A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius

Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.Peer reviewe

Динамика частоты встречамости уропатогенов и антимикробных детерминант резистентности при детской значимой бактериурии в 2017 и 2019 годах: моноцентровое исследование

Urinary tract infections are the second most common infections in children with spreading of antimicrobial resistance among uropathogens currently poses a high epidemiological threat.Purpose. Analysis of species prevalence and the presence of genetic determinants of antibiotic resistance.Materials and methods. In the study 215 midstream urine samples were retrospectively analyzed. Samples were obtained during 2017 and 2019 from patients aged 4 weeks to 17 years at the National Medical Research Center for Children's Health Federal State Autonomous Institution of the Ministry of Health of the Russian Federation.Results. Species of pathogen were identified in 93 samples, while the bacterial composition of other samples was classified as «intestinal flora» (n = 17), «coccus flora» (n = 16) or «mixed flora» (n = 89). The most common types of uropathogens in monopathogenic infections in 2017 and 2019 were Escherichia coli (37.5% and 29.2%, respectively). Among infections caused by multiple pathogens, the most common etiological agents were Pseudomonas aeruginosa and Staphylococcus spp. Among all studied samples, 31.9% contained CTX-M-like genes, 5% VIM genes, 1.8% NDM genes, and 3.0% — OXA-48-like genes, and 5.6% of samples contained two and more genetic determinants associated with resistance, with the most prevalent gene combination being the combination of CTX-M- and OXA-48-like genes. In 69 samples with identified species of uropathogens, resistance profile to antimicrobial, determined by microbiological methods, correlated with detected resistance genetic determinants.Conclusion. Authors suggest that introduction of testing for the presence of genes associated with antibacterial resistance to general clinical practice would not only provide an opportunity to conduct epidemiological monitoring of the genetic determinants of antibiotic resistance, but also provide an opportunity to select the correct timely treatment of childhood bacteriuria caused by antibiotic-resistant infectious agents.Инфекции мочевыводящих путей (ИМП) являются вторыми по частоте встречаемости инфекциями у детей, в то время как распространение среди уропатогенов антимикробной резистентности представляет в настоящее время высокую эпидемиологическую угрозу.Цель. Провести анализ видового состава и наличия генетических детерминант антибиотикорезистентности.Материалы и методы. В ходе исследования был проведен ретроспективный анализ 215 образец средней порций мочи. Образцы были получены в течение 2017 и 2019 годов от пациентов в возрасте от 4 недель до 17 лет в ФГАУ «Национальный медицинский исследовательский Центр Здоровья Детей» Министерства здравоохранения Российской Федерации.Результаты. Видовая принадлежность патогенов была установлена в 93 образцах, в то время как бактериальный состав других образцов был классифицирован как «кишечная флора» (n = 17), «кокковая флора» (n = 16) или «смешанная флора» (n = 89). Наиболее распространенными видам уропатогенов при монопатогенных инфекциях в 2017 и 2019 являлась Escherichia coli (37,5% и 29,2%, соответственно). Среди инфекций, вызванных множественными патогенами, наиболее часто встречающимися этиологическими агентами являлись Pseudomonas aeruginosa и Staphylococcus spp. Среди всех исследованных образцов 31,9% содержали CTX-M-подобные гены, 5% гены VIM, 1,8% гены NDM, а также 3,0 % — OXA-48-подобные гены, а также 5,6% образцов содержали две и более генетические детерминанты, ассоциированные с резистентностью, при этом наиболее превалирующей комбинацией генов было сочетание CTX-M- и OXA-48-подобных генов. В 69 образцах с идентифицированными видами уропатогенов профиль устойчивости к противомикробным препаратам, определенный микробиологическими методами, соответствовал обнаруженным генам устойчивости.Выводы. Авторы полагают, что введение в общую клиническую практику тестирования на наличие генов, ассоциированных с антибактериальной резистентностью, предоставит не только возможность проведения эпидемиологического мониторинга за генетическими детерминантнами антибиотикоустойчивости, но также предоставит возможность подбирать корректное своевременное лечение детских бактериурий, вызванных антибиотикорезистентными инфекционными агентами

Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis

BACKGROUND: Restriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. RAD-Seq has been extensively utilised, both at the population level and across species, for example in the construction of phylogenetic trees. However, the consistency of RAD-Seq data generated in different laboratories, and the potential use of cross-species orthologous RAD loci in the estimation of genetic relationships, have not been widely investigated. This study describes the use of SbfI RAD-Seq data for the estimation of evolutionary relationships amongst ten teleost fish species, using previously established phylogeny as a benchmark. RESULTS: The number of orthologous SbfI RAD loci identified decreased with increasing evolutionary distance between the species, with several thousand loci conserved across five salmonid species (divergence ~50 MY), and several hundred conserved across the more distantly related teleost species (divergence ~100–360 MY). The majority (>70%) of loci identified between the more distantly related species were genic in origin, suggesting that the bias of SbfI towards genic regions is useful for identifying distant orthologs. Interspecific single nucleotide variants at each orthologous RAD locus were identified. Evolutionary relationships estimated using concatenated sequences of interspecific variants were congruent with previously published phylogenies, even for distantly (divergence up to ~360 MY) related species. CONCLUSION: Overall, this study has demonstrated that orthologous SbfI RAD loci can be identified across closely and distantly related species. This has positive implications for the repeatability of SbfI RAD-Seq and its potential to address research questions beyond the scope of the original studies. Furthermore, the concordance in tree topologies and relationships estimated in this study with published teleost phylogenies suggests that similar meta-datasets could be utilised in the prediction of evolutionary relationships across populations and species with readily available RAD-Seq datasets, but for which relationships remain uncharacterised. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-015-1261-2) contains supplementary material, which is available to authorized users

Phylogenetic and Taxonomic Relationships of Northern Far Eastern Phoxinin Minnows, Phoxinus and Rhynchocypris (Pisces, Cyprinidae), as Inferred from Allozyme and Mitochondrial 16S rRNA Sequence Analyses

Analyses of allozyme (18 loci) and partial mitochondrial DNA (mtDNA) sequences (1295 bp, 16S rRNA) support the classification of phoxinin minnows from the northern Far East into 2 genera of 8 species: Phoxinus phoxinus, Rhynchocypris oxycephalus, R. perenurus, R. czekanowskii, R. kumgangensis, R. semotilus, R. lagowskii and R. sp. (bergi ?). Although R. lagowskii from Japan and the Amur basin and R. sp. from Vladivostok region to Korea have been classified into a single species by many authors as R. lagowskii, they form separate clusters in both analyses, suggesting different specific status. Some R. oxycephalus and R. perenurus had the mtDNA haplotypes of R. lagowskii and R. czekanowskii, respectively, which probably indicates that local introgression of mtDNA occurred through inter-specific hybridization. Rhynchocypris forms a monophyletic cluster with dace genera Tribolodon and Pseudaspius, not with Phoxinus. Eurasian and American Phoxinus are suggested to be paraphyletic