Phylogenetics of the marine sculpins (Teleostei: Cottidae) of the North American Pacific Coast

With 92 species along the North American Pacific Coast, marine sculpins represent the most species-rich radiation of fishes in this region. I used the mitochondrial cytochrome b gene and the nuclear ribosomal S7 intron for 99 species (76 North American, 19 Asian, and four North Atlantic) to produce the most complete phylogenetic hypothesis yet generated for this assemblage. Maximum likelihood and Bayesian analyses produced highly similar tree topologies. While many previously proposed groupings based on morphology are recovered, the molecular data suggest that a number of genera are para- or polyphyletic. However, this analysis supports the monophyly of one large clade that is found exclusively along the North American Pacific Coast (Chitonotous–Ruscarius–Artedius–Orthonopius–Clinocottus–Leiocottus–Oligocottus). Some sibling species have disjunct ranges, suggesting allopatric speciation. However, many other sibling species have largely overlapping ranges, and repeated habitat shifts appear to have facilitated diversification.     

Transatlantic disjunction in fleshy fungi. I. The Sparassis crispa complex

Phylogenies based on ITS and LSU sequences show that the Sparassis crispa complex comprises several monophyletic clades, in some cases co\rresponding to named taxa (i.e. S. crispa, S. radicata), but others lacking names (i.e. eastern and southwestern North American S. “crispa”). In our study, morphological examination of numerous collections also distinguished subtle differences correlated with geographic distribution. Underlying these problems, several taxa lacked type specimens for taxonomic analysis. In this paper, appropriate epitypes are designated and names assigned. Extensive sexual compatibility experiments, described within, indicate that monokaryon, haploid isolates of collections from North America and Europe are consistently sexually compatible to some degree. Inherent in the study, different “species concepts” were tested, with the “biological species concept,” based on sexual compatibility, being the least restrictive. We propose two new taxa, S. americana and S. americana f. arizonica.     

Phylogenetic Analyses of Teleki Grapevine Rootstocks Using Three Chloroplast DNA Markers

Teleki rootstocks are used in grapevine-producing countries all over the world. They represent one of the largest groups of available rootstocks but their origin is still in dispute although they have been regarded as Vitis berlandieri × V. riparia hybrids. To investigate their possible origin, we amplified and sequenced three chloroplast regions, two non-coding spacers (trnL-F, trnS-G) and the trnL group I intron in a core collection of Teleki rootstocks representing widespread accessions and related wild North American grape species (V. berlandieri, V. riparia and V. rupestris). Concatenated sequence data coupled with microstructural changes discovered in the chloroplast regions provided data to trace the maternal ancestry of the Teleki lines. All chloroplast regions showed both nucleotide and length variation. Length mutations in the non-coding regions represented mostly simple sequence repeats of poly-A and -T stretches. These indel characters exhibited additional diversity comparable with the nucleotide diversity and increased resolution of the phylogenetic trees. We found that a group of Teleki accessions position together with the wild grape species V. riparia. Another group of Teleki rootstocks formed a sister group to the other North American species V. berlandieri. These clades had moderate support values, and they do not share ancestry with other accessions of Teleki rootstocks resolved with high support value in the V. riparia clade. It seems that Teleki-Kober 5BB and 125 AA accessions might have a V. berlandieri maternal background. We also found great differences within putative clones of Teleki 5C and Teleki-Kober 5BB suggesting that the selection of these accessions was performed on heterogenous or mislabeled plant material collectively maintained under these names.     

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.     

Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement,plasmid diversity,and streptomycin resistance

Erwinia amylovora is a destructive pathogen of Rosaceous plants and an economic concern worldwide. Herein, we report 93 new E. amylovora genomes from North America, Europe, the Mediterranean, and New Zealand. This new genomic information demonstrates the existence of three primary clades of Amygdaloideae (apple and pear) infecting E. amylovora and suggests all three independently originate from North America. The comprehensive sequencing also identified and confirmed the presence of 7 novel plasmids ranging in size from 2.9 to 34.7 kbp. While the function of the novel plasmids is unknown, the plasmids pEAR27, pEAR28, and pEAR35 encoded for type IV secretion systems. The strA-strB gene pair and the K43R point mutation at codon 43 of the rpsL gene have been previously documented to confer streptomycin resistance. Of the sequenced isolates, rpsL-based streptomycin resistance was more common and was found with the highest frequency in the Western North American clade.     

Evidence for ongoing introduction of non-native earthworms in the Washington,DC metropolitan area

Earthworm introductions and invasions are ongoing, with significant consequences for ecological characteristics and function where populations of invasive species reach high densities. In North America the influx of people, goods and materials to coastal cities has long been recognized to be related to introduction and establishment of many different invasive organisms. We conducted surveys for soil invertebrates in the Washington, DC area along the Potomac River corridor to examine the influence of historic soil profile disrupting disturbances on the composition of soil invertebrate communities. Here we report three earthworm taxa that either (1) had never been previously reported in North America (Lumbricidae: Helodrilus oculatus), (2) had never been reported from “wild” caught samples in forested soils (Lumbricidae: Eisenia fetida), or (3) represented a notable range expansion for an introduced species (Lumbricidae: Murchieona muldali). All three species reported here have attributes that give reason for concern over their expansion into North American soils, not least of which is their potential for competitive interactions with the remaining native earthworm species.     

The Music Indici: its authors, types and localities

The sixty new taxa described in Musci Indici are reviewed. As a result of validation of 54 of these by plates alone, authorities, original specimens and provenance of many have been widely misinterpreted. Evidence from published material, unpublished correspondence and herbarium material demonstrates that W. H. Harvey (1836) is the sole validating author of most of the names; three were validated by J. D. Hooker in 1837, and two names jointly by J. D. Hooker and Harvey in 1840. None was validated by W. J. Hooker, in the past often considered to be the author of some of the names. It is shown that Musci Indici names should be typified by lectotypes; recent typifications of four of the names by ‘holotypes’ and six out of eight published ‘lectotypes’ are untenable as the specimens selected were not original material studied by Harvey, and should be superseded by new lectotypes. Five specimens are selected as new lectotypes. Original material, mostly in Harvey's herbarium in TCD, is identified as most suitable for future lectotypification of the other names. Types for the three names based solely on Royle material are located in LIV and BM. Original Harvey material is also preserved in GL, but most of the Wallich collections in BM, E and elsewhere are not part of the original material. For Neckera blanda no suitable type specimen was located; the original published plate is selected as lectotype with a specimen in BM as a supporting ‘epitype’. Many of the original localities published in 1840 as ‘Nepal’ are shown to be erroneous. As far as possible these are corrected but for some taxa provenance remains doubtful. Twenty-two of the new names are shown not to have been based on material from Nepal; as a result ten species (Acanthorrhynchium papillatum, Brachythecium kamounense, Chaetomitriopsis glaucocarpa, Meiothecium microcarpum, Mitthyridium repens, Rozea fulva, Splachnobryum flaccidum, Sterophyllum radiculosum, Trichosteleum boschii and Trismegistia lancifolia) and Trismegistia lancifolia) are deleted from the Nepal checklist. Twenty-eight of the new species are considered to be reliably based on material from Nepal, and a further five doubtfully so. Rozea microcarpa Broth. is shown to be an synonym of R. fulva (Harv.) M. Fleisch. Past taxonomic confusion between Hypnum cordatum Harv. and Neckera cordata [Hook. ex] Harv. is untangled; the first is shown to be a synonym of Eurhynchium hians (Hedw.) Sande Lac. and the second is the basionym of Penzigiella cordata (Harv.) M. Fleisch.     

Turning to the dark side: LED light at night alters the activity and species composition of a foraging bat assemblage in the northeastern United States

Artificial light at night (ALAN) is a rapidly intensifying form of environmental degradation that can impact wildlife by altering light‐mediated physiological processes that control a broad range of behaviors. Although nocturnal animals are most vulnerable, ALAN''s effects on North American bats have been surprisingly understudied. Most of what is known is based on decades‐old observations of bats around street lights with traditional lighting technologies that have been increasingly replaced by energy‐efficient broad‐spectrum lighting, rendering our understanding of the contemporary effects of ALAN on North American bats even less complete. We experimentally tested the effects of broad‐spectrum ALAN on presence/absence, foraging activity, and species composition in a Connecticut, USA bat community by illuminating foraging habitat with light‐emitting diode (LED) floodlights and comparing acoustic recordings between light and dark conditions. Lighting dramatically decreased presence and activity of little brown bats (Myotis lucifugus), which we detected on only 14% of light nights compared with 65% of dark (lights off) and 69% of control (lights removed) nights. Big brown bat (Eptesicus fuscus) activity on light nights averaged only half that of dark and control nights. Lighting did not affect presence/absence of silver‐haired bats (Lasionycteris noctivagans), but decreased their activity. There were no effects on eastern red bats (Lasiurus borealis) or hoary bats (L. cinereus), which have been described previously as light‐tolerant. Aversion to lighting by some species but not others caused a significant shift in community composition, thereby potentially altering competitive balances from natural conditions. Our results demonstrate that only a small degree of ALAN can represent a significant form of habitat degradation for some North American bats, including the endangered little brown bat. Research on the extent to which different lighting technologies, colors, and intensities affect these species is urgently needed and should be a priority in conservation planning for North America''s bats.     

Risk of infection of white-nose syndrome in North American vespertilionid bats in Mexico

Emerging diseases in wildlife pose challenges for conservation due to their usually rapid spread and high cause of mortality. The transmission of these diseases is a complex ecological process that involves interactions between groups of individuals, particularly in gregarious species. White-nose syndrome, caused by the fungus Pseudogymnoascus destructans, is increasingly infecting species of vespertilionid North American bats causing, in some cases, high population mortality. In this study, we modeled ecological niches projected as potential distributions for three strains of P. destructans (Asian, European and North American) and a group of species of verpertilionid bats in North America. Our model showed that the ecological niches of North American and Asian fungi strains are projected to expand into new geographic areas, with statistical significance between the two strains. In addition, our model identified the presence of all three strains of fungi in areas where the fungus has previously been documented as well as new suitable climatic areas for the establishment of P. destructans in North America: large regions of the central USA and highlands of Mexico in the Peninsula of Baja California, the Sierra Madre Occidental and Oriental, and Transvolcanic Mexican Belt. Our models identified 10 species of vespertilionid bats distributed similarly to P. destructans. Bats had a high risk of infection with WSN and a strong likelihood of dispersing the fungus.     

Mitochondrial DNA phylogeny of North American field crickets: perspectives on the evolution of life cycles,songs, and habitat associations

North American field crickets (genus Gryllus) exhibit a diversity of life cycles, habitat associations, and calling songs. However, patterns of evolution for these ecological and behavioral traits remain uncertain in the absence of a robust phylogenetic framework. Analyses of morphological variation have provided few clues about species relationships in the genus Gryllus. Here we use comparisons of mitochondrial DNA restriction site maps for 29 individuals representing 11 species (including potential outgroups) to examine relationships among eastern North American field crickets. Initially chosen as likely outgroup taxa, the two European species of Gryllus do not obviously fall outside of an exclusively North American clade and (based on amount of sequence divergence) appear to have diverged from North American lineages at about the same time that major North American lineages diverged from each other. The egg-overwintering crickets comprise a strongly supported monophyletic group, but relationships among these three closely related species cannot be resolved. The mtDNA data are consistent with a single origin of egg diapause and do not support a model of recent life cycle divergence and allochronic speciation for Gryllus pennsylvanicus and G. veletis. The two crickets are not sister species, despite remarkable similarity in morphology, habitat, and calling song. This conclusion is consistent with published data on allozyme variation in North American field crickets. The habitat associations of eastern North American field crickets have been labile, but calling songs sometimes have remained virtually unchanged across multiple speciation events.     

Neogene geese and ducks (Aves: Anatidae) from localities of the Great Lakes Depression, western Mongolia

New material of ducks and geese from Late Miocene-Early Pliocene localities of the Great Lakes Depression in western Mongolia is described and the previously described material is revised. This study confirms the presence of four goose species, four dabbling ducks, and three diving ducks. A large goose previously described as Heterochen vicinus is assigned to a separate genus, Heteroanser. Bonibernicla ponderosa is transferred to Anserinae, and North American Branta woolfendeni is regarded as a junior synonym of Bonibernicla ponderosa. The validity of two goose species, Anser devjatkini and A. liskunae, is confirmed and both are assigned here to the subgenus Chen. It is also shown that the holotype of Anas molesta actually belongs to a diving duck of the genus Aythya. The presence of Anas soporata in the Hyargas Nuur Formation is not confirmed.     

Systematics and diversity of the giant soft-shelled turtles (Cryptodira,Trionychidae) from the earliest Eocene of Belgium

In 1909, the famous paleontologist Louis Dollo identified two putative new species of giant soft-shelled turtles from the lowest Eocene record of Belgium, ‘Trionyx erquelinnensis’ and ‘Trionyx levalensis’, from Erquelinnes and Leval, respectively. However, these proposals did not meet the requirements of the International Code of Zoological Nomenclature, so they were considered as nomina nuda. The information on these specimens or about any other specimen of this lineage of giant turtles from the Belgian record is currently extremely limited. Relatively scarce material from giant trionychids has been described for the lower Eocene record of other European regions. Considering the available information, all the European material has recently been recognized as belonging to the genus Axestemys, which has a North American origin, and possibly attributable to a single species, Axestemys vittata, which currently lacks a diagnosis. Numerous and well-preserved Belgian specimens are deposited in the Royal Belgian Institute of Natural Sciences. In addition to the cited individuals from Erquelinnes and Leval, additional specimens from both localities, as well as others from Orp-le-Grand, are part of this collection. These specimens, found between the decades of 1910 and 1930, have been recently restored, and their study is carried out here. The presence of Axestemys vittata in Belgium (in Leval and Orp-le-Grand) is confirmed. Knowledge about this species is significantly improved, and a diagnosis is proposed. However, the hypothesis proposed by Dollo is here confirmed, this species being not the only identified in the Belgian record. So, Axestemys erquelinnensis nov. sp. is defined based on the carapace from Erquelinnes known by Dollo, suggesting that the genus probably reached Europe during the Paleocene Eocene Thermal Maximum.     

Types of names of Orobanche taxa described from North Africa

In the framework of the revision of the genus Orobanche (including Phelipaea) in the Mediterranean area, the original material for 31 names of new taxa described from North Africa by Ball, Battandier, Forsskål, Maire (partly with Emberger and Jahandiez), Persoon, Poiret and Pomel has been analysed. Typification is discussed, and where necessary types are designated. Accepted names and synonyms of the recognized taxa are given. Three species are illustrated, and one new combination (O. inexspectata) is proposed.     

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.     

Review of the marsupials (Mammalia: Metatheria) from the late Paleogene (Chadronian–Arikareean: late Eocene–late Oligocene) of North America

The taxonomy of marsupials from the late Paleogene of North America (Chadronian to Arikareean North American land mammal ages: late Eocene–late Oligocene) is reviewed based on new and previously undescribed fossil material as well as reevaluation of previously described material. Two families are recognized, the Herpetotheriidae and Peradectidae. Nine species of herpetotheriids are recognized within two genera: Herpetotherium Cope, 1873a and Copedelphys Korth, 1994, including one new species, H. tabrumi. The greatest diversity of herpetotheriids was in the Chadronian (four species). By the late Arikareean, only a single species is recognized. The range of Copedelphys is extended into the early Whitneyan (previously limited to Chadronian–Orellan). Among species of Herpetotherium, the ranges of two species have been extended: H. valens (Lambe, 1908) from the Chadronian is reported from the Orellan, and H. marsupium (Troxell, 1923) from the Uintan and Duchesnean is reported from the early Chadronian. The range of H. merriami (Stock and Furlong, 1922), previously only known from the Arikareean of Oregon, is expanded geographically eastward to Montana. Within the Peradectidae only three species are recognized: Peradectes cf. californicus (Stock, 1936) and Didelphidectes pumilis Hough, 1961 from the Chadronian, and Nanodelphys hunti (Cope, 1873b) from the Orellan to early Arikareean. Specimens previously identified as an unnamed new species of Nanodelphys from the Whitneyan and Arikareean are referred here to N. hunti.     

Generic names in the Orbiliaceae (Orbiliomycetes) and recommendations on which names should be protected or suppressed

A list of all generic names that have been connected with the Orbiliomycetes is provided. Recommendations are made as to which names should be used in accordance with the rules and the different generic concepts. There is a mismatch in the current generic concepts within Orbiliomycetes regarding the two morphs: a narrow concept is used for the asexual morphs, but a broad concept relies on the sexual morphs. As a consequence, many more generic names have been established for the asexual morphs. A number of previous generic concepts are artificial, since they were based on single characters without molecular support. In order to provide solutions for this mismatch, we present three different generic concepts within the Orbiliomycetes. A broad concept recognizes a large genus Orbilia, with which most of the listed names fall into synonymy, but could be maintained as infrageneric names. Due to the lack of data proving phylogenetic relationships, this broad concept, at present, is the most practicable and recommended one. A moderate concept subdivides Orbilia into several genera, with all nematode-trapping fungi merged in Arthrobotrys. A narrow generic concept accepts genera based on differences in trapping organs, but also subdivides the remaining groups of Orbilia into additional genera. Trapping of invertebrates (zoophagy) is not restricted to Arthrobotrys in a broad sense, but occurs also in the more distant basal genera Hyalorbilia and Lecophagus, which mainly prey on rhizopods and rotifers. Whether these predatory capabilities trace back to a common ancestor is not clear. The following new combinations are proposed: Hyalorbilia oviparasitica, Hyalorbilia quadridens, Hyalorbilia tenuifusaria, and Orbilia fissilis.