DNA analysis of a non-native lineage of Sinanodonta woodiana species complex (Bivalvia: Unionidae) from Middle Asia supports the Chinese origin of the European invaders

The Sinanodonta woodiana species complex includes several cryptic species-level phylogenetic lineages, the taxonomic placement of which is unclear. Here, we present the results of molecular analyses of a Sinanodonta sample from Middle Asia (Uzbekistan). The COI haplotype of the Uzbekistan lineage is similar to those of invasive Sinanodonta populations from Europe, Russia and Myanmar. We show that the non-native Sinanodonta flocks in Europe and Middle Asia originated from a single source population in China. Our results reveal that the Sinanodonta woodiana species complex comprises at least six distinct biological species: S. cf. gibba (=temperate invasive lineage), S. cf. woodiana (=tropical invasive lineage), S. schrenkii (=S. amurensis), S. ovata, S. jourdyi, and S. lucida, and two phylogenetic lineages with uncertain taxonomic names.

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PCR-Based Identification of MAT-1 andMAT-2 in the Gibberella fujikuroi Species Complex

Applied and Environmental Microbiology ◽

10.1128/aem.66.10.4378-4382.2000 ◽

2000 ◽

Vol 66 (10) ◽

pp. 4378-4382 ◽

Cited By ~ 114

Author(s):

Emma T. Steenkamp ◽

Brenda D. Wingfield ◽

Teresa A. Coutinho ◽

Kurt A. Zeller ◽

Michael J. Wingfield ◽

...

Keyword(s):

Species Complex ◽

Fusarium Verticillioides ◽

Fusarium Culmorum ◽

Biological Species ◽

Gibberella Fujikuroi ◽

Additional Species ◽

Individual Mating ◽

Sexual Cross ◽

Phylogenetic Lineages ◽

Gibberella Fujikuroi Species Complex

ABSTRACT All sexually fertile strains in the Gibberella fujikuroi species complex are heterothallic, with individual mating types conferred by the broadly conserved ascomycete idiomorphsMAT-1 and MAT-2. We sequenced both alleles from all eight mating populations, developed a multiplex PCR technique to distinguish these idiomorphs, and tested it with representative strains from all eight biological species and 22 additional species or phylogenetic lineages from this species complex. In most cases, either an ∼800-bp fragment from MAT-2 or an ∼200-bp fragment from MAT-1 is amplified. The amplified fragments cosegregate with mating type, as defined by sexual cross-fertility, in a cross of Fusarium moniliforme (Fusarium verticillioides). Neither of the primer pairs amplify fragments from Fusarium species such as Fusarium graminearum, Fusarium pseudograminearum, andFusarium culmorum, which have, or are expected to have,Gibberella sexual stages but are thought to be relatively distant from the species in the G. fujikuroi species complex. Our results suggest that MAT allele sequences are useful indicators of phylogenetic relatedness in these and otherFusarium species.

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Evaluating Metagenomic Analysis for Pathogen Transmission in Healthcare Settings

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.768 ◽

2020 ◽

Vol 41 (S1) ◽

pp. s224-s224

Author(s):

Curt Hewitt ◽

Katharina Weber ◽

Danielle LeSassier ◽

Anthony Kappell ◽

Kathleen Schulte ◽

...

Keyword(s):

Antibiotic Resistance ◽

Dna Analysis ◽

Pathogen Transmission ◽

Species Level ◽

Metagenomic Analysis ◽

Skin Microbiome ◽

Limited Information ◽

Culture Methods ◽

Data Set ◽

Skin Contact

Background: The prevalence of healthcare-acquired infections (HAIs) and rising levels of antimicrobial resistance place a significant burden on modern healthcare systems. Cultures are typically used to track HAIs; however, culture methods provide limited information and are not applicable to all pathogens. Next-generation sequencing (NGS) can detect and characterize pathogens present within a sample, but few research studies have explored how NGS could be used to detect pathogen transmission events under HAI-relevant scenarios. The objective of this CDC-funded project was to evaluate and correlate sequencing approaches for pathogen transmission with standard culture-based analysis. Methods: We modeled pathogen transfer via hand contact using synthetic skin. These skin coupons were seeded with a community of commensal organisms to mimic the human skin microbiome. Pathogens were added at physiologically relevant high or low levels prior to skin-to-skin contact. The ESKAPE pathogens: E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp plus C. difficile were employed because they are the most common antibiotic resistant HAIs. Pathogen transfer between skin coupons was measured following direct skin contact and fomite surface transmission. The effects of handwashing or fomite decontamination were also evaluated. Transferred pathogens were enumerated via culture to establish a robust data set against which DNA and RNA sequence analyses of the same samples could be compared. These data also provide a quantitative assessment of individual ESKAPE+C pathogen transfer rates in skin contact scenarios. Results: Metagenomic and metatranscriptomic analysis using custom analysis pipelines and reference databases successfully identified the commensal and pathogenic organisms present in each sample at the species level. This analysis also identified antibiotic resistance genes and plasmids. Metatranscriptomic analysis permitted not only gene identification but also confirmation of gene expression, a critical factor in the evaluation of antibiotic resistance. DNA analysis does not require cell viability, a key differentiator between sequencing and culturing reflected in simulated handwashing data. Sensitivity remains a key limitation of metagenomic analysis, as shown by the poor species identification and gene content characterization of pathogens present at low abundance within the simulated microbial community. Species level identification typically failed as ratios fell below 1:1,000 pathogen CFU:total community CFU. Conclusions: These findings demonstrate the strengths and weaknesses of NGS for molecular epidemiology. The data sets produced for this study are publicly available so they can be employed for future metagenomic benchmarking studies.Funding: NoneDisclosures: None

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Puparia Cleaning Techniques for Forensic and Archaeo-Funerary Studies

Insects ◽

10.3390/insects12020104 ◽

2021 ◽

Vol 12 (2) ◽

pp. 104

Author(s):

Jennifer Pradelli ◽

Fabiola Tuccia ◽

Giorgia Giordani ◽

Stefano Vanin

Keyword(s):

Sodium Hydroxide ◽

Molecular Identification ◽

Sodium Hydroxide Solution ◽

Species Level ◽

Post Mortem ◽

Molecular Analyses ◽

Chemical Treatments ◽

Wrong Identification ◽

Physical And Chemical

Diptera puparia may represent both in forensic and archaeo-funerary contexts the majority of the entomological evidence useful to reconstruct the peri and post-mortem events. Puparia identification is quite difficult due to the lack of identification keys and descriptions. In addition, external substances accumulated during the puparia permanence in the environment make the visualization of the few diagnostic characters difficult, resulting in a wrong identification. Six different techniques based on physical and chemical treatments have been tested for the removal of external substances from puparia to make identification at species level feasible. Furthermore, the effects of these methods on successful molecular analyses have also been tested as molecular identification is becoming an important tool to complement morphological identifications. The results of this study indicate that cleaning via warm water/soap, the sonication and treatment with a sodium hydroxide solution are the best methods to achieve a good quality of the samples.

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Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

Invertebrate Systematics ◽

10.1071/is18019 ◽

2018 ◽

Vol 32 (6) ◽

pp. 1298 ◽

Cited By ~ 4

Author(s):

Feng Zhang ◽

Daoyuan Yu ◽

Mark I. Stevens ◽

Yinhuan Ding

Keyword(s):

Species Complex ◽

Instar Larva ◽

Molecular Data ◽

Integrative Taxonomy ◽

Species Level ◽

Integrative Approach ◽

Gene Markers ◽

Late Neogene ◽

Taxonomic Approach ◽

Colour Patterns

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

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Bioacoustic investigations and taxonomic considerations on the Cicadetta montana species complex (Homoptera: Cicadoidea: Tibicinidae)

Anais da Academia Brasileira de Ciências ◽

10.1590/s0001-37652004000200020 ◽

2004 ◽

Vol 76 (2) ◽

pp. 316-324 ◽

Cited By ~ 22

Author(s):

Matija Gogala ◽

Tomi Trilar

Keyword(s):

Cryptic Species ◽

Species Complex ◽

Similar Case ◽

Genetic Differences ◽

Species Level ◽

Sister Species ◽

Type Locality

Recent bioacoustic investigations have shown that Cicadetta montana Scopoli 1772 is a complex of morphologically similar sister species that are best characterized by their song patterns. At the type locality of C. montana, only mountain cicadas with simple, long lasting song phrases were heard, recorded and collected. Therefore, we have good reasons to suggest that this type of song is characteristic for C. montana s. str. Boulard described a song of C. montana from France with phrases composed of a long and a short echeme; this type of song is characteristic for cicadas morphologically corresponding to C. montana var. brevipennis Fieber 1876; we suggest to raise this taxon to species level. On the basis of specific song, Puissant and Boulard described C. cerdaniensis from Pyrénées. A similar case was the discovery and description of C. montana macedonica Schedl 1999 from Macedonia; since these Macedonian cicadas are sympatric with at least two other cryptic species in the C. montana group and molecular investigations showed substantial genetic differences between C. macedonica and C. montana or C. brevipennis, we conclude that this taxon should also be raised to species level. Songs of closely related C. podolica and Korean mountain cicada are presented as well.

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Environment drives high phylogenetic turnover among oceanic bacterial communities

Biology Letters ◽

10.1098/rsbl.2011.0990 ◽

2012 ◽

Vol 8 (4) ◽

pp. 562-566 ◽

Cited By ~ 15

Author(s):

Thomas Pommier ◽

Emmanuel J. P. Douzery ◽

David Mouillot

Keyword(s):

Bacterial Communities ◽

Environmental Gradient ◽

Regional Scale ◽

Environmental Filtering ◽

Species Level ◽

Geographical Distance ◽

Abiotic Conditions ◽

High Connectivity ◽

Phylogenetic Lineages ◽

Marine Microbial Communities

Although environmental filtering has been observed to influence the biodiversity patterns of marine bacterial communities, it was restricted to the regional scale and to the species level, leaving the main drivers unknown at large biogeographic scales and higher taxonomic levels. Bacterial communities with different species compositions may nevertheless share phylogenetic lineages, and phylogenetic turnover (PT) among those communities may be surprisingly low along any biogeographic or environmental gradient. Here, we investigated the relative influence of environmental filtering and geographical distance on the PT between marine bacterial communities living more than 8000 km apart in contrasted abiotic conditions. PT was high between communities and was more structured by local environmental factors than by geographical distance, suggesting the predominance of a lineage filtering process. Strong phenotype-environment mismatches observed in the ocean may surpass high connectivity between marine microbial communities.

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From computer operating systems to biodiversity: co-emergence of ecological and evolutionary patterns

10.7287/peerj.preprints.2367v2 ◽

2016 ◽

Author(s):

Petr Keil ◽

Joanne M Bennett ◽

Bérenger Burgeois ◽

Gabriel E García-Peña ◽

Andrew M MacDonald ◽

...

Keyword(s):

Operating Systems ◽

Phylogenetic Signal ◽

Biological Species ◽

System Level ◽

Evolutionary Patterns ◽

Data Accessibility ◽

Software Packages ◽

Empirical Argument ◽

Phylogenetic Lineages ◽

Mean Variance

Comparisons between biodiversity and other complex systems can facilitate cross-disciplinary exchange of theories and the identification of key system processes and constraints. For example, due to qualitative structural and functional analogies to biological systems, coupled with good data accessibility, computer operating systems offer opportunities for comparison with biodiversity. However, it remains largely untested if the two systems also share quantitative patterns. Here, we employ analogies between GNU/Linux operating systems (distros) and biological species, and look for a number of well-established ecological and evolutionary patterns in the Linux universe. We demonstrate that patterns of the Linux universe match the macroecological patterns: Linux distro commonness and rarity (popularity of a distro) follow a lognormal distribution, power law mean-variance scaling of temporal fluctuation, and there is a significant relationship between niche breadth (number of software packages) and commonness. The diversity in the Linux universe also follows general macroevolutionary patterns: The number of phylogenetic lineages increases linearly through time, with clear per-species diversification and extinction slowdowns, something that is unobservable in biology. Moreover, the composition of functional traits (software packages) exhibits significant phylogenetic signal. Our study provides foundations for using Linux as a model system for eco-evolutionary studies, as well as insights into patterns and dynamics of computer operating systems, which may be used to inform their future development and maintenance. The co-emergence of patterns across systems suggests that some patterns might be produced by system-level properties, independently of system identity, which offers an empirical argument for non-biological explanations of fundamental biodiversity patterns.

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Plantago campestris (Plantaginaceae), a rare new species from southern Brazil, supported by phylogenomic and morphological evidence

PeerJ ◽

10.7717/peerj.11848 ◽

2021 ◽

Vol 9 ◽

pp. e11848

Author(s):

Gustavo Hassemer ◽

Elliot M. Gardner ◽

Nina Rønsted

Keyword(s):

New Species ◽

Species Complex ◽

High Throughput Sequencing ◽

Morphological Characters ◽

High Elevation ◽

Species Level ◽

Morphological Evidence ◽

Southern Brazil ◽

A New Species ◽

Iucn Criteria

High-throughput sequencing, when combined with taxonomic expertise, is a powerful tool to refine and advance taxonomic classification, including at the species level. In the present work, a new species, Plantago campestris, is described out of the P. commersoniana species complex, based on phylogenomic and morphological evidence. The main morphological characters that distinguish the new species from P. commersoniana are the glabrous posterior sepals and the slightly broader leaves. The new species is known from only three localities, all in natural high-elevation grasslands in Paraná and Santa Catarina states, southern Brazil. According to the IUCN criteria new species should be assessed as Endangered (EN). We present field photographs of P. campestris and related species, and we provide an identification key to the species previously included within the circumscription of P. commersoniana.

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Isochilostachya Mytnik & Szlach., gen. nov., a new genus of Polystachyinae Schltr. (Orchidaceae)

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2011.011 ◽

2011 ◽

Vol 80 (1) ◽

pp. 79-85 ◽

Cited By ~ 1

Author(s):

Joanna Mytnik-Ejsmont ◽

Dariusz L. Szlachetko

Keyword(s):

New Genus ◽

Species Level ◽

New Combinations ◽

Comprehensive Description ◽

Molecular Analyses ◽

Taxonomic Key ◽

North East ◽

Restricted Distribution ◽

Eastern Arc ◽

Floral Bracts

A new genus of Orchidaceae (Polystachyinae), Isochilostachya, is described. It is morphologically similar to Polystachya Hook. but is distinct by the narrower, grass-like leaves arranged in the upper part of the stem, long and acuminate floral bracts and sepals, and long clavate or capitate hairs densely arranged on the lip. A comprehensive description of the new genus is provided. A list of examined specimens and information about distribution, habitat, and altitude for each species are presented. A position of the members of the new genus in the cladogram recently obtained from molecular analyses of Polystachyinae is briefly discussed. A taxonomic key to Polystachyinae is included. Eleven new combinations on species level are validated. Eight lectotypes are designated. Most of the species of Isochilostachya are endemic to particular mountains of the Eastern Arc (Eastern Afromontane hotspot) in north-east Tanzania therefore a brief discussion about their restricted distribution is provided.

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Morphological and molecular characterisation of Xiphinema mazandaranense n. sp. (Dorylaimida: Longidoridae), a new member of the Xiphinema pyrenaicum species complex

Nematology ◽

10.1163/138855411x580768 ◽

2012 ◽

Vol 14 (1) ◽

pp. 109-119 ◽

Cited By ~ 5

Author(s):

Majid Pedram ◽

Ebrahim Pourjam ◽

Robert T. Robbins ◽

Weimin Ye ◽

Mohammad Reza Atighi ◽

...

Keyword(s):

New Species ◽

Species Complex ◽

Small Subunit ◽

Molecular Characterisation ◽

Molecular Analyses ◽

Small Subunit Rdna ◽

Group 6 ◽

Close Relationship ◽

Juvenile Stages ◽

Female Genital

Xiphinema mazandaranense n. sp. is described and illustrated. The new species belongs to morphospecies group 6, which is characterised by having two equally developed female genital branches that have spines in the uteri and a short, rounded tail. The new species is characterised by having spines in the tubular portion of the uterus, body 3.7-5.2 mm long, odontostyle 163-173 μm long, odontophore 96-100 μm long, body 62-80 μm diam., rounded tail, four juvenile stages, males rare with three ventromedian supplements next to the adcloacal pair and spicules 85 μm long. The polytomous identification codes of the new species are: A4-B3-C7b-D6-E456-F45-G4-H2-I23-J7b-K2-L1. The new species appears closely related to the members of X. pyrenaicum group which are characterised by a rounded tail with or without an inconspicuous projecting bulge and a uterus devoid of Z-differentiation but showing spiniform structures. The new species differs from members of the X. pyrenaicum group, which includes the recently described X. iranicum, by a more rounded tail without any projection. Beside morphological and morphometric data, molecular analyses of the near-full-length small subunit rDNA gene (SSU) placed the new species in close relationship with some species belonging to Xiphinema morphospecies group 6 and further separated this species from the X. pyrenaicum complex.

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