Molecular phylogeny,taxonomy, and distribution of French Unio species (Bivalvia,Unionidae)

A plethora of unionid names was established in the nineteenth century by the “Nouvelle Ecole”. Although naiad morphological plasticity is well documented, the currently recognized fauna, with 17 species and subspecies included in the French checklist for the Unio genus, is still based upon morphological characters only. Insights have been provided from molecular data elsewhere in Europe and North Africa, but the French fauna remains unstudied. We present a molecular phylogeny of the Unio genus in France based on COI, 16S and 28S genes; taking up all available data in Europe plus 273 specimens collected in all main French drainages. The results show that there are either three valid species in France, with U. pictorum and U. mancus synonymized, or five, with the subspecies U. crassus courtillieri elevated to species level. Subspecies were generally not recovered, which questions the evolutionary units tacitly implied by subspecific names. Although sampling topotypes is the most reliable way to evaluate the status of a nominal subspecies, major human-induced changes in aquatic hydrosystems challenge the method. Nevertheless, operational taxonomy has to rely on ground-truthed data and we propose to reduce the actual number of valid taxa in France to the seven observed operational taxonomic units.     

Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars

Ten well-annotated genomes of “Sulfolobus islandicus” strains from different geographic locations have been released at the NCBI database. Whole genome based composition vector trees indicate that these strains show the same branching patterns as originally reported by multi-locus sequence analysis. To determine whether the ten strains meet the criteria for separate species, DNA–DNA hybridization (DDH) was performed in silico. DDH values of strains from the same geographic location, i.e., Iceland, Kamchatka and North America, ranged from 82.4 to 95.4 %, clearly qualifying them as members of the same species. The lowest DDH values found between locations ranged from 75.5 to 76.6 %, which exceed the 70 % DDH threshold for a species thereby indicating they are all members of the same species based on the currently accepted definition. The clear divergences of strains from the different geographic locations are sufficiently great to consider them as separate geovars. “S. islandicus” has not yet been validly named and a type strain has not been deposited in culture collections. We urgently recommend that those who study the organism fulfill the criteria of the International Code of Nomenclature of Bacteria in order to designate a type strain and to identify and deposit related strains of this species to make them available to the broader scientific community.     

Seed Coat Microsculpturing Is Related to Genomic Components in Wild Brassica juncea and Sinapis arvensis

It has been reported that wild Brassica and related species are widely distributed across Xinjiang, China, and there has been an argument for species identification. Seed coat microsculpturing (SCM) is known to be an excellent character for taxonomic and evolutionary studies. By identifying collections from Xinjiang, China, and combining SCM pattern, flow cytometry, and genome-specific DNA markers as well as sexual compatibility with known species, this study aimed to detect potential relationships between SCM and genomic types in wild Brassica and related species. Three wild collections were found to be tetraploid with a SCM reticulate pattern similar to B. juncea, and containing A and B genome-specific loci, indicating relatively high sexual compatibility with B. juncea. The others were diploid, carrying S-genome-specific DNA markers, and having relatively high sexual compatibility with Sinapis arvensis. Moreover, their SCM was in a rugose pattern similar to that of S. arvensis. It was suggested that SCM, as a morphological characteristic, can reflect genomic type, and be used to distinguish B-genome species such as B. juncea from the related S. arvensis. The relationship between SCM and genomic type can support taxonomic studies of the wild Brassica species and related species.     

Description of three new Alteromonas species Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. isolated from marine environments,and proposal for reclassification of the genus Salinimonas as Alteromonas

In the course of a bioprospective study of marine prokaryotes for cosmetic purposes, four strains, MD_567^T, MD_652^T, MD_674 and PS_109^T, were isolated that 16S rRNA gene affiliation indicated could represent three new species within the family Alteromonadaceae. A thorough phylogenetic, genomic and phenotypic taxonomic study confirmed that the isolates could be classified as three new taxa for which we propose the names Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. In addition, the consistent monophyletic nature of the members of the genera Alteromonas and Salinimonas showed that both taxa should be unified, and therefore we also propose the reclassification of the genus Salinimonas within Alteromonas, as well as new combinations for the species of the former. As the specific epithets profundi and sediminis are already used for Alteromonas species, we created the nomina nova “Alteromonas alteriprofundi” nom. nov. and Alteromonas alterisediminis nom. nov. to accommodate the new names for “Salinimonas profundi” and Salinimonas sediminis. Whole genome comparisons also allowed us to detect the unexpected codification of aromatic hydrocarbon biodegradative compounds, such as benzoate and catechol, whose activity was then demonstrated phenotypically. Finally, the high genomic identity between the type strains of Alteromonas stellipolaris and Alteromonas addita indicated that the latter is a junior heterotypic synonym of Alteromonas stellipolaris.     

Taxonomische Studien in der Gattung Xerula R. Mre. (IV)

The taxonomically important characteristics of Xerula melanotricha Dörfelt are constant in fruit bodies, also in such which have been formed in culture. Studies on the development of the fruit bodies in culture showed that the macrosetae are formed already in the primordium. At first they are hyaline and colourless. A dark fluid (guttation) is secreted by the macrosetae. This is a specific characteristic of Xerula melanotricha. The fluid has an influence on the colours of the fruit bodies. The American specimens of “Collybia longipes” are revised by Mitchel & Smith (1978). These autors consider all the American collections to be a special variety, “Oudemansiella longipes (St. Amans) Moser var. americana Mitchel et Smith”. Investigations of the holotypus and of other collections suggested that this variety is a well characterized, seperate species. This taxon is an endemit of the Southern Rocky Mountains. In this paper it is described as Xerula americana Dörfelt sp. nov.     

The alkaloid profiles of Sophora nuttalliana and Sophora stenophylla

Sophora is a diverse genus in the family Fabaceae, comprised of herbs, shrubs, and trees that occurs throughout the world, primarily in the northern hemisphere. Species of Sophora are known to contain quinolizidine alkaloids that are toxic and potentially teratogenic. Two perennial herbaceous species occur in North America, Sophora stenophylla and Sophora nuttalliana. The quinolizidine alkaloid composition of these two species was investigated throughout their geographical distribution using field collections and herbarium specimens. Both species contain quinolizidine alkaloids, and S. nuttalliana contains the teratogen anagyrine. Lastly, neither species contains the neurotoxin swainsonine as implied by the common name “white loco” for S. nuttalliana.     

Reappraisal of two of Witham's species of fossil wood with taxonomical and nomenclatural notes on Planoxylon Stopes, Protocedroxylon Gothan and Xenoxylon Gothan

Fossil wood collections at the Natural History Museum, London, were searched for the type material of two important species, described as early as 1831 by Witham, on the basis of material at least partly furnished by Nicol and collected in the Liassic of Whitby (Yorkshire, UK). The names given to these two species by Witham are the basionyms for more than ten other species names, while these species names also provide syntypes for several generic names. Despite this, the original material has been only rarely and partly revised, leading to much confusion.We managed to locate some of the original material. Several topotypes were also studied. On the basis of this review we propose here a neotypification for Peuce huttoniana Witham, a lectotypification for Cupressinoxylon barberi Seward and a lectotypification for Tiloxylon Hartig. We evidence several taxonomical and nomenclatural synonymies, assign Peuce lindleyana Witham to Protocedroxylon and P. huttoniana to Xenoxylon Gothan, and introduce the new combination Xenoxylon huttonianum (Witham) nov. comb. as the correct name for Xenoxylon ellipticum Gottwald & Holleis ex Schultze-Motel.A topotype of Araucariopitys americana Hollick & Jeffrey was also reviewed, which, together with previous results, leads us to suggest that Araucariopitys Hollick & Jeffrey, Protocedroxylon Gothan and Planoxylon Stopes should not be considered as taxonomical synonyms. This point is crucial to the interpretation of the fossil record of Early Abietinae.     

The “miacids” (Carnivoraformes,Mammalia) from the Early Eocene locality of Le Quesnoy (MP7, France); first occurrence of Vassacyon in Europe

We describe here “miacid” taxa from the Early Eocene Paris Basin locality of Le Quesnoy (Oise, France). We describe the new species Vassacyon taxidiotis, the first European record of this genus. The other “miacids” identified from Le Quesnoy are Miacis latouri and Gracilocyon solei. The P4 of G. solei is described here for the first time. Its morphology (e.g., wide protocone, short postmetacrista) supports a close relationship with Miacis rundlei from Abbey Wood (MP8 + 9, England). The latter species is therefore classified as Gracilocyon rundlei. Three new tooth positions are known for Miacis latouri: P4, p4 and m2. They support its reference to Miacis. These specimens imply that the European species is more basal than the North American species. The fauna from Le Quesnoy shares with Dormaal the presence of Miacis latouri and Gracilocyon solei, but the “miacid” fauna from Le Quesnoy also contains Vassacyon taxidiotis. The presence in Le Quesnoy of the two former taxa supports a reference to MP7 level of the French locality. The presence of three distinct genera in European localities show that the “Miacidae” were diversified in Europe, as previously observed in North America. The genera Gracilocyon, Miacis, and Vassacyon probably dispersed from Europe to North America during the Palaeocene/Eocene boundary.     

The taxonomy,chronostratigraphy and paleobiogeography of glyptosaurine lizards (Glyptosaurinae,Anguidae)

Glyptosaurine lizards (Glyptosaurinae, Anguidae) are an extinct group of heavily armored lizards known from North America, Europe and Asia. Glyptosaurine lizards, taxa that possess fully developed tuberculated dermal armor, appear to have been established in North America by late early Puercan time (To3). “Proxestops,” a taxon distinguished by a combination of vermiculate and tuberculated osteoderm sculpturing, is considered to be a non-glyptosaurine, a sister taxon of the Glyptosaurinae. Known from only fragmentary remains, its wide chronostratigraphic distribution suggests that “Proxestops” is a form genus that, in all probability, represents more than one taxon, that ranges from the middle Paleocene to the early Eocene of North America. Moreover, the taxa Odaxosaurus piger, Parodaxosaurus sanjuanensis and “Proxestops” are best considered “proto-glyptosaurines”. “Melanosaurins” and glyptosaurins were well-established by the early Eocene, especially in North America, and are here documented by their type species and chronostratigraphic levels. Both tribes are present in Europe (MP7), too, but the record is not as estensive as that of North America. The North American taxon Gaultia silvaticus (Wa0) is transitional between a “melanosaurin” and glyptosaurin. Because it lacks the well-defined hexagonal osteoderms that characterize the Glyptosaurini, it is removed from that group and considered to be a “melanosaurin”. The “melanosaurin” taxon “Xestops” savagei (Wa4–Wa6) cannot be referred to Xestops (Br2) based on non-corresponding elements and because superficial similarity does not justify assignment to this taxon. Arpadosaurus sepulchralis (Wa6?), whose holotype is a fragmentary right frontal, is considered a subjective junior synonym of A. gazinorum, based on minor differences in the epidermal scale pattern that probably represent individual variation. “Glyptosaurus” agmodon (Wa6?), based on a partial right maxilla, cannot be referred to Glyptosaurus (sensu stricto), and the material upon which this taxon is based bears strong resemblance to material identified as cf. “?Paraglyptosaurus” yatkolai (Wa5–Wa6). “Glyptosaurus” rhodinos (Wa5) is based on an incomplete parietal, and its reference to Glyptosaurus is considered problematic. Eoglyptosaurus donohoei (Wa7) is probably valid and is re-established here. Glyptosaurus (sensu stricto) is known solely from the middle Eocene (Br2) by G. sylvestris. Dimetoposaurus wyomingensis (Br3) is removed from Xestops vagans because its synonymy was based on superficial similarities. Helodermoides tuberculatus, the largest and last glyptosaurin (Ch3), is restricted to the Chadronian of North America. Only the “melanosaurin” Peltosaurus granulosus (Or2–Or3), which includes the species P. abbotti, seems to have crossed the Eocene-Oligocene boundary, and appears to be largely restricted to the Orellan, but extended into the Arikareean. European glyptosaurines are also represented by both glyptosaurins and “melanosaurins” early in the Eocene (MP7). Placosauriops-like “melanosaurins” are known from Dormaal (MP7), and the glyptosaurin taxon?Placosaurus ragei occurs at the same level. “Placosauriops abderhaldeni” has been identified from the Grube Messel (MP11), but this assignment remains dubious because the species has not been adequately diagnosed, and the holotype species is from the Geiseltal (MP13), which is some 4.5 million years younger. Placosauriops weigelti (MP13) is the only valid species of this genus. Paraxestops stehlini (MP14) is not referable to the North American taxon Xestops, and its relationship to Placosauriops has not been studied. The late Eocene glyptosaurins Placosaurus estesi (MP17) and P. rugosus (MP18) are the last glyptosaurines known from Europe and appear to have gone extinct at the Eocene-Oligocene boundary, casulties perhaps of the “Grande Coupure”. Asian glyptosaurines are known solely from one species, Stenoplacosaurus mongoliensis, from the middle Eocene (Sharamurunian) of China. Glyptosaurines most likely originated in North America, diversified by late Paleocene time, and rapidly spread across the North Atlantic into Europe by the early Eocene. Both “melanosaurins” and glyptosaurins took a foothold in Europe by the early Neustrian, but the glyptosaurins, aside from one occurrence (Dormaal, MP7), were conspicuously absent for most of Neustrian through early Robiacian time. In North America, glyptosaurins diversified during the early and middle Eocene, while in Europe small “melanosaurins” were a prominent part of the paleoherpetofauna, and glyptosaurins are unknown for most of the Neustrian through the Geiseltalian, in both the fossilferous Lagerstätten of Messel and Geiseltal. Stenoplacosaurus is the only known glyptosaurin glyptosaurine from Asia, and its abrupt appearance during the late Eocene suggests the possiblity of a Beringian dispersal from North America into Asia.     

REPRODUCTIVE COMPATIBILITY AND RDNA SEQUENCE ANALYSES IN THE SELLAPHORA PUPULA SPECIES COMPLEX (BACILLARIOPHYTA)1

We tested whether internal transcribed spacer (ITS) rDNA sequence differences are correlated with sexual compatibility in the Sellaphora pupula complex, a model system for investigations of the species concept and speciation in diatoms. The phylogenetic relationships among the demes and the systematic position of the genus within the raphid diatoms were also investigated. The division of clones of S. pupula and S. laevissima into groups, based on sequence similarities and phylogenetic analyses, resembled groupings based on sexual compatibility: A high ITS sequence divergence, making full alignment difficult or impossible, was found among clones whose gametangia do not interact, whereas there was little sequence divergence among interfertile clones. This is clearly consistent with the idea that “Z clades” exhibit less intraclade than interclade variation in ITS and, as comparisons of secondary structure models for the RECT and PSEUDOCAP clones showed, that there is an equivalence of “CBC” and Z clades in the rectangular and pseudocapitate demes of S. pupula, as earlier hypothesized for chlorophytes. Intraclonal, presumably intraindividual, variation in ITS was found in S. pupula, though with a degree of variation less than that found within a single Z clade; it was too minor to affect the interclonal relationships in the ITS phylogeny. Sellaphora, which appears monophyletic in 18S phylogenies, with Pinnularia and “Navicula”pelliculosa as its closest allies, may also include some species currently classified in Eolimna. The S. pupula–S. laevissima group began to diversify in or before the Miocene.     

Origin, diversification, and evolution of Samolus valerandi (Samolaceae, Ericales)

The almost cosmopolitan distribution of Samolus valerandi is unique in the genus Samolus L. (Samolaceae), which also includes 12–15 taxa with distributions restricted to smaller areas of the Southern Hemisphere. Recent molecular phylogenetic studies based on chloroplast and nuclear DNA sequences showed that the widespread S. valerandi and the North American S. parviflorus are both part of a strongly supported clade, together with the North American S. vagans, S. spathulatus, and S. latifolius. To better understand the origin, distribution, and diversification of S. valerandi and to clarify the relationships within this clade, we performed molecular phylogenetic analyses based on the plastid trnS-G intergenic spacer and the nuclear ribosomal ITS region. We have also sought further support for relationships by examining flower and leaf characters. On the basis of new results, we propose that S. valerandi, S. parviflorus, and S. vagans are considered as part of a widespread “species complex”, with its centre of diversity in North America. No clear vicariance patterns were found regarding the phylogeography of S. valerandi, which thus seems to have dispersed secondarily to various places around the world, possibly as a result of human activities.     

Analysis of digitized herbarium records and community science observations provides a glimpse of downy mildew species diversity of North America,reveals potentially undescribed species,and documents the need for continued digitization and collecting

Downy mildew diseases caused by Peronosporaceae cause significant crop losses globally, with several emerging and resurgent threats in recent decades. Biodiversity data from digitized herbarium specimens provide an opportunity to develop a baseline census of species diversity, however, these resources may represent aggregations of nonrandom and opportunistic collecting efforts, which could lead to spurious results. Here, the MyCoPortal census of digitized herbarium records for downy mildew species collected from North America 1800 to present were analyzed. From 9838 unique records, 196 species were identified, reflecting ∼28% of known species diversity. Temporal and geographic collecting biases were observed, with 90% of the collections made prior to 1960 and the efforts of six “super-collectors” accounting for 25% of the collections. The presence of 50–100 undescribed species in North America was inferred from the records. Together, these results highlight the need for continued downy mildew collections, taxonomic research and digitization efforts.     

Phylogenetic relationships of Korean Sparassis latifolia based on morphological and ITS rDNA characteristics

Recent studies based on morphological characteristics and molecular analyses have revealed that the characteristics of Sparassis crispa from Asia are not concordant with those of collections from Europe and North America. Consequently, the Asian isolate was redefined as Sparassis latifolia. This study is the first report of Sparassis latifolia collected in Korea. The taxonomic relationships and replacement of Sparassis species were inferred from a comparison of the morphological characteristics and by molecular sequence analysis of the internal transcribed spacer (ITS) rDNA regions. In particular, this study focused on the phylogenetic relationships inferred from the biogeographical distribution of isolates within the genus Sparassis.     

Earthworms newly from Mongolia (Oligochaeta,?Lumbricidae,Eisenia)

Two new megadrile earthworms from the steppes, the first species wholly from Outer Mongolia, are ascribed to the partially parthenogenetic Eisenia nordenskioldi (Eisen, 1879) species-complex. Taxonomic justification of sympatric Eisenia nordenskioldi mongol and Eisenia nordenskioldi onon ssp. n. are supported by mtDNA COI barcodes. The unreliability of molecular differentiation based on voucher names compared to definitive types is again demonstrated, as pertains to the ultimate Eisenia andrei Bouché, 1972 synonym of the Eisenia fetida (Savigny, 1826) sibling species-complex composed of more than a dozen prior names. Similar species described from Northeast China [formerly Manchuria] and North Korea are briefly considered, albeit they are intermittently held in synonymy of cosmopolitan Aporrectodea rosea (Savigny, 1826) along with many other taxa including some exotic lumbricids initially found in India. Japanese and North American lumbricids are also mentioned. Distributions are discussed and an annotated checklist of all nine Siberian/sub-arctic Eisenia nordenskioldi ssp. is appended.     

On the Evolutionary and Biogeographic History of Saxifraga sect. Trachyphyllum (Gaud.) Koch (Saxifragaceae Juss.)

Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss.) provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud.) Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i) a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii) a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and plants inhabiting the North Pacific Rim.     

A gap analysis methodology for collecting crop genepools: a case study with phaseolus beans

Background

The wild relatives of crops represent a major source of valuable traits for crop improvement. These resources are threatened by habitat destruction, land use changes, and other factors, requiring their urgent collection and long-term availability for research and breeding from ex situ collections. We propose a method to identify gaps in ex situ collections (i.e. gap analysis) of crop wild relatives as a means to guide efficient and effective collecting activities.

Methodology/Principal Findings

The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps. We apply the gap analysis methodology to wild taxa of the Phaseolus genepool. Of 85 taxa, 48 (56.5%) are assigned high priority for collecting due to lack of, or under-representation, in genebanks, 17 taxa are given medium priority for collecting, 15 low priority, and 5 species are assessed as adequately represented in ex situ collections. Gap “hotspots”, representing priority target areas for collecting, are concentrated in central Mexico, although the narrow endemic nature of a suite of priority species adds a number of specific additional regions to spatial collecting priorities.

Conclusions/Significance

Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions. A more detailed prioritization of taxa and geographic areas for collection can be achieved by including in the analysis predictive threat factors, such as climate change or habitat destruction, or by adding additional prioritization filters, such as the degree of relatedness to cultivated species (i.e. ease of use in crop breeding). Furthermore, results for multiple crop genepools may be overlaid, which would allow a global analysis of gaps in ex situ collections of the world''s plant genetic resources.     

Spirometra species from Asia: Genetic diversity and taxonomic challenges

Despite considerable controversy concerning the taxonomy of species within the genus Spirometra, human sparganosis and spirometrosis mainly in Asia and Europe has long been confidently ascribed to Spirometra erinaceieuropaei. Recently, the mitochondrial genomes of purported “S. erinaceieuropaei”, “Spirometra decipiens” and “Spirometra ranarum” from Asia have been determined. However, it has been pointed out that the morphological criteria used for identifying these species are unsuitable and thus these identifications are questionable. In the present study, therefore, Spirometra samples from Asia were re-examined based on mitochondrial cytochrome c oxidase subunit 1 gene sequences and the identification of these species was discussed. Haplotype network and phylogenetic analyses revealed that: i) two distinct Spirometra species, Type I and Type II, are present in Asia and neither of which is close to likely European “S. erinaceieuropaei”; ii) Type I is genetically diverse and widely distributed, however Type II is known so far from Japan and Korea; iii) “S. decipiens” and “S. ranarum” reported from Asia are conspecific with Type I; iv) Type I is probably conspecific with Spirometra mansoni, and Type II may represent an undescribed species.