to the genus Odontostemma. The present work is aimed to solve this ambiguity.

Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

Cyanobacteria, the primordial oxygenic photosynthetic prokaryotes encompass a wide spectrum of morphologies and ecologies. The diversity of twelve marine unicellular cyanobacteria isolated from different marine habitats was analyzed morphologically. The evolutionary relationship among the investigated strains was examined by phylogenetic analysis of nearly complete 16S rRNA gene and 16-23S internal transcribed spacer region. Phylogenetic analysis of both 16S rRNA genes and internal spacer regions exhibited coherent clustering patterns. The genetic relatedness of the investigated strains was largely congruent with morphology-based taxonomic groupings. All the investigated strains possess both the types of tRNA (tRNAIle and tRNAAla) in their 16-23S internal spacer regions and significantly varied GC contents and spacer sequence lengths. Further, ultrastructural studies provide a more valuable insight into the cyanobacterial taxa studied. Our study helps to apply the polyphasic approach (use of morphology, ultra-structure, ecology, and molecular analysis of complete 16S rRNA genes and 16-23S internal spacer regions) to resolve taxonomic ambiguities and provide a fairly robust cyanobacterial classification system among the unicellular forms studied.

Altitudinal Variability in Wing Patterns of Phyllonorycter salictella (Zeller, 1846) (Lepidoptera: Gracillariidae)

Individual variability of wing patterns is not frequent in European species of the genusPhyllonorycterHübner, 1822. It is unusually distinct inPhyllonorycter salictella(Zeller, 1846) which causes some taxonomic ambiguities and oversights. We found on numerous material of adults reared from overwintering pupae collected in the Czech and Slovak Republics since 1950 that this variability is related with altitude (temperature). Adults with the distinct generotypic (plesiomorphic) wing patterns dominated in submountain populations while individuals with the strongly reduced (apomorphic) wing drawings were represented quite negligibly. This ratio was reversed in lowland populations. The observed variability is continuous between extreme variants, it is regionally and trophic unaffected, and more pronounced in males than in females. The results support the view that the questionable taxa such asPhyllonorycter viminiella(Sircom, 1848) andP. heringiella(Grønlien, 1932) represent only individual (local or regional) forms of the above species.

Taxonomic Notes on Mystus Species of Northern Kerala

Systematic studies conducted on Mystus species of northern Kerala are very rare. It is due the taxonomic ambiguity which had existed in many species of this genus? To solve this dilemma, during this study, all Mystus species were collected from their type localities and taxonomically analysed. Examination of meristic, metric and major morphometric characters helped to prove the identity of all Mystus species of these regions.