Cryptic genetic lineages in Eisenia nordenskioldi pallida (Oligochaeta, Lumbricidae)

Eisenia nordenskioldi (Eisen, 1879) is the only autochthonous Siberian earthworm with a large distribution that ranges from tundra to steppe and broadleaved forests. This species has a very high morphological, ecological, karyological, and genetic diversity, so it was proposed that E. nordenskioldi should be split into several species. However, the phylogeny of the complex was unclear due to the low resolution of the methods used and the high diversity that should have been taken into account. We investigated this question by (1) studying the diversity of the COI gene of E. nordenskioldi throughout its range and (2) sequencing transcriptomes of different genetic lineages to infer its phylogeny. We found that E. nordenskioldi is monophyletic and is split into two clades. The first one includes the pigmented genetic lineages widespread in the northern and western parts of the distribution, and the second one originating from the southern and southeastern part of the species' range and representing both pigmented and non-pigmented forms. We propose to split the E. nordenskioldi complex into two species, E. nordenskioldi and Eisenia sp. 1 (aff. E. nordenskioldi), corresponding to these two clades. The currently recognized non-pigmented subspecies E. n. pallida will be abolished as a polyphyletic and thus a non-natural taxon, while Eisenia sp. 1 will be expanded to include several lineages earlier recognized as E. n. nordenskioldi and E. n. pallida.

Download Full-text

Cold Resistance and the Distribution of Genetic Lineages of the Earthworm Eisenia nordenskioldi (Oligochaeta, Lumbricidae)

Biology Bulletin ◽

10.1134/s1062359019050042 ◽

2019 ◽

Vol 46 (5) ◽

pp. 430-437

Author(s):

D. I. Berman ◽

N. A. Bulakhova ◽

E. N. Meshcheryakova ◽

S. V. Shekhovtsov

Keyword(s):

Cold Resistance ◽

Genetic Lineages ◽

Eisenia Nordenskioldi

Download Full-text

Variation in nuclear genome size within the Eisenia nordenskioldi complex (Lumbricidae, Annelida)

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj21.073 ◽

2021 ◽

Vol 25 (6) ◽

pp. 647-651

Author(s):

S. V. Shekhovtsov ◽

Ya. R. Efremov ◽

T. V. Poluboyarova ◽

S. E. Peltek

Keyword(s):

Genome Size ◽

Phylogenetic Trees ◽

Russian Far East ◽

Far East ◽

Nuclear Genome ◽

Ancestral Population ◽

Separate Species ◽

Genetic Lineages ◽

Cryptic Taxa ◽

Eisenia Nordenskioldi

The size of the nuclear genome in eukaryotes is mostly determined by mobile elements and noncoding sequences and may vary within wide limits. It can differ significantly both among higher-order taxa and closely related species within a genus; genome size is known to be uncorrelated with organism complexity (the so-called C-paradox). Less is known about intraspecific variation of this parameter. Typically, genome size is stable within a species, and the known exceptions turn out be cryptic taxa. The Eisenia nordenskioldi complex encompasses several closely related earthworm species. They are widely distributed in the Urals, Siberia, and the Russian Far East, as well as adjacent regions. This complex is characterized by significant morphological, chromosomal, ecological, and genetic variation. The aim of our study was to estimate the nuclear genome size in several genetic lineages of the E. nordenskioldi complex using flow cytometry. The genome size in different genetic lineages differed strongly, which supports the hypothesis that they are separate species. We found two groups of lineages, with small (250–500 Mbp) and large (2300–3500 Mbp) genomes. Moreover, different populations within one lineage also demonstrated variation in genome size (15–25 %). We compared the obtained data to phylogenetic trees based on transcriptome data. Genome size in ancestral population was more likely to be big. It increased or decreased independently in different lineages, and these processes could be associated with changes in genome size and/or transition to endogeic lifestyle.

Download Full-text

Chapter 11: General epidemiology of TBE

Tick-borne encephalitis - The Book ◽

10.33442/26613980_11-3 ◽

2020 ◽

Keyword(s):

Eastern Siberia ◽

Genetic Lineages ◽

Phylogenetic Studies ◽

Tick Borne Encephalitis ◽

Natural Foci ◽

Genetic Sequences ◽

Tick Borne Encephalitis Virus ◽

Almost All ◽

Far Eastern ◽

Reservoir Hosts

Tick-borne encephalitis virus (TBEV) exists in natural foci, which are areas where TBEV is circulating among its vectors (ticks of different species and genera) and reservoir hosts (usually rodents and small mammals). Based on phylogenetic studies, four TBEV subtypes (Far-Eastern, Siberian, European, Baikalian) and two putative subtypes (Himalayan and “178-79” group) are known. Within each subtype, some genetic lineages are described. The European subtype (TBEV-EU) (formerly known also as the “Western subtype”) of TBEV is prevalent in Europe, but it was also isolated in Western and Eastern Siberia in Russia and South Korea. The Far-Eastern subtype (TBEV-FE) was preferably found in the territory of the far-eastern part of Eurasia, but some strains were isolated in other regions of Eurasia. The Siberian (TBEV-SIB) subtype is the most common and has been found in almost all TBEV habitat areas. The Baikalian subtype is prevalent around Lake Baikal and was isolated several times from ticks and rodents. In addition to the four TBEV subtypes, one single isolate of TBEV (178-79) and two genetic sequences (Himalayan) supposed to be new TBEV subtypes were described in Eastern Siberia and China. The data on TBEV seroprevalence in humans and animals can serve as an indication for the presence or absence of TBEV in studied area.

Download Full-text

Comparative Study of Highly Pathogenic Avian Infl uenza Strains Isolated in Ukraine in 2005 and 2008

Agricultural science and practice ◽

10.15407/agrisp1.01.068 ◽

2014 ◽

Vol 1 (1) ◽

pp. 68-71

Author(s):

A. Gerilovych ◽

B. Stegniy ◽

A. Stegniy ◽

M. Stegniy ◽

K. Smietanka ◽

...

Keyword(s):

Western Europe ◽

Rna Extraction ◽

Experimental Studies ◽

Molecular Characteristics ◽

Eastern European ◽

Highly Pathogenic ◽

Genetic Lineages ◽

Phylogenetic Studies ◽

Polymerase Chain ◽

Pathogenic H5n1

Objective. To research the molecular characteristics of two HPAI strains – A/Ch/Syvash/02/05/H5N1 and A/Ch/Krasnogvardeysk/58/08/H5N1, which were identifi ed as representatives of the highly pathogenic H5N1 viruses. Methods. RNA extraction, real-time polymerase chain reaction (PCR). Results. The phylogenetic studies revealed that the above mentioned strains belong to two various genetic lineages originated from the Eastern European strains isolated in 2005, but differ from the viruses introduced to the Central and Western Europe in 2005/2006, and also the lineages consisting of H5N1 viruses isolated in the Europe and Middle East in late 2007. Conclusions. Relying on experimental studies, it can be concluded that the strains of A/Ch/Syvash/02/05/H5N1 and A/Ch/Krasnogvardeysk/58/08/H5N1 are highly pathogenic.

Download Full-text

Identification of Phytoplasmas Representing Multiple New Genetic Lineages from Phloem-Feeding Leafhoppers Highlights the Diversity of Phytoplasmas and Their Potential Vectors

Pathogens ◽

10.3390/pathogens10030352 ◽

2021 ◽

Vol 10 (3) ◽

pp. 352

Author(s):

Wei Wei ◽

Valeria Trivellone ◽

Christopher H. Dietrich ◽

Yan Zhao ◽

Kristi D. Bottner-Parker ◽

...

Keyword(s):

Host Range ◽

Quantitative Polymerase Chain Reaction ◽

Rflp Analysis ◽

Natural Habitats ◽

Genetic Lineages ◽

Genetic Subgroup ◽

Polymerase Chain ◽

Phloem Feeding ◽

Fresh Insight

Phytoplasmas are obligate transkingdom bacterial parasites that infect a variety of plant species and replicate in phloem-feeding insects in the order Hemiptera, mainly leafhoppers (Cicadellidae). The insect capacity in acquisition, transmission, survival, and host range directly determines the epidemiology of phytoplasmas. However, due to the difficulty of insect sampling and the lack of follow-up transmission trials, the confirmed phytoplasma insect hosts are still limited compared with the identified plant hosts. Recently, quantitative polymerase chain reaction (qPCR)-based quick screening of 227 leafhoppers collected in natural habitats unveiled the presence of previously unknown phytoplasmas in six samples. In the present study, 76 leafhoppers, including the six prescreened positive samples, were further examined to identify and characterize the phytoplasma strains by semi-nested PCR. A total of ten phytoplasma strains were identified in leafhoppers from four countries including South Africa, Kyrgyzstan, Australia, and China. Based on virtual restriction fragment length polymorphism (RFLP) analysis, these ten phytoplasma strains were classified into four distinct ribosomal (16Sr) groups (16SrI, 16SrIII, 16SrXIV, and 16SrXV), representing five new subgroups (16SrI-AO, 16SrXIV-D, 16SrXIV-E, 16SrXIV-F, and 16SrXV-C). The results strongly suggest that the newly identified phytoplasma strains not only represent new genetic subgroup lineages, but also extend previously undiscovered geographical distributions. In addition, ten phytoplasma-harboring leafhoppers belonged to seven known leafhopper species, none of which were previously reported insect vectors of phytoplasmas. The findings from this study provide fresh insight into genetic diversity, geographical distribution, and insect host range of phytoplasmas. Further transmission trials and screening of new potential host plants and weed reservoirs in areas adjacent to collection sites of phytoplasma harboring leafhoppers will contribute to a better understanding of phytoplasma transmission and epidemiology.

Download Full-text

An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods

Scientific Reports ◽

10.1038/s41598-021-87244-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Juan Moles ◽

Shahan Derkarabetian ◽

Stefano Schiaparelli ◽

Michael Schrödl ◽

Jesús S. Troncoso ◽

...

Keyword(s):

Machine Learning ◽

Deep Sea ◽

Weddell Sea ◽

Nucleotide Polymorphisms ◽

Sea Levels ◽

Suitable Material ◽

Genetic Lineages ◽

Genome Wide ◽

Gastropod Mollusks ◽

Double Digestion

AbstractSampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.

Download Full-text

Prevalence and Characteristics of Multidrug-Resistant Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) CC398 Isolated from Quails (Coturnix Coturnix Japonica) Slaughtered for Human Consumption

Animals ◽

10.3390/ani11072038 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2038

Author(s):

Vanessa Silva ◽

Madalena Vieira-Pinto ◽

Cândido Saraiva ◽

Vera Manageiro ◽

Lígia Reis ◽

...

Keyword(s):

Methicillin Resistant Staphylococcus Aureus ◽

Clonal Complex ◽

Sccmec Type ◽

Multidrug Resistant ◽

Coturnix Japonica ◽

Human Consumption ◽

Coturnix Coturnix Japonica ◽

Genetic Lineages ◽

Coturnix Coturnix ◽

Type V

Livestock-associated MRSA (LA-MRSA) is a zoonotic pathogen that has been reported in several animals, and it is often associated with clonal complex (CC) 398. We aimed to isolate MRSA from quails and to characterize their antimicrobial resistance and genetic lineages. One hundred swab samples were recovered from quails at the slaughterhouse. The swabs were inoculated onto CHROMagar™ MRSA agar plates for MRSA isolation. The presence of antimicrobial-resistant genes and virulence factors was investigated by PCR. All strains were typed by MLST, SCCmec-, spa- and agr-typing. From the 100 samples, 29 MRSA were isolated. All strains were resistant to penicillin, cefoxitin, ciprofloxacin, erythromycin and clindamycin and carried the blaZ, mecA, ermB and ermC genes. All strains, except one, showed resistance to tetracycline and harbored the tetM, tetK and tetL genes in different combinations. Twenty strains belonged to ST398 and SCCmec type V, and nine strains belonged to the new ST6831. Twenty-eight out of twenty-nine strains were ascribed to t011 and one to t108. As far as we know, this is the first report of MRSA from quails slaughtered for human consumption. Most strains belonged to ST398-t011, which is the most common LA-MRSA clone found in livestock in Europe.

Download Full-text

Biogeography of Italy revisited: genetic lineages confirm major phylogeographic patterns and a pre-Pleistocene origin of its biota

Frontiers in Zoology ◽

10.1186/s12983-021-00418-9 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Thomas Schmitt ◽

Uwe Fritz ◽

Massimo Delfino ◽

Werner Ulrich ◽

Jan Christian Habel

Keyword(s):

Meta Analysis ◽

Balkan Peninsula ◽

Po Plain ◽

Genetic Lineages ◽

Biogeographic Patterns ◽

Italian Peninsula ◽

Biogeographic Pattern ◽

History Of ◽

Multiple Species ◽

Micro Plates

AbstractWarm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.

Download Full-text

Chemical Fingerprinting of Cryptic Species and Genetic Lineages of Aneura pinguis (L.) Dumort. (Marchantiophyta, Metzgeriidae)

Molecules ◽

10.3390/molecules26041180 ◽

2021 ◽

Vol 26 (4) ◽

pp. 1180

Author(s):

Rafał Wawrzyniak ◽

Wiesław Wasiak ◽

Beata Jasiewicz ◽

Alina Bączkiewicz ◽

Katarzyna Buczkowska

Keyword(s):

Cluster Analysis ◽

Cryptic Species ◽

Plant Material ◽

Chemical Constituents ◽

Principal Component ◽

Molecular Data ◽

Rapid Identification ◽

Multivariate Statistical ◽

Genetic Lineages ◽

Marker Compounds

Aneura pinguis (L.) Dumort. is a representative of the simple thalloid liverworts, one of the three main types of liverwort gametophytes. According to classical taxonomy, A. pinguis represents one morphologically variable species; however, genetic data reveal that this species is a complex consisting of 10 cryptic species (named by letters from A to J), of which four are further subdivided into two or three evolutionary lineages. The objective of this work was to develop an efficient method for the characterisation of plant material using marker compounds. The volatile chemical constituents of cryptic species within the liverwort A. pinguis were analysed by GC-MS. The compounds were isolated from plant material using the HS-SPME technique. Of the 66 compounds examined, 40 were identified. Of these 40 compounds, nine were selected for use as marker compounds of individual cryptic species of A. pinguis. A guide was then developed that clarified how these markers could be used for the rapid identification of the genetic lineages of A. pinguis. Multivariate statistical analyses (principal component and cluster analysis) revealed that the chemical compounds in A. pinguis made it possible to distinguish individual cryptic species (including genetic lineages), with the exception of cryptic species G and H. The classification of samples based on the volatile compounds by cluster analysis reflected phylogenetic relationships between cryptic species and genetic lineages of A. pinguis revealed based on molecular data.

Download Full-text