Chromosomal locations of U2 snDNA clusters in <Emphasis Type="Italic">Megaleporinus</Emphasis>, <Emphasis Type="Italic">Leporinus</Emphasis> and <Emphasis Type="Italic">Schizodon</Emphasis> (Characiformes: Anostomidae)

The U small nuclear RNA (U snRNA) genes comprise a multigene family and are required for splicing of pre-mRNA. In this paper, we aimed to study the chromosomal location of the U2 snRNA gene in Megaleporinus, Leporinus and Schizodon species, which constitute interesting models for the study of repetitive DNA and genomic evolution in fish once the group comprises species with and without heteromorphic sex chromosomes. The all six species showed 2n?=?54 chromosomes: Megaleporinus elongatus, Megaleporinus macrocephalus, Leporinus striatus, Leporinus friderici, Schizodon borelli and Schizodon isognathus. The U2 snDNA clusters were evident in only one medium-sized submetracentric pair in all analyzed species and this may represent a condition shared by Anostomidae family.     

Redescription and systematic position of nominal loach species <Emphasis Type="Italic">Nemacheilus compressirostris</Emphasis> and <Emphasis Type="Italic">N. sibiricus</Emphasis> (Nemacheilidae)

Type specimens of nominal species Nemacheilus compressirostris Warpachowsky, 1897, and N. sibiricus Gratzianov, 1907, from the upper Ob River basin were redescribed, and lectotypes for both species were selected. Although some traits were not preserved well enough, it was established that both names should be classified with Barbatula cf. toni, corresponding to the “snub-nosed” morphotype fide Prokofiev (2007). None of the names are suitable for designation of the morph “tigris” fide Gundrizer (1975) and Prokofiev (2007). A comparison table of diagnostic traits of the genus Barbatula from the Asian part of the range was compiled.     

Evaluation of the Diversity of Probiotic <Emphasis Type="Italic">Bacillus</Emphasis>, <Emphasis Type="Italic">Clostridium</Emphasis>, and <Emphasis Type="Italic">Bifidobacterium</Emphasis> Using the Illumina-Based Sequencing Method

Bacterial species of Bacillus, Lactobacillus, and Bifidobacterium in the intestinal tract have been used as probiotics. Selections for probiotic candidates by the culture-based approaches are time-consuming and labor-consuming. The aim of this study was to develop a new method based on sequencing strategies to select the probiotic Bacillus, Lactobacillus, and Bifidobacterium. The Illumina-based sequencing strategies with different specific primers for Bacillus, Clostridium, and Bifidobacterium were applied to analyze diversity of the genera in goat feces. The average number of different Bacillus, Clostridium, and Bifidobacterium OTUs (operational taxonomic units) at the 97% similarity level ranged from 1922 to 63172. The coverage index values of Bacillus, Clostridium, and Bifidobacterium calculated from the bacterial OTUs were 0.89, 0.99, and 1.00, respectively. The most genera of Bacillus (37.9%), Clostridium (53%), and Bifidobacterium (99%) were detected in goat feces by the Illumina-based sequencing with the specific primers of the genera, respectively. Higher phylogenetic resolutions of the genera in goat feces were successfully established. The results suggest that the selection for probiotic Bacillus, Clostridium, and Bifidobacterium based on the Illumina sequencing with their specific primers is reliable and feasible, and the core Bacillus, Clostridium, and Bifidobacterium species of healthy goats possess the potentials as probiotic microbial consortia.     

<Emphasis Type="Italic">Bruguiera hainesii</Emphasis>, a critically endangered mangrove species,is a hybrid between <Emphasis Type="Italic">B. cylindrica</Emphasis> and <Emphasis Type="Italic">B. gymnorhiza</Emphasis> (Rhizophoraceae)

Bruguiera hainesii (Rhizophoraceae) is one of the two Critically Endangered mangrove species listed in the IUCN Red List of Threatened Species. Although the species is vulnerable to extinction, its genetic diversity and the evolutionary relationships with other Bruguiera species are not well understood. Also, intermediate morphological characters imply that the species might be of hybrid origin. To clarify the genetic relationship between B. hainesii and other Bruguiera species, we conducted molecular analyses including all six Bruguiera species using DNA sequences of two nuclear genes (CesA and UNK) and three chloroplast regions (intergenic spacer regions of trnL-trnF, trnS-trnG and atpB-rbcL). For nuclear DNA markers, all nine B. hainesii samples from five populations were heterozygous at both loci, with one allele was shared with B. cylindrica, and the other with B. gymnorhiza. For chloroplast DNA markers, the two haplotypes found in B. hainesii were shared only by B. cylindrica. These results suggested that B. hainesii is a hybrid between B. cylindrica as the maternal parent and B. gymnorhiza as the paternal one. Furthermore, chloroplast DNA haplotypes found in B. hainesii suggest that hybridization has occurred independently in regions where the distribution ranges of the parental species meet. As the IUCN Red List of Threatened Species currently excludes hybrids (except for apomictic plant hybrids), the conservation status of B. hainesii should be reconsidered.     

On some <Emphasis Type="Italic">Rarecostites</Emphasis> (Parkinsoniidae,Ammonoidea) from the Upper Bajocian <Emphasis Type="Italic">Parkinsoni</Emphasis> zone of the Northern Caucasus

The ammonites of the genus Rarecostites (subfamily Parkinsoniinae) are studied from the lower part of the Upper Bajocian Parkinsonia parkinsoni Zone of the Kyafar River (Bolshoi Zelenchuk River Basin, Karachai-Cherkessia, Russia). The locality contains numerous microconch shells of R. subarietis (Wetzel). We follow de Grossouvre (1919) in considering the names R. acris (Wetzel) and R. arietis (Wetzel) to be subjective synonyms of R. subarietis and, thus, the standard Acris should be replaced by the Subarietis Subzone. The lower part of the section also contains numerous microconchs of R. sherstyukovi sp. nov. and, less commonly, macroconchs of R. kyafarensis sp. nov. The phylogeny of Rarecostites species is reconstructed; the above species are described and figured and the sherstyukovi and subarietis faunal horizons are established.     

Parasitism rates and parasitoid complexes of the wheat midges, <Emphasis Type="Italic">Sitodiplosis mosellana</Emphasis>, <Emphasis Type="Italic">Contarinia tritici</Emphasis> and <Emphasis Type="Italic">Haplodiplosis marginata</Emphasis>

Three species of cecidomyiid midges (Diptera: Cecidomyiidae), whose larvae overwinter in the soil, can cause significant yield losses on wheat in Europe: the orange wheat blossom midge, Sitodiplosis mosellana (Géhin), the yellow wheat blossom midge, Contarinia tritici (Kirby), and the saddle gall midge, Haplodiplosis marginata (von Roser). The biological control of wheat midges by their parasitoids can contribute to reduce the midge populations. Soil samples were collected in several fields in Belgium in 2012–2014 in order to characterize the parasitism rates and parasitoid complexes in overwintering larvae. The parasitism rates varied greatly between the sampled fields: 3–100, 0–100 and 2% for S. mosellana, H. marginata and C. tritici, respectively. The parasitism rate was not related to the larval density of wheat midge. The three wheat midges have totally distinct parasitoid complexes in Belgium. Eight species (Hymenoptera: Pteromalidae and Platygastridae) were found as parasitoid of S. mosellana: Macroglenes penetrans (Kirby), Amblypasis tritici (Walker), Euxestonotus error (Fitch), Euxestonutus sp. Fouts, Leptacis sp. Foerster, Platygaster gracilipes (Huggert), Platygaster nisus Walker, and Platygaster tuberosula (Kieffer). According to their abundance, M. penetrans, E. error and P. tuberosula appeared as the main parasitoids of S. mosellana in Belgium. For the two other wheat midges, only one species of the family Platygastridae was found for each midge: Platygaster equestris (Spittler) for H. marginata and Synopeas myles (Walker) for C. tritici.     

Tracking an invasion: community changes in hardwood forests following the arrival of <Emphasis Type="Italic">Amynthas agrestis</Emphasis> and <Emphasis Type="Italic">Amynthas tokioensis</Emphasis> in Wisconsin

Because Upper Midwest temperate forests lack native earthworms, the invasions of European and Asian earthworms can significantly alter soils and understory vegetation. Earthworms’ ability to increase leaf litter decay, alter nutrient cycling by mixing the organic layer with mineral soil, and decrease plant species richness leads to concern about the Asian ‘jumping earthworm’ (Amynthas agrestis and A. tokioensis) species that were recorded in the University of Wisconsin—Madison Arboretum in 2013. In 2015, we found A. agrestis and A. tokioensis in a distinct 8-ha region of a 23-ha hardwood forest surveyed in the Arboretum; by 2016 A. agrestis and A. tokioensis had spread over an additional 7 ha. Plots also contained the European earthworm species Lumbricus terrestris, L. rubellus, and Apporectodea spp., whose distributions decreased from 2015 to 2016. While leaf litter, plant species richness, and tree and shrub seedling abundance were generally reduced in areas with European earthworms, they were typically slightly increased in areas with A. agrestis and A. tokioensis versus those without. Although our results do not show substantial impacts of A. agrestis and A. tokioensis on vegetation in the initial years of invasion, the rapid replacement of European earthworms by A. agrestis and A. tokioensis suggests continued monitoring of these new invasive species is important to better understand their potential to change the Upper Midwest’s forests.     

Co-invasion of three Asian earthworms, <Emphasis Type="Italic">Metaphire hilgendorfi</Emphasis>, <Emphasis Type="Italic">Amynthas agrestis</Emphasis> and <Emphasis Type="Italic">Amynthas tokioensis</Emphasis> in the USA

Earthworm invasions are one of the most serious causes of ecological deterioration in the temperate deciduous forests of North America. Non-native earthworms impact understory vegetation, leaf litter layer, carbon dynamics, nutrient availability, and the associated food webs. Here we report a significant status change and confirm expansion of known range of Amynthas agrestis, one of the most serious invasive species in North America, and two of its close relatives, A. tokioensis and Metaphire hilgendorfi. The three species have never been confirmed to co-occur in North American ecosystems. We examined 1760 earthworms collected from 30 sites across northeastern USA, and identified them using a new morphological key. Our data show that sympatric occurrence of at least two, and often all three, species is more common than having only one species. In addition, A. tokioensis was dominant in many of these earthworm communities. The status change in species composition from only one species to two or three and the shift in dominance are most likely caused by previous incorrect species identification. Our results support expansion of known range of A. tokioensis and M. hilgendorfi northward and westward into states with colder winters. This range expansion may have taken place alongside that of A. agrestis in the last 10–20 years, but has long been overlooked. Altogether, results highlight an urgent need for correct species identification. The recognition of an expanding multi-species system represents a unique opportunity to further evaluate complex interactions among co-invading and resident species, and to investigate whether interspecific interactions have unexpected non-additive impacts on ecological processes.     

Association between <Emphasis Type="Italic">cagA</Emphasis>, <Emphasis Type="Italic">vacAi</Emphasis>, and <Emphasis Type="Italic">dupA</Emphasis> genes of <Emphasis Type="Italic">Helicobacter pylori</Emphasis> and gastroduodenal pathologies in Chilean patients

In addition to the already known cagA gene, novel genetic markers have been associated with Helicobacter pylori (H. pylori) virulence: the dupA and vacAi genes. These genes might play an important role as specific markers to determine the clinical outcome of the disease, especially the vacAi gene, which has been expected to be a good marker of severe pathologies like gastric adenocarcinoma. In the present study, the association of cagA, dupA, and vacAi genes with gastroduodenal pathologies in Chilean patients was studied. One hundred and thirty-two patients positive for H. pylori were divided into two groups—non-severe and severe gastric pathologies—and investigated for the presence of cagA, dupA, and vacAi H. pylori virulence genes by PCR. The cagA gene was detected in 20/132 patients (15.2%), the vacAi1 gene was detected in 54/132 patients (40.9%), the vacAi2 gene was detected in 26/132 patients (19.7%), and the dupA gene was detected in 50/132 (37.9%) patients. Logistic regression model analysis showed that the vacAi1 isoform gene in the infected strains and the severity of the diseases outcome were highly associated, causing severe gastric damage that may lead to gastric cancer (p < 0.0001; OR = 8.75; 95% CI 3.54–21.64). Conversely, cagA (p = 0.3507; OR = 1.62; 95% CI 0.59–4.45) and vacAi2 (p = 0.0114; OR = 3.09; 95% CI 1.26–7.60) genes were not associated with damage, while the dupA gene was associated significantly with non-severe clinical outcome (p = 0.0032; OR = 0.25; 95% CI 0.09–0.65). In addition, dupA gene exerts protection against severe gastric pathologies induced by vacAi1 by delaying the outcome of the disease by approximately 20 years.     

Identification of <Emphasis Type="Italic">Bacillus</Emphasis> Probiotics Isolated from Soil Rhizosphere Using 16S rRNA, <Emphasis Type="Italic">recA</Emphasis>, <Emphasis Type="Italic">rpoB</Emphasis> Gene Sequencing and RAPD-PCR

Some Bacillus species, especially Bacillus subtilis and Bacillus pumilus groups, have highly similar 16S rRNA gene sequences, which are hard to identify based on 16S rDNA sequence analysis. To conquer this drawback, rpoB, recA sequence analysis along with randomly amplified polymorphic (RAPD) fingerprinting was examined as an alternative method for differentiating Bacillus species. The 16S rRNA, rpoB and recA genes were amplified via a polymerase chain reaction using their specific primers. The resulted PCR amplicons were sequenced, and phylogenetic analysis was employed by MEGA 6 software. Identification based on 16S rRNA gene sequencing was underpinned by rpoB and recA gene sequencing as well as RAPD-PCR technique. Subsequently, concatenation and phylogenetic analysis showed that extent of diversity and similarity were better obtained by rpoB and recA primers, which are also reinforced by RAPD-PCR methods. However, in one case, these approaches failed to identify one isolate, which in combination with the phenotypical method offsets this issue. Overall, RAPD fingerprinting, rpoB and recA along with concatenated genes sequence analysis discriminated closely related Bacillus species, which highlights the significance of the multigenic method in more precisely distinguishing Bacillus strains. This research emphasizes the benefit of RAPD fingerprinting, rpoB and recA sequence analysis superior to 16S rRNA gene sequence analysis for suitable and effective identification of Bacillus species as recommended for probiotic products.     

Revision of the genus <Emphasis Type="Italic">Melamphaes</Emphasis> (Melamphaidae). 5. Oligo-raker species: <Emphasis Type="Italic">M. indicus</Emphasis>, <Emphasis Type="Italic">M. eurous</Emphasis>, and <Emphasis Type="Italic">M. typhlops</Emphasis>

Three oligo-raker species (?19 rakers on the first gill arch) of the genus Melamphaes out of the “M. typhlops” group are considered. The validity of M. indicus Ebeling is restored. This species inhabits equatorial and tropical waters of the Indian Ocean and the western part of the Pacific Ocean. M. eurous sp. n., which is related to M. indicus, is described from equatorial waters of the eastern part of the Pacific Ocean. M. typhlops (Lowe) inhabiting the northern part of the Atlantic Ocean, from the equatorial zone about to 45° N, is redescribed.     

Revision of the <Emphasis Type="Italic">Serrulati</Emphasis> species of <Emphasis Type="Italic">Penstemon</Emphasis> section <Emphasis Type="Italic">Saccanthera</Emphasis> subsection <Emphasis Type="Italic">Serrulati</Emphasis>

A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations.     

The homologous identification of the stem rust resistance genes <Emphasis Type="Italic">Rpg5</Emphasis>, <Emphasis Type="Italic">Adf3</Emphasis> and <Emphasis Type="Italic">RGA1</Emphasis> in the relatives of barley

The barley genes Rpg5, RGA1 and Adf3, which provide a strong resistance to many pathotypes of stem rust, were cloned a few years ago, but it was still unclear whether their homologues were represented in wheat and in related species. The paper describes the results of a bioinformatic research to determine the homologues of Rpg5, RGA1 and Adf3 in the genomes of Triticum aestivum and several wild grasses, which breeders usually use as sources of stem rust resistance, and which are available in the genome databases. It was found that the Th. elongatum sequence Q9FEC6 and T. aestivum sequence Q43655 were the highly identical homologues of the Adf3 sequence. T. urartu M8A999 sequence and T. aestivum W5FCU1 sequence were found to be the closest homologues of Rpg5 complete protein sequence, but the identity of their kinase domains was not as clear as that of the other domains. The separate Rpg5 kinase part analysis did not provide the strong evidences that its orthologs were present in our corn species. T. urartu M7ZZX9 sequence and T. aestivum W5FFP0 and W5FI33 sequences were shown to be the homologues of RGA1. The analysis of the predicted active sites allowed finding out the difference between sequences of Rpg5, RGA1, Adf3 protein and their homologues.     

Niche dynamics of two cryptic <Emphasis Type="Italic">Prosopis</Emphasis> invading South American drylands

Whether or not species track native climatic conditions during invasions (i.e., climate match hypothesis) is fundamental to understand and prevent potential impacts of invasive species. Recent empirical work suggests that climatic mismatches between native and invasive ranges are pervasive. Whether these differences are due to adaptation to new climatic spaces in the invasive range or due to partial filling of the potential climatic space are still subject to debate. Here, we analyze climatic niche dynamics associated with the invasion of the two most common invasive plants in Brazilian semi-arid areas, Prosopis juliflora and Prosopis pallida. These species have been simultaneously introduced in the region, which creates a unique opportunity to compare their niche dynamics during invasion. Given that P. juliflora have a much wider native range size, we expect these species would present different dispersal potentials, which might translate into different unfilling levels. Using an ordination method with kernel smoother and null models, we contrasted climate spaces occupied by each species in both native and invasive ranges. We further used ecological niche models (ENMs) to compare reciprocal predictions of potentially suitable areas. Against our expectation based on differences in native range sizes, climatic niches of P. juliflora and P. pallida overlapped greatly, both in their native and invasive ranges. Our results support niche conservatism during the invasion process. Climatic mismatches among native and invaded ranges were exclusively attributed to unfilling of native climates in the invasive range. Both species showed similar unfilling levels. Likewise, ENMs predicted regions not yet occupied in the invasive range, revealing a potential for further expansion. We discuss colonization time lag and founder effect as potential mechanisms that may have prevented these species to fully occupy their native niches in the invasive range.     

<Emphasis Type="Italic">Cantharellus</Emphasis> sect. <Emphasis Type="Italic">Amethystini</Emphasis> in Asia

In this contribution on the genus Cantharellus in Asia, C. subvaginatus is described from the Republic of Korea as a close relative to the Chinese C. vaginatus, which is here reported for the first time from India. Both species are here placed in Cantharellus subg. Cantharellus sect. Amethystini, together with the Indian C. pseudoformosus (syn.: C. umbonatus) and the Malayan C. subamethysteus. As such, Asia has suddenly become the continent with the highest diversity for Amethystini. Species delimitation in sect. Amethystini is molecularly supported by a combined phylogenetic analysis of rDNA sequences obtained for LSU and ITS and additionally suggests the existence of a still undescribed species in North America. Character variability is discussed for all known members of Amethystini, including atypical specimens of the North American C. lewisii that are morphologically more reminiscent of the South Korean C. subvaginatus.