Single Variable Species Research Articles

Anthomyza gilviventris in Palaearctic Region: integrative taxonomy, variability and habitat associations of North European population (Diptera: Anthomyzidae)

Anthomyza gilviventris Roháček & Barber, 2016, hitherto known only from the Nearctic Region, is recorded from the Palaearctic Region (NE Sweden) for the first time. Specimens from the Swedish population have been compared with those of A. gilviventris from Canada and the USA and those of A. tschirnhausi Roháček, 2009 from the Kamchatka Peninsula (Far East of Russia). Both morphological and molecular analyses (BI and RAxML, based on seven DNA markers: 12S, 16S, 28S, COI, COII, CytB, ITS2) confirmed that the Swedish specimens belong to A. gilviventris. Because no specimen of A. tschirnhausi has been available for molecular study, the most diagnostic morphological characters used for separation of this species from A. gilviventris have been re-evaluated with respect to Swedish specimens, and their variability discussed. However, these differences, although stable, are relatively small and, consequently, the possibility that they fall within the limits of a single variable species has not been entirely eliminated. New biological information (habitat and host-plant associations) on the Swedish population of A. gilviventris is presented.

Cytogeography of Gagea bohemica (Liliaceae) outside the Mediterranean: two ploidy levels, spatial differentiation of cytotypes, and occurrence of mixed-ploidy populations

Gagea bohemica s.l. is a morphologically and karyologically highly variable group with many morphologically similar “narrow” taxa currently considered as a single variable species. It is predominantly distributed in Mediterranean and warmer parts of temperate belt of Europe. The large-scale data on its cytogeography and population cytotype structure which could provide a basis for taxonomy are lacking, only scattered data on ploidy have been published from various parts of its range. In this study, we sampled 106 populations in broader Central Europe, the northeastern Balkan Peninsula and the northwestern Black Sea coast in order to analyze their ploidy level, genome size and pollen stainability. Two cytotypes, i.e., tetraploid (2n = 48) and pentaploid (2n = 60), were found in the study area using chromosome counting and flow cytometry, both in pure and mixed-ploidy populations. Pure pentaploid populations are mainly distributed in Austria, Czechia, northwestern Hungary and Slovakia while tetraploid cytotype in pure and mixed-ploidy populations forming two lineages which are concentrated into two disjunct geographical areas: a western lineage in Germany and Switzerland and an eastern one in Bulgaria, southeastern Hungary, northern Greece, Romania, Serbia and Ukraine. The two lineages differ in their genome size regardless of their ploidy, indicating their independent origin. Analysis of pollen stainability using a modified Alexander stain revealed an unusual pattern with tetraploids having a lower pollen stainability (mean 44.29%) than pentaploids (mean 70.70%), but the western and eastern populations differed again from each other.

Burchellia R.Br. (Rubiaceae: Ixoroideae), a monotypic genus endemic to southern Africa

Burchellia R.Br. (Rubiaceae: Ixoroideae) is endemic to southern Africa. The type species, B. bubalina (L.f.) Sims, is based on Lonicera bubalina L.f., for which we designate a lectotype. We provide an account of the genus with comprehensive nomenclature and synonymy, including a taxonomic history of all names, and morphological descriptions for the genus and species, as well as distribution and ecological notes. The occurrence of hairy pocket-domatia in the species is variable. Examination of material from throughout the range of the species reveals a continuous pattern of variation in leaf size, shape and density of the vestiture, as well as in the size and colour of the corolla. We accordingly recognise a single variable species.

Morphology-Based Identification of Bemisia tabaci Cryptic Species Puparia via Embedded Group-Contrast Convolution Neural Network Analysis

The Bemisia tabaci species complex is a group of tropical–subtropical hemipterans, some species of which have achieved global distribution over the past 150 years. Several species are regarded currently as among the world’s most pernicious agricultural pests, causing a variety of damage types via direct feeding and plant-disease transmission. Long considered a single variable species, genetic, molecular and reproductive compatibility analyses have revealed that this “species” is actually a complex of between 24 and 48 morphologically cryptic species. However, determinations of which populations represent distinct species have been hampered by a failure to integrate genetic/molecular and morphological species–diagnoses. This, in turn, has limited the success of outbreak-control and eradication programs. Previous morphological investigations, based on traditional and geometric morphometric procedures, have had limited success in identifying genetic/molecular species from patterns of morphological variation in puparia. As an alternative, our investigation focused on exploring the use of a deep-learning convolution neural network (CNN) trained on puparial images and based on an embedded, group-contrast training protocol as a means of searching for consistent differences in puparial morphology. Fifteen molecular species were selected for analysis, all of which had been identified via DNA barcoding and confirmed using more extensive molecular characterizations and crossing experiments. Results demonstrate that all 15 species can be discriminated successfully based on differences in puparium morphology alone. This level of discrimination was achieved for laboratory populations reared on both hairy-leaved and glabrous-leaved host plants. Moreover, cross-tabulation tests confirmed the generality and stability of the CNN discriminant system trained on both ecophenotypic variants. The ability to identify B. tabaci species quickly and accurately from puparial images has the potential to address many long-standing problems in B. tabaci taxonomy and systematics as well as playing a vital role in ongoing pest-management efforts. [Aleyrodidae; entomology; Hemiptera; machine learning; morphometrics; pest control; systematics; taxonomy; whiteflies.]

A review of Dendrobium kingianum Bidwill ex Lindl. (Orchidaceae) with morphological and molecular-phylogenetic analyses

Populations of Dendrobium kingianum Bidwill ex Lindl. from near Newcastle, New South Wales to southern and central west Queensland and encompassing all regions of the distribution were studied using field observations, morphometric analysis and nrITS sequences. A total of 281 individuals were used to construct regional descriptions of D. kingianum and 139 individuals were measured for 19 morphological characters, and similarities and differences among specimens summarised using multivariate statistical methods. Patterns of morphological variation within D. kingianum are consistent with a single variable species that expresses clinal variation, with short growing plants in the south and taller plants in the northern part of the distribution. The nrITS gene tree suggests two subgroups within D. kingianum subsp. kingianum, one comprising northern, the other southern individuals, which may overlap in the vicinity of Dorrigo, New South Wales. The disjunct D. kingianum subsp. carnarvonense in central west Queensland, which can be distinguished by a predominately subterranean habit and a narrower labellum midlobe, was resolved sister to D. moorei, which renders D. kingianum paraphyletic in the nrITS gene tree, but this position was not supported. Regional descriptions documenting clinal variation are provided. All previously described varieties, including D. kingianum var. pulcherrimum Rupp, are colour and growth forms of D. kingianum subsp. kingianum.

Morphological plasticity of the Aden Nerite, Nerita adenensis Mienis, 1978 (Gastropoda: Cycloneritida: Neritidae)

ABSTRACT Fourteen morphotypes of the Aden nerite (Nerita adenensis) from Chabahar Bay, the northern Gulf of Oman, were sequenced for mitochondrial cytochrome c oxidase I and nuclear ATPSα genes. COI sequences across all morphotypes yielded uncorrected intraspecific genetic distances (p) of between 0.013 and 0.017, whereas interspecific p was 0.11–0.16 among congeneric species. For ATPSα, across all morphotypes, p was 0.00–0.03, whereas between N. adenensis and congeneric species, p was 0.07–0.19. Morphological analysis revealed a high degree of plasticity in shell colour, pattern and structure, while characters of the operculum and crenulations on the outer lip were more stable. Our descriptions provided here will be helpful in identifying this problematic taxon, which our genetic analyses show is best regarded as a single variable biological species.

A species complex within the red-reticulate Goniobranchus Pease, 1866 (Nudibranchia: Doridina: Chromodorididae)

The taxonomy and diversity of chromodorid nudibranchs (Mollusca: Gastropoda: Nudibranchia) are relatively well-studied, although molecular analyses have only been applied to test few species-level groups. Within Chomodorididae, the genus Goniobranchus Pease, 1866 contains many different groups based on external colouration, including the red-reticulate group. Previously, most of the red-reticulate group has been considered as either a single variable species, identified as either Goniobranchus reticulatus Pease, 1866 or Goniobranchus tinctorius (Ruppell & Leuckart, 1828), or as a species complex. In this study, red-reticulate nudibranchs were collected from different locations spanning the Indo-Pacific. From these specimens, DNA data were derived, consisting of mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA (16S rDNA) sequences. COI data were analysed using a distance-based species delimitation approach (ABGD), and the combined dataset (COI+16S rDNA) was analysed using maximum likelihood (ML) and Bayesian inference (BI) methods. The analyses identified five species-level clades, but none of the clades’ morphotypes matched exactly with the original descriptions of G. tinctorius or G. reticulatus. The non-reticulate, spotted species Goniobranchus splendidus (Angas, 1864) falls inside this complex. The existence of multiple species-level clades in the Goniobranchus red-reticulate group suggests this is a group of closely related species, comprising at least five undescribed taxa.

A Taxonomic Revision ofPassiflorasect.Xerogona(Passifloraceae) Using Principal Component Analysis

In subgenus Decaloba (DC.) Rchb. of Passiflora L., the section Xerogona (Raf.) Killip (Passifloraceae) is a group of herbaceous vines found in subtropical and tropical regions of the Americas. Primarily distributed in Central America, with a few also found in the West Indies and South America, the species of Passiflora sect. Xerogona are recognized by their unusual dehiscent capsular fruit, the absence of bracts and laminar nectaries, and their transversely grooved seeds. Passiflora tenella Killip is the only species included in Passiflora sect. Xerogona with a fruit that does not appear to be a capsule, but the shape of the leaves and the absence of floral bracts and laminar nectaries suggest affiliation with this section. Fifteen species, including two subspecies, are recognized within Passiflora sect. Xerogona. Passiflora cobanensis Killip is distinguished as two subspecies, P. cobanensis subsp. cobanensis and P. cobanensis subsp. brevipes (Killip) T. Boza, with the latter subspecies transferred from P. brevipes Killip. From previous species circumscriptions, this section contains two problematic species complexes for P. capsularis L. and P. rubra L. The morphological variation between and within these two species complexes was examined in this study, using Principal Component Analysis and correlation matrices of morphological characters, and this variation was studied throughout their distributional ranges. Passiflora capsularis is recognized as a single variable species. Two species are recognized within the P. rubra complex, based primarily on floral characters, as P. cisnana Harms and P. rubra. Passiflora cisnana is lectotypified.

Taxonomic status of Protankyra ramiurna and Protankyra benedeni (Holothuroidea: Apodida: Synaptidae)

This study presents a review of the species Protankyra ramiurna Heding, 1928 and Protankyra benedeni (Ludwig, 1881) from the Brazilian coast. Some authors consider that these two taxa represent a single variable species. Our comparative analysis of external characters, anatomy and ossicle morphology indicates that they represent distinct species. This is the first record of Protankyra ramiurna from Brazil.

Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus.

The genus Conus comprises approximately 700 species of venomous marine cone snails that are highly efficient predators of worms, snails, and fish. In evolutionary terms, cone snails are relatively young with the earliest fossil records occurring in the Lower Eocene, 55 Ma. The rapid radiation of cone snail species has been accompanied by remarkably high rates of toxin diversification. To shed light on the molecular mechanisms that accompany speciation, we investigated the toxin repertoire of two sister species, Conus andremenezi and Conus praecellens, that were until recently considered a single variable species. A total of 196 and 250 toxin sequences were identified in the venom gland transcriptomes of C. andremenezi and C. praecellens belonging to 25 and 29 putative toxin gene superfamilies, respectively. Comparative analysis with closely (Conus tribblei and Conus lenavati) and more distantly related species (Conus geographus) suggests that speciation is associated with significant diversification of individual toxin genes (exogenes) whereas the expression pattern of toxin gene superfamilies within lineages remains largely conserved. Thus, changes within individual toxin sequences can serve as a sensitive indicator for recent speciation whereas changes in the expression pattern of gene superfamilies are likely to reflect more dramatic differences in a species’ interaction with its prey, predators, and competitors.

A review of the Pseudobarbus afer (Peters, 1864) species complex (Teleostei, Cyprinidae) in the eastern Cape Fold Ecoregion of South Africa.

The Eastern Cape redfin, Pseudobarbus afer, has long been considered to be a single widespread and variable species occurring in multiple isolated river systems in the Cape Fold Ecoregion (CFE) at the southern tip of Africa. Mitochondrial cytochrome b and control region sequence data of individuals from populations currently assigned to Pseudobarbus afer across the species’ distribution range revealed existence of four deeply divergent taxonomic units: (i) the Mandela lineage confined to the Sundays, Swartkops and Baakens river systems, (ii) the Krom lineage endemic to the Krom River system, (iii) the St Francis lineage occurring in the Gamtoos and adjacent river systems, and (iv) the Forest lineage occurring in several coastal river systems from the Tsitsikamma to the Klein Brak River system. The Forest lineage is closely related to Pseudobarbus phlegethon from the Olifants River system on the west coast of South Africa, suggesting that it does not belong to Pseudobarbus afer s.l. Herein we focus on the three lineages within the Pseudobarbus afer s.l. complex and provide new diagnosis for Pseudobarbus afer s.s (Mandela lineage), revalidate Pseudobarbus senticeps (Krom lineage) as a distinct species, and describe a new species Pseudobarbus swartzi (St Francis lineage). The three species exhibit subtle differences, which explains why they were previously considered to represent a single variable and widespread species. Pseudobarbus senticeps differs from both Pseudobarbus afer and Pseudobarbus swartzi by having fewer (i.e. larger) scales (25–33, mode 29 lateral line scale series; 10–12, mode 11 circumpeduncular scales) and presence of a lateral stripe which terminates in a conspicuous triangular blotch at the base of the caudal fin. Long barbels which reach or surpass the vertical through the posterior edge of the eye further separate Pseudobarbus senticeps from Pseudobarbus afer s.s. which possesses simple short barbels which do not reach the vertical through the posterior margin of the eye. Pseudobarbus afer s.s differs from Pseudobarbus swartzi sp. n. by possession of fewer scale rows along the lateral line (29–35, mode 32 vs 34–37, mode 36 in Pseudobarbus swartzi), fewer scales around the caudal peduncle (12–16, mode 12 vs 13–17, mode 16 in Pseudobarbus swartzi) and a distinct mesh or net-like pigmentation pattern on latero-ventral scales.

Mandibular ramus shape of Australopithecus sediba suggests a single variable species

The fossils from Malapa cave, South Africa, attributed to Australopithecus sediba, include two partial skeletons—MH1, a subadult, and MH2, an adult. Previous research noted differences in the mandibular rami of these individuals. This study tests three hypotheses that could explain these differences. The first two state that the differences are due to ontogenetic variation and sexual dimorphism, respectively. The third hypothesis, which is relevant to arguments suggesting that MH1 belongs in the genus Australopithecus and MH2 in Homo, is that the differences are due to the two individuals representing more than one taxon. To test these hypotheses, we digitized two-dimensional sliding semilandmarks in samples of Gorilla, Pan, Pongo, and Homo, as well as MH1 and MH2. We document large amounts of shape variation within all extant species, which is related neither to ontogeny nor sexual dimorphism. Extant species nevertheless form clusters in shape space, albeit with some overlap. The shape differences in extant taxa between individuals in the relevant age categories are minimal, indicating that it is unlikely that ontogeny explains the differences between MH1 and MH2. Similarly, the pattern of differences between MH1 and MH2 is inconsistent with those found between males and females in the extant sample, suggesting that it is unlikely that sexual dimorphism explains these differences. While the difference between MH1 and MH2 is large relative to within-species comparisons, it does not generally fall outside of the confidence intervals for extant intraspecific variation. However, the MH1-MH2 distance also does not plot outside and below the between-species confidence intervals. Based on these results, as well as the contextual and depositional evidence, we conclude that MH1 and MH2 represent a single species and that the relatively large degree of variation in this species is due to neither ontogeny nor sexual dimorphism.

Reconstructed Homo habilis type OH 7 suggests deep-rooted species diversity in early Homo.

Besides Homo erectus (sensu lato), the eastern African fossil record of early Homo has been interpreted as representing either a single variable species, Homo habilis, or two species. In the latter case, however, there is no consensus over the respective groupings, and which of the two includes OH 7, the 1.8-million-year-old H. habilis holotype. This partial skull and hand from Olduvai Gorge remains pivotal to evaluating the early evolution of the Homo lineage, and by priority names one or other of the two taxa. However, the distorted preservation of the diagnostically important OH 7 mandible has hindered attempts to compare this specimen with other fossils. Here we present a virtual reconstruction of the OH 7 mandible, and compare it to other early Homo fossils. The reconstructed mandible is remarkably primitive, with a long and narrow dental arcade more similar to Australopithecus afarensis than to the derived parabolic arcades of Homo sapiens or H. erectus. We find that this shape variability is not consistent with a single species of early Homo. Importantly, the jaw morphology of OH 7 is incompatible with fossils assigned to Homo rudolfensis and with the A.L. 666-1 Homo maxilla. The latter is morphologically more derived than OH 7 but 500,000years older, suggesting that the H. habilis lineage originated before 2.3 million years ago, thus marking deep-rooted species diversity in the genus Homo. We also reconstructed the parietal bones of OH 7 and estimated its endocranial volume. At between 729 and 824ml it is larger than any previously published value, and emphasizes the near-complete overlap in brain size among species of early Homo. Our results clarify the H. habilis hypodigm, but raise questions about its phylogenetic relationships. Differences between species of early Homo appear to be characterized more by gnathic diversity than by differences in brain size, which was highly variable within all taxa.

The Plio-Pleistocene scimitar-toothed felid genus Homotherium Fabrini, 1890 (Machairodontinae, Homotherini): diversity, palaeogeography and taxonomic implications

The systematics of the Plio-Pleistocene scimitar toothed felid Homotherium have remained problematic after more than a century of fossil findings in Eurasia, Africa and the Americas. Ranging in age between around 4 million and 10,000 years, fossils of this genus display considerable variation, but the distribution of that variation has largely failed to fit a consistent pattern that would allow a clear distinction between species, especially in the Eurasiatic record. The study of undescribed mandibular and cranial fossils of Homotherium from Pleistocene sites in Spain and Alaska provides new insights into the morphological variability within this widespread genus. The results of our study and comparison of the new material with the published fossils of Homotherium confirm the difficulty in dividing the sample into clear-cut species. The new mandible from Incarcal (Spain) shows in a more dramatic way than before how the sample from that Spanish site encompasses the range of variability observed in the Villafranchian and Pleistocene Eurasiatic record, while older, possibly Ruscinian fossils of Homotherium from East Europe display less reduced lower premolars and probably correspond to a different species. The Alaskan fossils, on the other hand, add to the variability in mandibular and cranial morphology of the late Pleistocene North American record. We find no evidence to allow a species-level division within the Villafranchian-Pleistocene Homotherium sample from Eurasia, which for now is best classified as a single variable species, Homotherium latidens, but there are indications of evolution within the lineage, such as the presence of a pocketed anterior margin of the mandibular masseteric fossa, a feature found in the younger fossils of middle or late Pleistocene age but consistently absent in older specimens. A comparable pattern is found in the American record, where the same mandibular feature is observed in late Pleistocene fossils, although in that continent the “primitive” features of some older Homotherium fossils of Blancan (Pliocene) age are consistent enough to justify their classification in a separate species, Homotherium ischyrus. Only the finding of more complete cranial fossils of middle and late Pleistocene age will reveal if there are additional morphological features (besides the pocketing of the masseteric fossa) that could one day allow the separation of younger populations from those of Late Pliocene and Early Pleistocene age.

Dollfusiella Campbell & Beveridge, 1994 (Trypanorhyncha: Eutetrarhynchidae) from elasmobranchs off Borneo, including descriptions of five new species

Sampling of a large number of elasmobranchs from coastal waters off Borneo revealed the presence of five new species of Dollfusiella Campbell & Beveridge, 1994 (Trypanorhyncha: Eutetrarhynchidae), namely D. angustiformis n. sp., D. hemispinosa n. sp., D. spinosa n. sp., D. imparispinis n. sp. and D. parva n. sp. Dollfusiella angustiformis n. sp. is described from the spiral intestines of four species of the dasyatid stingray genus Himantura Müller & Henle from both the Indonesian and Malaysian parts of Borneo. All the other species were obtained from Malaysian Borneo. Dollfusiella hemispinosa n. sp. is described from the spiral intestines of three species of Himantura, whereas D. spinosa n. sp. was obtained from several specimens of Pastinachus solocirostris Last, Manjaji & Yearsley (Dasyatidae) as well as from Taeniura lymma 1 (sensu Naylor et al., 2012) (Dasyatidae), Neotrygon kuhlii 2 (sensu Naylor et al., 2012) (Dasyatidae), and Glaucostegus cf. typus (sensu Naylor et al., 2012) (Rhinobatidae). Dollfusiella imparispinis n. sp. is described from the spiral intestine of a single specimen of Chiloscyllium punctatum Müller & Henle (Hemiscyllidae) from the South China Sea off Sarawak, whereas D. parva n. sp. was obtained from several species of Himantura. Specimens of the five novel taxa possess scoleces covered with enlarged microtriches, a morphological characteristic exhibited by several other congeners. However, the new species differ from all congeners by possessing unique patterns of oncotaxy as well as combinations of additional morphological features. The number of valid species within Dollfusiella is increased to 26. For this reason, a key for the species of Dollfusiella is provided. Furthermore, novel information on hosts and geographic distribution is provided for two previously described species of Dollfusiella, D. michiae (Southwell, 1929) and D. spinulifera (Beveridge & Jones, 2000). The latter species differs slightly from the original description and shows a much higher variability with regard to the lengths of the scolex and muscular bulbs and the number of testes. These variable characters subdivided specimens of D. spinulifera into relatively distinct groups. However, the specimens did not differ in their oncotaxy and are considered to represent a single variable species.

Litoporus iguassuensis (Araneae, Pholcidae): Camouflaged retreat, sexual dimorphism, female color polymorphism, intra-specific genital variation, and description of the male

We describe the previously unknown male of Litoporus iguassuensisMello-Leitão, 1918 and document the exceptional biology of this species: (1) females and juveniles but not adult males construct camouflaged retreats; (2) there is a strong sexual dimorphism involving coloration, leg length, and behavior; (3) females at some localities are color polymorphic, i.e., discontinuously variable within the population. The species, previously only known from Rio de Janeiro, is widely distributed in the Brazilian Atlantic Forest. Among some of the localities studied it shows genital and male cheliceral variation that is here interpreted as being intraspecific. Preliminary molecular data (16S, H3) reveal low p-distances and no significant grouping information, leading us to hypothesize a single variable species rather than two or more species. Finally, we argue that Mello-Leitão's original assignment to Litoporus (instead of Tupigea) may be correct, and discuss the implications: (1) Litoporus may be nested within Mesabolivar and represent a case of evolutionary shift among microhabitats with the correlated morphological changes; (2) extreme sexual dimorphism may be common in Litoporus and may explain the fact that females continue to be unknown in several species (because they were not recognized as being conspecific with the males).

A Subspecific Revision of North American Saltmarsh Mallow Kosteletzkya pentacarpos (L.) Ledeb. (Malvaceae)

Kosteletzkya pentacarpos (L.) Ledeb. (syn. = Kosteletzkya virginica (L.) C. Presl ex A. Gray) has been treated as a single variable species or as a species including four varieties: K. virginica var. althaeifolia, var. aquilonia, var. smilacifolia, and var. virginica. The aim of this study was to test the validity of formally recognizing these putative infraspecific taxa with a statistical analysis of morphological data. Loans were received from 15 herbaria, for 1,114 specimens; 224 were selected. Measurements were taken from these 224 specimens for 42 characters and analyzed by canonical discriminant analysis, which recognized two dimensions. Var. smilacifolia and var. aquilonia were separated from the other two groupings and correctly predicted at 100%. Var. smilacifolia is morphologically distinct from the other taxa in having linear hastate leaves with reflexed linear lobes, an unbranched inflorescence, a slender stem, and a mostly entire leaf margin. A new combination is proposed: Kosteletzkya pentacarpos (L.) Ledeb. var. smilacifolia (Chapm.) S.N. Alexander. All other former putative infraspecific taxa are synonymous with Kosteletzkya pentacarpos var. pentacarpos.

Molecular analyses of Pythium irregulare isolates from grapevines in South Africa suggest a single variable species

The Pythium irregulare species complex is the most common and widespread Pythium spp. associated with grapevines in South Africa. This species complex has been subdivided into several morphological and phylogenetic species that are all highly similar at the sequence level [internal transcribed spacer (ITS) and cytochrome c oxidase ( cox) regions]. The complex includes Pythium regulare and Pythium cylindrosporum, which are morphologically distinct, and P. irregulare sensu stricto ( s.s.) and Pythium cryptoirregulare, which are morphologically similar. The aim of the current study was to determine whether 50 South African grapevine P. irregulare isolates represented more than one phylogenetically distinct species. The isolates were characterised using nuclear (ITS and β-tubulin) and mitochondrial ( cox1 and cox2) gene region phylogenies and two isozyme loci [glucose-6-phosphate isomerase ( Gpi) and malate dehydrogenase ( Mdh-1)]. Some of the gene sequence data were difficult to interpret phylogenetically, since some isolates contained two or more polymorphic ITS copies within the same isolate (intra-isolate variation) that clustered into different ITS sub-clades, i.e. the P. irregulare s.s. and P. cryptoirregulare sub-clades. The molecular data furthermore only revealed the presence of one phylogenetic species, P. irregulare. Morphological analyses of a subset of the isolates confirmed that the isolates were P. irregulare, and further showed that the P. cylindrosporum ex-type strain formed typical P. irregulare oogonia, and not the previously reported distinct elongated oogonia. Some of the molecular analyses suggested the occurrence of outcrossing events and possibly the formation of aneuploids or polyploids since (i) the nuclear and mitochondrial gene data sets were incongruent, (ii) polymorphic ITS copies were present within the same isolate, (iii) heterozygosities were observed in the β-tubulin gene and Gpi and Mdh-1 loci in some isolates and (iv) more than two β-tubulin alleles were detected in some isolates. Altogether, the data suggest that P. irregulare, P. cryptoirregulare, P. cylindrosporum, and possibly P. regulare should be synonimised under the name P. irregulare.

Polyphasic analysis of intraspecific diversity in Epicoccum nigrum warrants reclassification into separate species.

Background Epicoccum nigrum Link (syn. E. purpurascens Ehrenb. ex Schlecht) is a saprophytic ascomycete distributed worldwide which colonizes a myriad of substrates. This fungus has been known as a biological control agent for plant pathogens and produces a variety of secondary metabolites with important biological activities as well as biotechnological application. E. nigrum produces darkly pigmented muriform conidia on short conidiophores on sporodochia and is a genotypically and phenotypically highly variable species. Since different isolates identified as E. nigrum have been evaluated as biological control agents and used for biocompound production, it is highly desirable that this species name refers to only one lineage. However, according to morphological and genetic variation, E. nigrum present two genotypes that may comprise more than one species.Methodology/Principal FindingsWe report the application of combined molecular (ITS and β-tubulin gene sequence analysis, PCR-RFLP and AFLP techniques), morphometric, physiological, genetic compatibility and recombination analysis to study the taxonomic relationships within an endophytic population that has been identified as E. nigrum. This combined analysis established two genotypes showing morphological, physiological and genetic divergence as well as genetic incompatibility characterized by colony inhibition, strongly indicating that these genotypes correspond to different species. Genotype 1 corresponds to E. nigrum while genotype 2 represents a new species, referred to in this study as Epicoccum sp.Conclusions/SignificanceThis research contributes to the knowledge of the Epicoccum genus and asserts that the classification of E. nigrum as a single variable species should be reassessed. In fact, based on the polyphasic approach we suggest the occurrence of cryptic species within E. nigrum and also that many of the sequences deposited as E. nigrum in GenBank and culture collection of microbial strains should be reclassified, including the reference strain CBS 161.73 sequenced in this work. In addition, this study provides valuable tools for differentiation of Epicoccum species.

Gagea bohemica (Liliaceae), a highly variable monotypic species within Gagea sect. Didymobulbos

Gagea bohemica s.l. (Liliaceae) consists of two morphologically extreme forms (saxatilis and bohemica) which depending on the varying opinions of the authors are considered as separate species, subspecies or as a single variable species. In this study, morphological (form and length of perianth segments, pilosity of pedicles and peduncles) and molecular data (cpDNA trnL–trnF IGS) of 55 samples corresponding to 43 populations from Western Europe to the Mediterranean area and eastern Caucasus were investigated. G. bohemica (Zauschn.) Schult. & Schult. f. represents a highly variable monotypic species from both morphological and karyological (2n = 24, 36, 48, 60, 72) aspects. Based on the molecular and morphological data presented here, a differentiation between specific and infraspecific taxa is not possible. We hypothesize that the morphological variability of this species is largely influenced by different site conditions and ploidy level.