Criteria For Delimitation Research Articles

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene—Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.

Integrative lineage delimitation in rodents of the Ctenomys Corrientes group

Abstract The tuco-tucos rodents (genus Ctenomys) of the Corrientes group comprise several populations that inhabit the vast area under the influence of the Iberá wetland. Lineage delimitation within the recently diverged Corrientes group is a challenging task as morphological differentiation is not conspicuous between populations. However, delimitation is crucial for evolutionary studies and conservation issues. In this study, we performed a phylogenetic analysis including cytochrome b (cyt-b) sequences from taxa that had never been studied in a comprehensive context. We integrated previously published chromosomal studies, mitochondrial phylogenies and simple sequence repeat (SSR) variability analyses, and applied a delimitation criterion over the basis of chromosomal incompatibilities and genetic exclusivity. Under this integrative approach seven independently evolving lineages were delimited in the Corrientes group: Ctenomys roigi, which conserves its former definition, Ctenomys dorbignyi and Ctenomys perrensi complex which were redefined, Sarandicito which includes the population of Paraje Sarandicito and probably a group of nearby poorly studied populations, and Iberá i, ii and iii distributed at both sides of the Iberá wetland. We discuss future perspectives to evaluate the proposed lineages and conservation issues concerning these tuco-tucos.

One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes

Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock “bass” cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.

Delimitation of functional transport regions: understanding the transport flows patterns at the micro-regional level

ABSTRACTThe main purpose of the article is the delimitation of functional regions in the Czech Republic based on the car transport flows. We argue that the traditionally used criteria for delimitation of functional regions (especially based on commuting to work flows) gradually losing their value. Therefore, we delimited functional regions as newly defined transport regions. Spatially expressed transport flows are unique indicators of complex spatial relations. We work with the daily intensities of car transport, which tend to create apparent nodal structures. Nodal structures are evident in particular at the micro-regional level, since transport flows reflect polarization between cities and their hinterlands. We use the concept of local minimum of transport intensities to delimit the boundaries of transport regions. As a result, we defined 235 functional transport regions (FTR) in the Czech Republic, which reflect the core-hinterland polarization. The delimited FTR represent logically arranged functional units, which we have subsequently compared with other types of functional regions. During these comparisons with various types of regions, we concluded that the greatest correlations are achieved with the regions of commuting to services.

TELEDETECCIÓN APLICADA AL RECONOCIMIENTO DE PRADERAS DE PASTOS MARINOS EN AMBIENTES DE BAJA VISIBILIDAD: LA GUAJIRA, COLOMBIA

Seagrass meadows are important ecosystems due to their high productivity and ecological value among tropical ecosystems, because of their high species diversity. In Colombia seagrasses are located around some islands, oceanic coral banks and along the Caribbean shelf, mainly in La Guajira Department, where more than 80% of the seagrass meadows of the country are present. In the world, the delimitation of this ecosystem has been successfully mapped during years, with assistance of remote sensing, using satellite image of different spatial scales. Nevertheless, the specific environmental conditions in La Guajira, such as high water turbidity and reduced light penetration restrict the use of traditional satellite images employed for those seascapes. With the aim of delimiting and establishing the extension of seagrass meadows in La Guajira, based on analyses between July 2013 and February 2014, a methodology of massive image interpretation that included fieldwork fast verification was applied, generating as a result one layer of seagrass habitats in Cabo de La Vela – Dibulla area at 1:100000 scale. Methodology included geometric correction, image fusion, fieldwork information, definition of thematic classes, determining of criteria for spatial delimitation, visual interpretation of images, thematic uncertainty qualification, and final cartography production. The process of cartographic production showed that Landsat 8 OLI satellite sensor images made easier the identification of seagrass meadows in deep areas (>10m). In total, 53621 ha of seagrass meadows were identified, and the largest meadows of Colombia were delimitated, which reach dimensions of up to 6018 ha.

Phylogenetic reassessment of Specklinia and its allied genera in the Pleurothallidinae (Orchidaceae)

The phylogenetic relationships within Specklinia (Pleurothallidinae; Orchidaceae) and related genera are re-evaluated using Bayesian analyses of nrITS and chloroplast matK sequence data of a wide sampling of species. Specklinia is found paraphyletic in the DNA based trees, with species alternatively assigned to Muscarella proven distinct, monophyletic and easily recognizable. Specklinia as such includes about 100 morphologically highly diverse species. Their phenotypic differences have prompted the creation of up to eleven generic names within this relatively small group. Here we show not only that these morphologically divergent species are closely related, but also that they can still be recognized by certain conserved morphological traits. The genera Acostaea, Areldia, Empusella, Cucumeria, Gerardoa, Pseudoctomeria, Sarcinula, Sylphia, Tribulago and Tridelta are found embedded within Specklinia, and therefore reduced under the synonymy of the latter. Specklinia is confirmed as sister to a clade that includes Platystele, Scaphosepalum and Teagueia. Five well-supported subgenera are proposed for Specklinia and are characterized both geographically and morphologically. The species belonging to each subgenus are listed. Incaea is synonymized with Dryadella, while Rubellia is reduced under Platystele. New combinations for several species are proposed. The criteria for the generic delimitation of Specklinia and other genera in the Pleurothallidinae are discussed.

Species-level divergences in multiple functional traits between the two endemic subspecies of Blue Chaffinches Fringilla teydea in Canary Islands

One of the biggest challenges in avian taxonomy is the delimitation of allopatric species because their reproductive incompatibility cannot be directly studied in the wild. Instead, reproductive incompatibility has to be inferred from multiple, divergent character sets that indicate a low likelihood of allopatric populations amalgamating upon secondary contact. A set of quantitative criteria for species delimitation has been developed for avian taxonomy. Here, we report a broad multi-trait comparison of the two insular subspecies of the Blue Chaffinch Fringilla teydea, endemic to the pine forests of Tenerife (ssp. teydea) and Gran Canaria (ssp. polatzeki) in the Canary Islands. We found that the two taxa were reciprocally monophyletic in their whole mitogenomes and two Z chromosome introns. The genetic distance in mitogenomes indicates around 1 Mya of allopatric evolution. There were diagnostic differences in body morphometrics, song and plumage reflectance spectra, whose combined divergence score (=11) exceeds the threshold level (=7) set for species delimitation by Tobias et al. (Ibis 152:724–746, 2010). Moreover, we found a marked divergence in sperm lengths with little range overlap. Relatively long sperm with low intra- and intermale CV compared to other passerines suggest a mating system with high levels of sperm competition (extrapair paternity) in these taxa. The large and diagnostic divergences in multiple functional traits qualify for species rank, i.e., Tenerife Blue Chaffinch (Fringilla teydea) and Gran Canaria Blue Chaffinch (Fringilla polatzeki). We encourage a wider use of sperm traits in avian taxonomy because sperm divergences might signal reproductive incompatibility at the postcopulatory prezygotic stage, especially in species with sperm competition.

Morphological study of the genus Herposiphonia (Rhodophyta, Rhodomelaceae) on the coast of eastern Guangdong, China, with a description of H. pinnata sp. nov.

We present a taxonomic study of taxa of the red algae genus Herposiphonia (Rhodophyta, Rhodomelaceae), collected from the coast of eastern Guangdong, China. We made detailed morphological studies and considered recent taxonomic criteria for species delimitation, and are making the first report of five different species on the coast of Guangdong, including a new species. The species identified were H. caespitosa Tseng, H. hollenbergii Dawson, H. pecten - veneris (Harvey) Falkenberg, H. subdisticha Okamura and H. pinnata Ding and Tan sp. nov. H. pinnata sp. nov. is characterized by bright green thalli; most parts of the feathery thalli are free of the substratum; determinate branches and indeterminate branches are arranged in a chaotic sequence; the primary axis has bare segments; the determinate branch has 9–11 periaxial cells per segment; vegetative trichoblasts are abundant; and tetrasporangia are formed on the middle of the determinate branch with 1–8 successive segments in a single rectilinear series. This paper is also the first record of sporophyte plants of H. pecten-veneris.

Carpological and receptacular morpho-anatomical characters of Inula, Dittrichia, Limbarda and Pulicaria species (Compositae, Inuleae): Taxonomic implications

Genus Inula L. is paraphyletic and heterogeneous with respect to several diverse characters, which makes delimiting taxa difficult. Dittrichia Greuter, Limbarda Adans. and Pulicaria Gaertn. were previously located in different sections within Inula, and subsequently segregated into separate genera. According to the latest molecular phylogenetic analyses based on plastid and nuclear DNA sequence data, supported by morphological and karyological data, it is suggested that type species of genus, Inula helenium L., should be separated from the remaining species to form a separate genus. The goals of this research are to (1) perform comparative micro-morphological and anatomical analysis of fruit and receptacle of species belonging to Inula, Pulicaria, Dittrichia and Limbarda genera in order to estimate their systematic value; (2) define further characters that would be useful in taxonomic delimitation of species that are often misidentified due to their morphological similarities; (3) investigate whether all these characters support the segregation of I. helenium into a separate genus. Using stereoscopic, light and scanning electron microscope, micro-morphological and anatomical characters of cypsela and receptacle were revealed. Cross sections of mature fruit were obtained using cryotechnic procedure. This study pertains to the evaluation of examined characters using correspondence analysis. The species’ characters, as well as those specific to the genera are identified and described. The findings reveal that the organisation of sclerenchyma tissue in a fruit and receptacle characteristics are features that tend to be diagnostic for genera. The results yielded by this study provide valuable criteria for delimitation of taxa belonging to Compositae tribe Inuleae, which are often misidentified due to their morphological similarities. Our results, based on anatomical and micro-morphological characteristics of the fruit and receptacle, also revealed that I. helenium can be distinguished as a separate taxon with equally small percentage of statistical support as Dittrichia, Limabarda and Pulicaria had.

Biodiversity undertakings call for extensive discussion on species concept and the criteria for species delimitation

Biodiversity undertakings call for extensive discussion on species concept and the criteria for species delimitation

Evolution of trichomes and its systematic significance inSalvia(Mentheae; Nepetoideae; Lamiaceae)

We have investigated the trichome characteristics in representative species of Salvia and Pleudia in order to evaluate this source of morphological evidence for addressing problems regarding generic delimitation and subgeneric classification. Trichomes of 46 Salvia spp., representing three subgenera in Iran, were investigated using light microscopy and scanning electron microscopy. General trichome characteristics were constant among different populations of a certain species, but showed a degree of variability useful in the delimitation of taxa, specifically at lower taxonomic levels. Trichome characters of taxonomic interest are as follows: types of glandular hair; number of composing cells (uni-, bi- or multicellular); size and thickness; branching pattern; and presence of papillae on the surface. Non-glandular trichomes can be simple and branched. Glandular trichomes can be stalked, subsessile or sessile. Our investigation reveals the usefulness of such characters in providing fundamental taxonomic criteria for taxon delimitation in these genera at various levels, especially at the specific rank. Furthermore, the data presented here indicate the potential applicability of such characters in the determination of evolutionary trends in Salvia and allies. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180, 241–257.

Coordinated ultrastructural and phylogenomic analyses shed light on the hidden phycobiont diversity of Trebouxia microalgae in Ramalina fraxinea

The precise boundary delineations between taxa in symbiotic associations are very important for evolutionary and ecophysiological studies. Growing evidence indicates that in many cases, the use of either morphological characters or molecular markers results in diversity underestimation. In lichen symbioses, Trebouxia is the most common genus of lichen phycobionts, however, the diversity within this genus has been poorly studied and as such there is no clear species concept. This study constitutes a multifaceted approach incorporating aspects of ultrastructural characterization by TEM and phylogenomics to evaluate the morphological and genetic diversity of phycobionts within the sexually reproducing lichen Ramalina fraxinea in the context of Mediterranean and temperate populations. Results reveal an association with at least seven different Trebouxia lineages belonging to at least two species, T. decolorans and T. jamesii, and diverse combinations of such lineages coexisting within the same thallus depending on the analyzed sample. Some of these lineages are shared by several other non-related lichen taxa. Our findings indicate the existence of a highly diverse assemblage of Trebouxia algae associating with R. fraxinea and suggest a possible incipient speciation within T. decolorans rendering a number of lineages or even actual species. This study stresses the importance of coordinated ultrastructural and molecular analyses to improve estimates of diversity and reveal the coexistence of more than one Trebouxia species within the same thallus. It is also necessary to have clearer species delimitation criteria within the genus Trebouxia and microalgae in general.

A reappraisal of Maxillaria (Orchidaceae)

It is argued that a broad and expanded circumscription of Maxillaria is to be preferred over a narrower one that necessitates the recognition of many segregate genera. These more narrowly circumscribed genera are often difficult to diagnose, increasing the risk of misidentifications, especially when material is only identified to genus level. The genera of the Maxillaria alliance as recognised in Genera orchidacearum are treated as sections of an expanded genus Maxillaria. Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium are here included in Maxillaria. Criteria for generic delimitation are discussed, the necessary combinations are made, and a key to the sections as well as a provisional checklist of the 634 species of Maxillaria arranged according to section are provided. Maxillaria prolifera is shown to be the correct name for M. pendens. Maxillaria humilis is a new combination for M. gracilis.

Erratum to: Distribution, morphological and histochemical characteristics of foliar trichomes of Plectranthus zuluensis (Lamiaceae)

There are problems in the delimitation/identification of Plectranthus species and this investigation aims to contribute toward solving such problems through structural and histochemical study of the trichomes. Considering the importance of P. zuluensis as restricted to semi-coastal forests of Natal that possess only two fertile stamens not four as the other species of this genus. The objective of this work was to study in detail the distribution, morphology and histochemistry of the foliar trichomes of this species using light and electron microscopy. Distribution and morphology of two types of non-glandular, capitate and peltate glandular trichomes are described on both leaf sides. This study provides a description of the different secretion modes of glandular trichomes. Results of histochemical tests showed a positive reaction to terpenoids, lipids, polysaccharides and phenolics in the glandular trichomes. We demonstrated that the presence, types and structure of glandular and non-glandular trichomes are important systematic criteria for the species delimitation in the genus.

Checklist of the species of Neoechinorhynchus (Acanthocephala:Neoechinorhynchidae) in fishes and turtles in Middle-America, and their delimitation based on sequences of the 28S rDNA.

Among the acanthocephalans, Neoechinorhynchus is one of the most speciose genera, with 116 described species distributed worldwide. The adults of Neoechinorhynchus are found in the intestine of freshwater and brackish water fish, as well as in freshwater turtles. In this study, a checklist of the congeneric species of Neoechinorhynchus occurring in Middle-American fish and turtles is presented. The checklist contains the records established in all published accounts, as well as novel data from survey work conducted in the region comprising Neotropical areas of Mexico, as well as some localities in Central America. The species delimitation criteria used to discriminate among species is based on molecular data. In the last years, a large database derived from sequences of the D2 + D3 domains of the large subunit of rDNA (28S) was generated for 262 specimens corresponding to nine species of Neoechinorhynchus. This molecular marker has shown to be useful in establishing species limits within Neoechinorhynchus and in resolving phylogenetic relationships at species level. Based on our results, the domains D2 + D3 of the 28S rDNA could be considered as potential DNA barcodes to complement mitochondrial DNA to discriminate among acanthocephalan species.

Formalized classification of species‐poor vegetation: a proposal of a consistent protocol for aquatic vegetation

AbstractAimsMost vegetation classification systems developed for large areas include various inconsistencies. Therefore, we (1) propose a new consistent Cocktail‐based approach to redefine the traditional phytosociological classification of species‐poor vegetation; (2) apply it to create a classification protocol for aquatic vegetation; (3) implement this protocol in a computer expert system; and (4) test it with a data set previously classified using an older version of the Cocktail method.MethodsThe new approach uses formal logic to provide formal definitions of vegetation units. In the classification protocol for aquatic vegetation we defined consistent criteria for delimitation of associations according to the concepts that are predominantly used in phytosociology, based on species cover, dominance patterns and functional species groups. We applied these criteria in a computer expert system running in the JUICE 7.0 program, and applied them to a test data set of 12 171 vegetation plots from the Czech Republic containing at least one aquatic species. The new classification was compared with (1) the previous national Cocktail classification based on species cover values and in few cases on sociological species groups, and (2) a non‐formalized expert‐based classification.ResultsThirteen functional species groups were created to build logical formulas of 64 aquatic associations and 5297 (44% of the total data set) vegetation plots were assigned to these associations, i.e. by 4% and 12% more than in the previous Cocktail and expert‐based classifications, respectively. There was 94% and 83% classification agreement with the previous Cocktail and expert‐based classification.ConclusionsThe new approach produces a formal, consistent and unequivocal classification of species‐poor vegetation with several advantages over similar approaches. It provides not only a set of formal definitions of vegetation units, but also a set of rules for building such definitions. All associations with common characteristics are defined by structurally identical formulas, ensuring consistency of the classification. While similar approaches for species‐rich vegetation use sociological species groups, which are not applicable to species‐poor vegetation, the new approach introduces the use of functional species groups, which reflect vegetation physiognomy and spatial structure and, in combination with species dominance, enable the classification of species‐poor vegetation in a similar manner as in traditional phytosociology.

Operational criteria for cryptic species delimitation when evidence is limited, as exemplified by North AmericanEntomobrya(Collembola: Entomobryidae)

Evaluating species boundaries remains a significant challenge in rare, difficult to collect, and/or understudied groups because of a lack of available data. Uninformative morphology, unknown ecologies and/or geographical distributions, inadequate comparative sequence data, and limited sample sizes present substantial challenges when applying commonly used methods for species delimitation. Here we present an approach that overcomes the challenges previously mentioned by integrating phylogeny, genetic distances, and a fixed diagnostic character (i.e. colour pattern) into the species delimitation process. The genus Entomobrya (Collembola) includes many species marked by complex and variable colour patterns. Many Entomobrya species have been named based exclusively on colour pattern, but the value of this character as a species-level diagnostic marker has been challenged. To test the hypothesis that colour forms in Entomobrya represent independent evolutionary lineages, i.e. distinct species, we used phylogenetic methods to evaluate the association between colour pattern and molecular variation in the cytochrome c oxidase I gene (COI) in 11 species of North American Entomobrya. The comparative analysis focused on 13 colour forms distributed amongst the species Entomobrya assuta, Entomobrya clitellaria, Entomobrya ligata, and Entomobrya quadrilineata. Phylogenetic analysis and genetic divergences sorted the 13 colour forms into seven independent evolutionary lineages, including three morphologically cryptic lineages diagnosable by colour pattern. However, genetic divergence did not always correlate with colour pattern variation, indicating that the diagnostic utility of colour pattern is species dependent and requires individual evaluation for each species. We propose that incorporation of the explicit species delimitation criteria developed for this study will result in a substantial advance in the identification and description of species in understudied taxa. © 2015 The Linnean Society of London

DNA barcoding of Japanese click beetles (Coleoptera, Elateridae).

Click beetles (Coleoptera: Elateridae) represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation). These findings urge taxonomic reinvestigation of these mismatched taxa.

Соотношение административных наркоправонарушений и наркопреступлений: прошлое, настоящее и будущее

The article concerns issues of correlation of administrative drug-related offences and drug-related crimes; substantiates the conclusion that administrative drug-related offences and drug-related crimes have a feature of public danger and the criteria for delimitation thereof are of a conditional and formal character. The author notes the dynamic character of correlation of administrative drug-related offences and drug-related crimes and the tendency to increase the number of administrative drug-related offences and crimes. The attention is drawn to the phenomenon of reciprocity of certain administrative drug-related offences and crimes when actions similar by the objective side are reflected both in the Criminal Code of the RF and the Code of Administrative-Law Offences of the RF. The author analyses the legislation of the People’s Republic of China and the Kingdom of Spain related to criminal responsibility of juridical persons for drugrelated crimes. Taking into consideration foreign practices the author considers the issue of necessity of adding to the administrative responsibility of juridical persons for drug-related offences of a new type of responsibility — criminal responsibility of juridical persons.

Defining rural areas of Visegrad countries

The article is focused on the introduction and categorization of various approaches to rurality, and the identification and delimitation of rural areas in Visegrad countries. Three substantively different groups of conceptualizations and definitions of rural and rurality are described as follows: functional definitions, rural as locality (political-economic approaches), and social representation. Latter, basic sorts of methods and appro - aches to the delimitation of rural areas in V4 countries are introduced emphasizing its historical development, differences in spatial level and criteria of delimitation in current research. Due to different nature of rural areas and even local administrative units (the basic units usually used for delimitation of rural areas), it is not possible to reach sufficient and reliable identification of rural areas for whole V4 area using any of criteria or definitions applied in the research at national levels. Therefore, the average population density of entire V4 area was used as a main criterion for distinguishing between urban and rural LAU 2 at the whole Visegrad area level. Such approach is also affected by generalization but it captures various conditions in each country relatively well and moreover, it is comparable with the OECD and European Union methods to some extent.