Genetic data,reproduction season and reproductive strategy data support the existence of biological species in Ophioderma longicauda

Cryptic species are numerous in the marine environment. The brittle star Ophioderma longicauda is composed of six mitochondrial lineages, encompassing brooders, which form a monophyletic group, and broadcasters, from which the brooders are derived. To clarify the species limits within O. longicauda, we compared the reproductive status of the sympatric lineages L1 and L3 (defined after sequencing a portion of the mitochondrial gene COI) during the month of May in Greece. In addition, we genotyped a nuclear marker, intron i51. Each L3 female was brooding, whereas all L1 specimens displayed full gonads, suggesting temporal pre-zygotic isolation between brooders and broadcasters. Statistical differences were found among lineages in morphology and bathymetric distribution. Finally, the intron i51 was polymorphic in L1 (60 individuals), but monomorphic in L3 (109 individuals), confirming the absence of gene flow between brooders and broadcasters. In conclusion, the broadcasting lineage L1 and the brooding lineage L3 are different biological species.     

Phylogenetic analyses of Japanese golden chanterelles and a new species description,Cantharellus anzutake sp. nov.

The Japanese golden chanterelle commonly identified as Cantharellus cibarius was sampled in a broad range of forest vegetation. A total of 90 fresh and 11 herbarium specimens were examined microscopically, subjected to sequencing analysis of their nuclear ribosomal RNA (rDNA) and tef-1 genes, and their characteristics were compared with those of European C. cibarius. Based on morphological and ecological characteristics, basidioma samples from Japan were divided into four species. While specimens of Cantharellus sp. 4 from Hokkaido Island were included in the European C. cibarius clade phylogenetically, the other three species formed three unique clades. Among these, Cantharellus anzutake sp. nov. is sister to the clade of C. cibarius and was widely sampled from the northern limit of Honshu Island to the southern limit of Kumejima Island in Ryukyu Islands. Although C. anzutake was morphologically similar to C. cibarius, the two species were phylogenetically distinct. Other morphologically similar but genetically distinct chanterelle species from India exhibited macroscopic and microscopic differences compared with C. anzutake.     

Molecular identification and relative abundance of cryptic Lophodermium species in natural populations of Scots pine,Pinus sylvestris L.

The multi-locus phylogenetic species recognition approach and population genetic analysis of Amplified Fragment Length Polymorphism (AFLP) markers were used to delineate Lophodermium taxa inhabiting needles of Scots pine (Pinus sylvestris) in native pinewoods within Scotland. These analyses revealed three major lineages corresponding to the morphological species Lophodermium seditiosum and Lophodermium conigenum, fruiting on broken branches, and Lophodermium pinastri, fruiting on naturally fallen needles. Within L. pinastri three well supported sister clades were found representing cryptic taxa designated L. pinastri I, L. pinastri II, and L. pinastri III. Significant differences in mean growth rate in culture were found among the cryptic taxa. Taxon-specific primers based on ITS sequences were designed and used to classify over 500 Lophodermium isolates, derived from fallen needles of P. sylvestris in three Scottish and one French pinewood site, into the three L. pinastri cryptic taxa. Highly significant differences in the relative abundance of the three taxa were found among the Scottish pinewood sites, and between the French and all of the Scottish sites.     

The Hoosier cavefish,a new and endangered species (Amblyopsidae,Amblyopsis) from the caves of southern Indiana

We describe a new species of amblyopsid cavefish (Percopsiformes: Amblyopsidae) in the genus Amblyopsis from subterranean habitats of southern Indiana, USA. The Hoosier Cavefish, Amblyopsis hoosieri sp. n., is distinguished from A. spelaea, its only congener, based on genetic, geographic, and morphological evidence. Several morphological features distinguish the new species, including a much plumper, Bibendum-like wrinkled body with rounded fins, and the absence of a premature stop codon in the gene rhodopsin. This is the first new cavefish species described from the United States in 40 years and exemplifies how molecular data can alert us to the presence of otherwise cryptic biodiversity.     

Molecular-genetic analyses reveal cryptic species of trematodes in the intertidal gastropod, Batillaria cumingi (Crosse)

Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philophthalmid, were detected using polymerase chain reaction-based restriction fragment-length polymorphism methodology and sequence analyses. These digeneans were all collected from the same species of gastropod first intermediate host, Batillaria cumingi (=Batillaria attramentaria). The mitochondrial cytochrome oxidase subunit 1 gene (approximately 800bp) and nuclear internal transcribed spacer 1 gene (approximately 400bp) were used for species level discrimination. Restriction fragment-length polymorphism analyses of cytochrome oxidase subunit 1 gene showed that C. batillariae included 10 distinguishable fragment patterns, and the philophthalmid included five patterns. On the basis of subsequent sequence analyses, the restriction fragment length polymorphism patterns of C. batillariae were grouped into eight phylogenetically distinct lineages and those of the philophthalmid into three phylogenetically distinct lineages. There was no evidence of gene flow among the different lineages due to the lack of heterozygosity within the observed internal transcribed spacer 1 gene fragment patterns. This suggests that all of these lineages are different species. Most of these species were widespread, but some exhibited restricted geographic distributions. We discuss the implications of these findings for host specificity of these trematodes. These results demonstrate the utility of genetic analysis to distinguish species of morphologically similar trematodes. Hence, trematode species diversity may often be underestimated when species identifications are limited to morphological features.     

Molecular and phylogenetic characterization of Ostreopsis (Dinophyceae) and the description of a new species,Ostreopsis rhodesae sp. nov., from a subtropical Australian lagoon

Cryptic and pseudo-cryptic species are common amongst marine phytoplankton, and may cause misleading inferences of ecological and physiological data of plankton community studies. Deciphering the diversity and distribution of species of the benthic dinoflagellate Ostreopsis is one example, as there are many morphologically indistinct clades that differ greatly genetically and toxicologically from one another. In this study, a new species, Ostreopsis rhodesae from the southern Great Barrier Reef was described. While it initially appeared to be highly similar to several other Ostreopsis species, we found O. rhodesae can be distinguished based on the relative size of the second apical plate (2′), which is twice as long as the APC plate, and separates the third apical (3′) from the third precingular (3′′) plate. Phylogenetic trees based on the SSU, ITS/5.8S and D1-D2 and D8-D10 regions of the LSU rRNA were well supported, and showed a clear difference to other Ostreopsis clades. Compensatory base changes (CBCs) were identified in helices of the ITS2 between O. rhodesae and O. cf. ovata and O. cf. siamensis, which were also present in the same habitat. Fish gill cell lines were toxic to O. rhodesae, cell extracts but no palytoxin-like analogues were found in them. The findings highlight a case of pseudo-cryptic speciation, found in sympatry with closely related and morphologically similar species, but biologically and functionally distinct.     

Pythium carbonicum,a new species isolated from a spoil heap in northern France,the ITS region,taxonomy and comparison with related species

Pythium carbonicum (F-72) sp. nov. was found in soil samples taken on the top of a spoil heap in northern France. The morphology of this new species resembles that of a recently described species: Pythium megacarpum. However, the antheridial and oogonial characteristics of this new species are unique, and the comparison of its ITS region of the nuclear ribosomal DNA indicates that this species is also related to the genus Phytophthora. The fungus does not sporulate, the sporangia germinate directly into mycelium through germ tubes. The oogonia of P. carbonicum are smooth-walled and also papillated, and are provided with monoclinous and diclinous antheridia that wrap around, forming a complicated knot. Morphological features of this new species, together with the sequences of the ITS region of its nuclear ribosomal DNA and its comparison with related species are discussed here.     

Two new Polyangium species,P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample

Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1^T, and two rose pink strains, designated SDU13 and SDU14^T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14^T formed solitary sporangioles under starvation conditions, while SDU3-1^T had no fruiting body structures. They showed 95.9–97.0% (SDU3-1^T) or 98.7–98.9% (SDU13 and SDU14^T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1^T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14^T) with the G + C content range of 68.3–69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C_18:1ω9c, C_16:0 and C_18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1^T (=CGMCC 1.16875^T = KCTC 72136^T) and SDU14^T (=CCTCC AB 2021123^T = KCTC 82625^T), respectively.     

Phylogenetic analysis of Allium subg. Melanocrommyum infers cryptic species and demands a new sectional classification

Allium subgenus Melanocrommyum (Alliaceae) from Eurasia comprises about 150 mostly diploid species adapted to arid conditions. The group is taxonomically complicated with different and contradictory taxonomic treatments, and was thought to include a considerable number of hybrid species, as the taxa show an admixture of assumed morphological key characters. We studied the phylogeny of the subgenus, covering all existing taxonomic groups and their entire geographic distribution. We analyzed sequences of the nuclear rDNA internal transcribed spacer region (ITS) for multiple individuals of more than 100 species. Phylogenetic analyses of cloned and directly sequenced PCR products confirmed the monophyly of the subgenus, while most sections were either para- or polyphyletic. The splits of the large sections are supported by differences in the anatomy of flower nectaries. ITS data (i) demand a new treatment at sectional level, (ii) do not support the hypotheses of frequent gene flow among species, (iii) indicate that multiple rapid radiations occurred within different monophyletic groups of the subgenus, and (iv) detected separately evolving lineages within three morphologically clearly defined species (cryptic species). In two cases these lineages were close relatives, while in Allium darwasicum they fall in quite different clades in the phylogenetic tree. Fingerprint markers show that this result is not due to ongoing introgression of rDNA (ITS capture) but that genome-wide differences between both lineages exist. Thus, we report one of the rare cases in plants where morphologically indistinguishable diploid species occurring in mixed populations are non-sister cryptic species.     

Characterisation of a new species of Pythium isolated from a wheat field in northern France and its antagonism towards Botrytis cinerea causing the grey mould disease of the grapevine

A new species, Pythium bifurcatum, isolated from soil samples taken from a wheat field in Lille in northern France is described here. The oomycete occurred thrice out of 50 samples. The type specimen is F-91, which is a slow-growing saprophyte living on vegetable debris and which can be recognised by its antheridial as well as oogonial characteristics, which are different from other known species of Pythium. When grown together with Botrytis cinerea, the causal agent of the grey mould disease of the grapevine, Pythium bifurcatum shows a pronounced antagonism and suppresses its growth. Morphological features of this new species, its antagonism to B. cinerea, the sequences of the ITS region of its nuclear ribosomal DNA, and its comparison with related species are discussed in this article.     

Genetic structure of natural populations of the California black abalone (Haliotis cracherodii Leach, 1814), a candidate for endangered species status

The black abalone (Haliotis cracherodii) has been severely depleted across much of its historic range by a combination of overexploitation and disease. Natural recovery of extirpated populations along the southern California coast will depend on the extent to which remnant populations can serve as larval sources to geographic locations formerly supporting abalone populations. Population genetic analyses of mitochondrial cytochrome oxidase subunit one (COI) DNA sequences, four nuclear microsatellites, and 142 amplified fragment length polymorphisms (AFLPs) were used to evaluate connectivity among populations of H. cracherodii sampled from the central California coast and four islands in the Southern California Bight. Global divergence among populations was significant at COI and the AFLP loci. The Hka28 microsatellite locus and AFLP data showed significant divergence in multiple pairwise population comparisons and exhibited a signal of isolation by distance. Although estimates of gene flow based on genetic analyses must be interpreted with caution, the observed level of interpopulation genetic divergence suggests that larval dispersal is restricted, and natural recovery of decimated H. cracherodii populations along the coast of California is unlikely to occur in the near future.     

Tylotus laqueatus,a new species of Dicranemataceae (Gigartinales,Rhodophyta) from the Hawaiian Islands

A rarely collected shallow‐subtidal Hawaiian macroalga has been determined anatomically and molecularly to belong to an undescribed species of Tylotus J. Agardh, the most widely distributed genus of the small, mostly Australian‐endemic family Dicranemataceae. Thalli are repent and imbricate on calcareous boulders at the type locality on O‘ahu, and are anchored both basally and by haptera arising marginally and ventrally on the (sub‐)dichotomous, linear axes. Simple or forked terete haptera can be a means of perennation by the occasional direct issuing of adventitious blades. Fronds are multiaxial and consist of a broad pseudoparenchymatous medulla of thick‐walled cells surrounded on both sides by a two‐ or three‐layered small‐celled pigmented cortex in which numbers of ‘glandular’ hairs are embedded. Tetrasporangia are zonate, and gametophytes are monoecious. Carpogonial branches are three‐celled, directed to the thallus surface, and borne laterally on inner‐cortical supporting cells; cystocarps are prominently protuberant and scattered sparingly on dorsal frond surfaces, the carposporophytes directed outwardly beneath an ostiolate pericarp and connected to the parent gametophyte across a broad placental base in which the remnant auxiliary cell persists centrally. The inner surface of the pericarp is unusual in producing extensive patches or isolated islands of short gonimoblast filaments with terminal carposporangia as an apparent result of the implantation of gonimoblasts into the tissue of the lining. Anatomy indicates that the new species is more closely related to the East‐Asian Tylotus lichenoides Okamura than to the only other described member of the genus, the type species T. obtusatus (Sonder) J. Agardh from southern Australia. An rbcL phylogeny supports placement of sequences for Hawaiian specimens within the genus Tylotus but distinct from all previously recorded sequences of Tylotus. As is widely reported in other molecular‐phylogenetic analyses of the Gigartinales, we find that support for generic and familial relationships within the order is strong whereas that for between‐family relationships is low.     

ITS region of the rDNA of Pythium longandrum, a new species; its taxonomy and its comparison with related species

Pythium longandrum (F-73.0) was isolated, from soil samples taken in Lille in northern France. Morphologically the fungus resembles closely Pythium rostratum, however its antheridial characters are unique. The oogonia of this species are provided with hypogynous and monoclinous antheridia. The antheridial cells are inflated and are probably the largest and longest for the genus. The internal transcribed spacer region of its nuclear ribosomal DNA indicates that it is entirely different from all other species of Pythium. This new species is characterized by its spherical to elongated sporangia, smooth-walled oogonia and hypogynous to monoclinous antheridia bearing long antheridial cells closely applied to the oogonia. Morphological features of this new species, together with the sequences of the ITS region of its nuclear ribosomal DNA and comparison with related species are discussed here.     

Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami Bay and its phylogenetic analysis

A new species of the genus Rhodotorula was isolated from a tubeworm (Lamellibrachia sp.) collected at a depth of 1156 m in Sagami Bay, Japan. Strain SY-89 had physiological properties quite similar to R. aurantiaca. Two phylogenetic trees, one based on internal transcribed spacer (ITS) regions and 5.8S rDNA sequences and the other based on the D1/D2 region of the large subunit (26S) rDNA sequences, united strain SY-89 to the type strain of Sakaguchia dacryoides through a considerable evolutionary distance. Strain SY-89 was differentiated from S. dacryoides by the G+C content of the nuclear DNA and differences in the ability to utilize specific carbon and nitrogen compounds. The low complementarity of strain SY-89 DNA to that of the type strain of S. dacryoides confirmed that this strain was genetically unrelated to previously known species. The tubeworm isolates are described as R. lamellibrachii sp. nov. The type strain of R. lamellibrachii is strain SY-89 (= JCM 10907). R. lamellibrachii formed a cluster with Erythrobasidium hasegawianum, R. lactosa, S. dacryoides and Sporobolomyces elongatus on the ITS and 5.8S rDNA phylogenetic tree. These five species shared a signature sequence in 26S rDNA, although this relationship was not supported by phylogeny based on the D1/D2 region of 26S rDNA.     

A new species of Haplophyllum A. Juss. (Rutaceae) from the Iberian Peninsula: evidence from morphological, karyological and molecular analyses

BACKGROUND AND AIMS: The discovery of a new species, Haplophyllum bastetanum F.B. Navarro, V.N. Suárez-Santiago & Blanca sp. nov., in the south-east of Spain has prompted the comparative study of species of the Iberian Peninsula, and others related, through morphological, cytogenetic, molecular, distributional and ecological characterization. METHODS: The morphological study involved a quantitative analysis of the species present in the Iberian Peninsula and a comparative analysis of the morphological characteristics between H. bastetanum and other related species. Mitotic analyses were made with root meristems taken from germinating seeds. Phylogenetic analyses of the internal transcribed spacer sequences of nuclear ribosomal DNA were performed using neighbour-joining (NJ) and maximum-parsimony methods. KEY RESULTS: Haplophyllum bastetanum is a diploid species (2n = 18) distinguished primarily for its non-trifoliate glabrous leaves, lanceolate sepals, dark-green petals with a dorsal band of hairs, and a highly hairy ovary with round-apex locules. The other two Iberian species (H. linifolium and H. rosmarinifolium) are tetraploid (2n = 36) and have yellow petals. Both phylogenetic methods generated a well-supported clade grouping H. linifolium with H. rosmarinifolium. In the NJ tree, the H. linifolium-H. rosmarinifolium clade is a sister group to H. bastetanum, while in the parsimony analysis this occurred only when the gaps were coded as a fifth base and the characters were reweighted according to the rescaled consistency index. This latter group is supported by the sequence divergence among taxa. CONCLUSIONS: The phylogenies established from DNA sequences together with morphological and cytogenetic analyses support the separation of H. bastetanum as a new species. The results suggest that the change in the number of chromosomes may be the key mechanism of speciation of the genus Haplophyllum in the Iberian Peninsula. An evolutionary scheme for them is propounded.     

ITS1 region of the rDNA of Pythium proliferatum, a new species: its taxonomy and its comparison with related species

A new species, Pythium proliferatum (F-382), was isolated from soil samples taken in Genlis in the burgundian region of France. The fungus is unique because of the character combinations of its large, spherical to elongated, proliferating sporangia, and its smooth walled oogonia supplied with different types of antheridia like hypogynous, monoclinous sessile, monoclinous stalked, diclinous and wrapping around the oogonia. Almost all types of antheridia that are found in the genus are present in this new species. Morphological features of this new species, together with the sequences of the ITS1 region of its nuclear ribosomal DNA and its comparison with related species are discussed in this article.