Austrian gudgeons of the genus Gobio (Teleostei: Gobionidae): A mixture of divergent lineages

Gudgeons of the genus Gobio are small Eurasian fishes whose systematics, taxonomy, and phylogenetic relationships have been the matter of a long-standing debate. Two species, Gobio gobio and G. obtusirostris have been reported for Austria, with a potential hybrid zone in the upper Danube. Phylogenetic and phylogeographic analysis of mitochondrial cytochrome oxidase subunit I and control region sequences, as well as nuclear ribosomal protein S7 sequences, however, shows that the proposed hybrid zone is not restricted to the upper Danube, but spans large parts of the Austrian Danube system (upper Danube, Rába & Mur systems). Moreover, our data show that also a third lineage, closely related to species from the southern Balkan, contributed to the gene pool of Austrian Gobio. Patterns of intra-lineage genetic diversity indicate that the distinct Gobio lineages expanded their distribution recently (most likely post-glacially) to come into secondary contact and hybridize in the Danube system.     

Genetic and morphological divergence within the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

Genetic and morphological divergence among the four subspecies in the Sebastes pachycephalus complex (S. pachycephalus pachycephalus, S. p. nigricans, S. p. nudus and S. p. chalcogrammus) was clarified. Principal coordinate analysis (PCoA) based on AFLP clearly divided 55 specimens of the complex into two groups, the S. p. pachycephalus?CS. p. nigricans group (P-Ni group) and the S. p. nudus?CS. p. chalcogrammus group (Nu-C group), although three specimens occupied intermediate positions. The minimum spanning network (MSN) based on partial sequences of the mitochondrial control region (mtCR) failed to separate either the P-Ni and Nu-C groups or the four subspecies into distinct clades, although restricted gene flow and genetic differentiation between the former were indicated by the F _ST estimation. Differences in morphological characters, including counts of pectoral fin rays and counts of dorsal fin spines lacking basal scales, were also evident between the two groups. However, little or no genetic or morphological difference was found between the two subspecies within each group. It was concluded that the P-Ni and Nu-C groups of the S. pachycephalus complex actually represent two different species, which is further supported by their sympatric distribution. Differences in dorsal body coloration and the presence or absence of brown spots on the ventral surface, which were formerly used to discriminate between four ??subspecies,?? may simply represent intraspecific variation. The three specimens occupying intermediate positions in the AFLP PCoA also occupied equivocal positions between the two species in the principal component analysis (PCA) based on morphometric characters, suggesting that they were hybrids between the two species. The star-shaped MSN of mtCR, which lacks distinct clades representing the two species, may be due to not only interspecific hybridization but also the sharing of ancestral haplotypes.     

Mitochondrial phylogeny and biogeography of the genus Gobio (Teleostei: Cyprinidae) in Turkey

Species of the cyprinid genus Gobio Cuvier, 1816 are widely distributed in freshwater lakes and rivers in Turkey, which is a hotspot for freshwater fish diversity and endemism. The mitochondrial 16S, coxI and cytb genes were sequenced for 217 individuals representing 15 species of Gobio from Turkey. A total of 23 haplotypes were identified for each mitochondrial gene. The genetic distance matrices show that Turkish Gobio species are clustered into three groups (northwestern, central and northeastern Anatolia). Phylogenetic trees constructed with combined dataset by using maximum parsimony, maximum likelihood and Bayesian inference methods revealed that the Turkish Gobio species belongs to three well-supported groups in accordance with their geographic distribution: Group I comprises species found in Central Anatolia, Group II species ranging from eastern Thrace to western Anatolia (northwestern Group) and Group III contains only one species from Western Transcaucasia (northeastern Group). The estimated divergence times between the three Gobio groups, calculated using a conventional 1% rate of mutation for a fish mitochondrial cytb gene per million years, coincide with the late Miocene period in which the tectonic uplift of Anatolia and global climate fluctuations occurred. The relatively low genetic distance between Gobio species in the Turkish Lake District indicate that they are not good species.     

Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae,Pucciniales) on Willows in China

The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was an effective approach for delimitating Melampsora species on willows in China.     

First genetic evidence that invasive bullhead (Cottus L. 1758) in Scotland is of English origin and the difficulty of resolving the European Cottus species taxonomy

The European bullhead (Cottus gobio) is widely distributed across Europe, and within the UK is native to England and Wales, where it is protected under the Habitats Directive. In Scotland, however, the species is considered invasive and thriving populations are recorded in the Forth and Clyde river catchments, and the Ale Water in the Scottish Borders. The genetic identity of the Scottish populations has not been established. There is also debate about the status of the European bullhead and its validity as single species, a species complex with several unresolved species, or distinct different species in its European distribution range. There is therefore a need to determine the taxonomy and likely source of the novel Scottish populations. Genetic analyses using cytochrome oxidase 1 (COI) mitochondrial DNA sequences were undertaken on specimens from the Forth and Clyde catchments, and combined with the results of morphological characteristics to provide a comprehensive assessment of the taxonomic classification for Scottish bullheads. There was considerable variation in morphological characteristics between populations within Scotland and a wider range of variability than previously recorded for English populations. Genetically the Scottish populations were very closely related to English specimens, supporting the hypothesis of introduction directly from England to Scotland. In terms of broader relationships, Scottish specimens are genetically more closely related to the ostensible species Chabot fluviatile Cottus perifretum, which has been suggested as one of a complex of species across Europe. Morphologically they exhibit characteristics on the spectrum between C. perifretum and C. gobio. There is an urgent need for the clarification of the taxonomy of Cottus sp(p). to avoid confusion in future publications, legislation and management practices relating to bullheads throughout the UK and Europe.     

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

Dendrobium spp. are traditional Chinese medicinal plants, and the main effective ingredients (polysaccharides and alkaloids) have pharmacologic effects on gastritis infection, cancer, and anti-aging. Previously, we confirmed endophytic xylariaceous fungi as the dominant fungi in several Dendrobium species of tropical regions from China. In the present study, the diversity, taxonomy, and distribution of culturable endophytic xylariaceous fungi associated with seven medicinal species of Dendrobium (Orchidaceae) were investigated. Among the 961 endophytes newly isolated, 217 xylariaceous fungi (morphotaxa) were identified using morphological and molecular methods. The phylogenetic tree constructed using nuclear ribosomal internal transcribed spacer (ITS), large subunit of ribosomal DNA (LSU), and beta-tubulin sequences divided these anamorphic xylariaceous isolates into at least 18 operational taxonomic units (OTUs). The diversity of the endophytic xylariaceous fungi in these seven Dendrobium species was estimated using Shannon and evenness indices, with the results indicating that the dominant Xylariaceae taxa in each Dendrobium species were greatly different, though common xylariaceous fungi were found in several Dendrobium species. These findings implied that different host plants in the same habitats exhibit a preference and selectivity for their fungal partners. Using culture-dependent approaches, these xylariaceous isolates may be important sources for the future screening of new natural products and drug discovery.     

A review of Semigenetta (Viverridae,Carnivora) from the Miocene of Eurasia based on material from the hominid locality of Hammerschmiede (Germany)

The present article offers a detailed review of the taxonomy, distribution and palaeoecology of the genus Semigenetta. The study is based on new craniodental and postcranial remains of the genus from the early late Miocene (Tortonian) locality of Hammerschmiede (Bavaria, Germany). Most of the new specimens are attributed to the medium-sized species Semigenetta sansaniensis, whereas one lower carnassial is assigned to the large-sized Semigenetta grandis, making Hammerschmiede 4 the first known locality with two species of the genus. The variability of the material of S. sansaniensis from Europe allows us to revise the taxonomic weight of some previously used characters, and to identify the smaller-sized late Miocene form Semigenetta ripolli as a junior synonym of the former. Such an evolutionary transition of S. sansaniensis towards smaller forms is explained by niche partitioning with larger carnivorans of similar ecology, such as the herein reported S. grandis. Additionally, the species Semigenetta huaiheensis is here considered as a junior synonym of Semigenetta elegans.     

Genetic and morphometric evidence that the jacks (Carangidae) fished off the coast of Rio de Janeiro (Brazil) comprise four different species

Individuals of jacks that were captured off the Rio de Janeiro coast were characterized using multivariate morphometrics and allozymes molecular markers. The main objectives were to determine the number of fish captured and their species. Classical taxonomic classification and multivariate morphometry indicated the existence of three species in the landings from Rio de Janeiro State (Caranx crysos, Carangoides bartholomaei and Caranx latus). The results of the genetic analyses performed were consistent with these results. However, Bayesian analysis revealed the possible presence of a fourth species, which could not be discriminated by classical taxonomy. Caranx crysos possibly comprises two different species. Other population indexes, such as unique alleles, degree of structuring and genetic identity, also pointed to different species. Therefore, based on evidences from classical taxonomy, geometric morphometric analyses together with genetic data from allozymes molecular markers it is possible to support that at least four different Carangidae species are present in fish landings from Niterói, Rio de Janeiro State, Brazil, whereas fish capture records for the same location have recorded only two species. These results are important for not only developing fisheries management strategies but also providing general information regarding the ecology and evolution of the genus.     

Hybridization in the section Mentha (Lamiaceae) inferred from AFLP markers

The amplified fragment length polymorphism (AFLP) method was used to evaluate genetic diversity and to assess genetic relationships within the section Mentha in order to clarify the taxonomy of several interspecific mint hybrids with molecular markers. To this end, genetic diversity of 62 Mentha accessions from different geographic origins, representing five species and three hybrids, was assessed. Three EcoRI/MseI AFLP primer combinations generated an average of 40 AFLP markers per primer combination, ranging in size from 50 to 500 base pairs (bp). The percentage of markers polymorphic ranged from 50% to 60% across all accessions studied. According to phenetic and cladistic analysis, the 62 mint accessions were grouped into two major clusters. Principal coordinates analysis separated species into well-defined groups, and clear relationships between species and hybrids could be described. Our AFLP analysis supports taxonomic classification established among Mentha species by conventional (morphological, cytological, and chemical) methods. It allows the assessment of phenetic relationships between species and the hybrids M. spicata and M. × piperita, largely cultivated all over the world for their menthol source, and provides new insights into the subdivision of M. spicata, based for the first time on molecular markers.     

Species Delimitation and Morphological Divergence in the Scorpion Centruroides vittatus (Say, 1821): Insights from Phylogeography

Scorpion systematics and taxonomy have recently shown a need for revision, partially due to insights from molecular techniques. Scorpion taxonomy has been difficult with morphological characters as disagreement exists among researchers with character choice for adequate species delimitation in taxonomic studies. Within the family Buthidae, species identification and delimitation is particularly difficult due to the morphological similarity among species and extensive intraspecific morphological diversity. The genus Centruroides in the western hemisphere is a prime example of the difficulty in untangling the taxonomic complexity within buthid scorpions. In this paper, we present phylogeographic, Ecological Niche Modeling, and morphometric analyses to further understand how population diversification may have produced morphological diversity in Centruroides vittatus (Say, 1821). We show that C. vittatus populations in the Big Bend and Trans-Pecos region of Texas, USA are phylogeographically distinct and may predate the Last Glacial Maximum (LGM). In addition, we suggest the extended isolation of Big Bend region populations may have created the C. vittatus variant once known as C. pantheriensis.     

Sibling species of fragrant orchids (Gymnadenia: Orchidaceae, Magnoliophyta) in Russia

Recent molecular phylogenetic studies of the genus Gymnadenia have demonstrated that it contains sibling taxa, i.e., species that are hardly distinguishable according to morphological traits, yet are phylogenetically rather distant and distinctly distinguishable by molecular methods, which is a rare phenomenon for angiosperms. By sequencing the ITS1-5.8S rDNA-ITS2 fragment the presence of G. densiflora was confirmed for Russia. Our data supported a high degree of genetic differentiation between G. conopsea s. str. and G. densiflora, which confirms their taxonomic rank of species. Morphological analysis has shown that the features that are best for the discrimination between these two species in Northwestern Russia are the length of the lower bract, length of the mid-lobe of the lip, and width of leaves. The ecological and phenological differentiation between G. conopsea s. str. and G. densiflora is briefly reviewed. The ITS sequence variation in these species has been analyzed; the molecular genetic differences of the G. conopsea individuals from the eastern part of the distribution area have been discovered for the first time. Different taxonomic interpretations of Gymnadenia phylogenetic tree topology taking into account the presence of sibling species are discussed in general.     

A new sculpin species Cottus sabaudicus sp. nova (Scorpaeniformes: Cottidae) from the Savoy district, France

Sculpins from mountain tributaries of the upper reaches of the Rhone River (Haute-Savoy district) in the collection of the National Museum of Natural History (Paris, France) are described as a new species Cottus sabaudicus. This species belongs to the species group C. gobio, but is characterized by several morphologically specific features. It differs from the typical species of the genus C. gobio in its monotonous body coloration, an increased postanal distance that equals preanal distance, an absence of dark stripes on ventral fins, the ratio of the length of caudal peduncle and depth (1.8–2.3 versus 2.3–2.8), and a greater number of pores in the trunk seismosensory canal (34–37 versus 31–33 + 1).     

A COI Nonsynonymous Mutation as Diagnostic Tool for Intraspecific Discrimination in the European Anchovy Engraulis encrasicolus (Linnaeus)

The European anchovy, Engraulis encrasicolus, is currently one of the principal target species for commercial fisheries in Europe. In this study, the mitochondrial Control Region (CR) and the Cytochrome Oxidase I (COI) mitochondrial gene were analyzed in 74 specimens of E. encrasicolus from four localities in the central Mediterranean. In both populations, the two markers revealed the presence of two main haplogroups, A and B, already detected in previous investigations of different classes of molecular markers. Both CR and COI markers consistently identified two haplogroups. The COI sequence analysis identified a non-synonymous transversion (T to G) at position 116 of the translated sequence, resulting in an amino acid change. All COI sequences of haplogroup A had an amino acid sequence with alanine in this position, while serine was present in the same position in haplogroup B. The two haplogroups A and B were also discriminated by the variable number of TACA elements at the 5’-end of the mitochondrial CR. The selection tests applied to the COI dataset revealed that codon 116 was not under positive selection, that seven amino acid changes were under purifying selection, and that two amino acids were under episodic positive selection.     

Towards resolving the identities of the Graphium butterflies (Lepidoptera: Papilionidae) of Peninsular Malaysia

Graphium butterflies are famous in Peninsular Malaysia for their colourful wings, yet their taxonomy remains unresolved. The popular guides to Malaysian butterflies, place the species in one, two or three genera and identification to species using obscure morphological characters can be difficult, especially for the closely related species, G. bathycles bathycloides and G. chironides malayanum. We sequenced the COI mtDNA barcode for Graphium specimens in the Museum of Zoology, University of Malaya to test the utility of DNA barcoding for the identification of Graphium species. Additionally, we sequenced 28S rRNA to examine, in conjunction with COI, the phylogenetic relationships of these species and investigate the validity of Pathysa and Paranticopsis as distinct genera. We found that all species of Graphium possessed a distinctive cluster of DNA barcodes with the exception of specimens originally identified as G. bathycles bathycloides and G. chironides malayanum which shared DNA barcodes. On further examination we found that the morphological determinations were ambiguous as the specimens overlapped for diagnostic characters reported for each species. The COI and 28S rRNA phylogenetic trees showed a similar topology with Paranticopsis species forming a clade nested within a larger clade also comprising Pathysa species. Based on this topology, in order for Pathysa to be a valid genus, at least three other clades within Graphium s.l. would also have to be raised as genera.     

The potential of AFLPs in biosystematics: A first application inSolanum taxonomy(Solanaceae)

Using the AFLP technique highly informative DNA fingerprints were generated from 19 taxa ofSolanum sect.Petota (potatoes) and three taxa ofSolanum sect.Lycopersicum (tomatoes). Both phenetic and cladistic analyses were conducted from the individual genotypic level to the species level. An AFLP fingerprint, using a combination of suitable AFLP primers, generated 12 to 71 scorable fragments per genotype which was sufficient for taxonomic interpretation. The classifications based on the molecular markers were generally in agreement with current taxonomic opinions. Unexpectedly,S. microdontum was associated with ser.Megistacroloba rather than with ser.Tuberosa, andS. demissum (ser.Demissa) and species of ser.Acaulia appeared closely affiliated. AFLP is an efficient and reliable technique to generate biosystematic data and therefore a promising tool for evolutionary studies.     

Phylogeny of firs (genus <Emphasis Type="Italic">Abies</Emphasis>, Pinaceae) based on multilocus nuclear markers (AFLP)

To study the phylogenetic relationships, evolutionary history, and molecular systematics of firs (genus Abies), the phylogenetic reconstruction, based on nuclear multilocus markers—amplified fragment length polymorphism (AFLP)—was conducted. Using seven combinations of selective primers, 84 samples of 39 taxa were genotyped for 553 polymorphic AFLP loci. A comparison with our earlier chloroplast and mitochondrial phylogenies of the genus (in 2014) shows that the nuclear phylogeny generally is more congruent to the chloroplast tree. Most of the clades resolved by the chloroplast phylogeny were supported also in the AFLP tree. Employing the nuclear DNA-based tree, we revealed the presence of new groups and the differences in the topology of several clades. AFLP confirmed the monophyly of Asian species of section Balsamea and their sister position in relation to the American group of species of this section. As shown by the tree of chloroplast DNA, Asian species of section Balsamea do not form a monophyletic group, but belong to the clade comprising the majority of Asian species. Phylogenetically mitochondrial DNA data to a large extent are not congruent to the nuclear and chloroplast DNA trees, and are more in line with geographical distribution of species. Conflicts between nuclear and cytoplasmic phylogeny were analyzed. Taking them into account, we consider the hypothesis of a hybrid origin of particular groups of firs, including ancient hybridization in section Balsamea. A comparison of molecular data with traditional taxonomy of the genus is discussed.     

Etude du cycle reproducteur du goujon, Gobio gobio L. 2 Variations saisonnières dans l'histologie des testicules

Study on the reproductive cycle of the gudgeon, Gobio gobio L. Part 2 Monthly samplings of male gudgeons, Gobio gobio L. reared in ponds were carried out to study the spermatogenesis of this cyprinid during an entire annual cycle. Together with macroscopic parameters (GSI, condition coefficients, K and K1, nuptial tubercles) the cytologic characteristics of the testis maturation were analysed. The relationship between environmental conditions and spermatogenesis was also examined. The spermatogenetic cycle of G. gobio was divided in two separate periods: a) from October until March, during which only the spermatogonia (SgA and SgB) were present, and b) a stage of active transformation, from April until August, when all the 5 testicular cells (SgA, SgB, Scyt, Spd, Spz) were determined. Dynamic aspects of spermatogenesis were also investigated by an estimation of the proportion of each cellular stage. Spermiation, by abdominal pressure, occurred from mid-April to end of July.     

Circumpolar analysis of morphological and genetic diversity in the Notostracan Lepidurus arcticus

This study presents a first circumpolar screening of the taxonomic and genetic diversity of the crustacean Lepidurus arcticus, belonging to the ‘living fossil’ order Notostraca. Sequencing of a 484 bp segment of the mitochondrial 12S rDNA from 48 populations revealed two distinct haplogroups, each consisting of separate haplotypes. Alignment with published sequences of other species of Lepidurus clearly revealed that all of the studied populations were distinctly different from other species. Some major geographical patterns for distribution of haplogroups and haplotypes were identified, perhaps the most remarkable being the difference in distribution of haplogroups between the neighbouring Svalbard and Bear Island where a larger number of populations were studied. On the Norwegian mainland both haplogroups co-occurred in the same areas, however, and strong conclusions of the distributional pattern are yet premature. The distribution of similar haplotypes over wide geographical ranges suggests high dispersal abilities by Lepidurus. Morphological taxonomic criteria assign all surveyed populations to L. arcticusin spite of a pronounced morphological plasticity. Analysis of major morphological features such as length:width ratio of cephalothorax, the cephalothorax:abdominal length ratio, size of supra-anal plate and eye morphology revealed some distinctive population specific properties. The two major haplogroups differed significantly with regard to the relative size of the supra-anal plate, which also is a standard taxonomic criterion. This first genetic screening of a limited number of populations suggests that a subtler genetic diversity will be revealed when including more populations over a larger geographic area as well as a finer geographical resolution.     

A synopsis of Rhynchospora sect. Pluriflorae (Cyperaceae)

A taxonomic revision of Rhynchospora sect. Pluriflorae revealed 22 species. Nine species are endemic to Brazil, one to Cuba, and another to Bolivia. Of the 22 species, seven were new to science and have been described and published. Two new lectotypes are designated here for R. consanguinea and R. consanguinea var. subrigida . A new name, Rhynchospora albobracteata, is also proposed. A key to species, information on types, illustrations, and discussions of geographic distributions and taxonomy are presented.