Myxozoa is a group of endoparasitic cnidarians covering almost 2600 species but merely 53 species, mostly from the genus Chloromyxum, have been reported from sharks, rays, and skates (Elasmobranchii). Elasmobranchs play a key role in the study of evolutionary trajectories of myxozoans as they represent ancestral vertebrate hosts. Our study provides new data on Chloromyxum spp. from 57 elasmobranchs, covering 20 species from geographical regions and host groups not previously investigated, such as Lamniformes and Hexanchiformes, the most basal phylogenetic shark lineage. In total, 28% of elasmobranchs were infected with Chloromyxum spp., indicating high diversity. Of the seven distinguished species, six are formally described based on morphological, morphometric, and genetic (18S rDNA) data. Comprehensive co-phylogenetic analyses and ancestral state reconstruction revealed that parasite and host phylogenies are clearly correlated, resulting in a distinct phylogenetic separation of chloromyxids from selachid (shark) vs. batoid (ray and skate) hosts. Species infecting the most ancient elasmobranchs formed a sublineage, branching off in the middle of the Chloromyxum sensu stricto clade. Our findings indicate that chloromyxids likely invaded an ancestral elasmobranch prior the time of divergence of shark and batoid lineages. Our analyses did not show a clear phylogeographic pattern of Chloromyxum parasites, probably due to the cosmopolitan distribution and migratory behaviour of many elasmobranch hosts, but geographical sampling must be extended to confirm or refute this observation. This study provides a complex view on species diversity, phylogeny, evolution, host-parasite co-phylogeny, and the phylogeographic origin of Chloromyxum species from elasmobranchs. Our results highlight the importance of adding missing data from previously un- or undersampled geographical regions and host species which results in a more accurate estimate of myxozoan biodiversity and a better understanding of the evolution of this parasite group in their hosts and in the different oceans of our planet.

• MeSH
• Elasmobranchii * genetika   parazitologie   MeSH
• fylogeneze MeSH
• Myxozoa * genetika   MeSH
• paraziti * MeSH
• ryby parazitologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug-resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.

• MeSH
• antibiotická rezistence genetika   MeSH
• Escherichia coli genetika   patogenita   MeSH
• fylogeneze MeSH
• genom bakteriální účinky léků   MeSH
• infekce vyvolané Escherichia coli farmakoterapie   genetika   MeSH
• lidé MeSH
• molekulární evoluce * MeSH
• regulační oblasti nukleových kyselin genetika   MeSH
• sekvenční analýza DNA MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Lineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. Myxozoa, a cnidarian subphylum of obligate parasites, are evolutionarily altered and highly reduced organisms with a simple body plan including cnidarian-specific organelles and polar capsules (a type of nematocyst). Minicollagens, a group of structural proteins, are prominent constituents of nematocysts linking Myxozoa and Cnidaria. Despite recent advances in the identification of minicollagens in Myxozoa, the evolutionary history and diversity of minicollagens in Myxozoa and Cnidaria remain elusive. RESULTS: We generated new transcriptomes of two myxozoan species using a novel pipeline for filtering of closely related contaminant species in RNA-seq data. Mining of our transcriptomes and published omics data confirmed the existence of myxozoan Ncol-4, reported only once previously, and revealed a novel noncanonical minicollagen, Ncol-5, which is exclusive to Myxozoa. Phylogenetic analyses support a close relationship between myxozoan Ncol-1-3 with minicollagens of Polypodium hydriforme, but suggest independent evolution in the case of the myxozoan minicollagens Ncol-4 and Ncol-5. Additional genome- and transcriptome-wide searches of cnidarian minicollagens expanded the dataset to better clarify the evolutionary trajectories of minicollagen. CONCLUSIONS: The development of a new approach for the handling of next-generation data contaminated by closely related species represents a useful tool for future applications beyond the field of myxozoan research. This data processing pipeline allowed us to expand the dataset and study the evolution and diversity of minicollagen genes in Myxozoa and Cnidaria. We identified a novel type of minicollagen in Myxozoa (Ncol-5). We suggest that the large number of minicollagen paralogs in some cnidarians is a result of several recent large gene multiplication events. We revealed close juxtaposition of minicollagens Ncol-1 and Ncol-4 in myxozoan genomes, suggesting their common evolutionary history. The unique gene structure of myxozoan Ncol-5 suggests a specific function in the myxozoan polar capsule or tubule. Despite the fact that myxozoans possess only one type of nematocyst, their gene repertoire is similar to those of other cnidarians.

• MeSH
• fylogeneze MeSH
• genom MeSH
• Myxozoa * genetika   MeSH
• paraziti * MeSH
• životní styl MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Species gain membership of regional assemblages by passing through multiple ecological and environmental filters. To capture the potential trajectory of structural changes in regional meta-communities driven by biological invasions, one can categorize species pools into assemblages of different residence times. Older assemblages, having passed through more environmental filters, should become more functionally ordered and structured. Here we calculate the level of compartmentalization (modularity) for three different-aged assemblages (neophytes, introduced after 1500 AD; archaeophytes, introduced before 1500 AD, and natives), including 2,054 species of vascular plants in 302 reserves in central Europe. Older assemblages are more compartmentalized than younger ones, with species composition, phylogenetic structure and habitat characteristics of the modules becoming increasingly distinctive. This sheds light on two mechanisms of how alien species are functionally incorporated into regional species pools: the settling-down hypothesis of diminishing stochasticity with residence time, and the niche-mosaic hypothesis of inlaid neutral modules in regional meta-communities.

• MeSH
• Asteraceae klasifikace   fyziologie   MeSH
• biodiverzita MeSH
• časové faktory MeSH
• distribuce rostlin fyziologie   MeSH
• druhová specificita MeSH
• ekosystém MeSH
• fylogeneze * MeSH
• fylogeografie MeSH
• fyziologická adaptace MeSH
• lidé MeSH
• lipnicovité klasifikace   fyziologie   MeSH
• Rosaceae klasifikace   fyziologie   MeSH
• šáchorovité klasifikace   fyziologie   MeSH
• zavlečené druhy MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

Background and Aims: The origin of different cytotypes by autopolyploidy may be an important mechanism in plant diversification. Although cryptic autopolyploids probably comprise the largest fraction of overlooked plant diversity, our knowledge of their origin and evolution is still rather limited. Here we study the presumed autopolyploid aggregate of Aster amellus, which encompasses diploid and hexaploid cytotypes. Although the cytotypes of A. amellus are not morphologically distinguishable, previous studies showed spatial segregation and limited gene flow between them, which could result in different evolutionary trajectories for each cytotype. Methods: We combine macroevolutionary, microevolutionary and niche modelling tools to disentangle the origin and the demographic history of the cytotypes, using chloroplast and nuclear markers in a dense population sampling in central Europe. Key Results: Our results revealed a segregation between diploid and hexaploid cytotypes in the nuclear genome, where each cytotype represents a monophyletic lineage probably homogenized by concerted evolution. In contrast, the chloroplast genome showed intermixed connections between the cytotypes, which may correspond to shared ancestral relationships. Phylogeny, demographic analyses and ecological niche modelling supported an ongoing differentiation of the cytotypes, where the hexaploid cytotype is experiencing a demographic expansion and niche differentiation with respect to its diploid relative. Conclusions: The two cytotypes may be considered as two different lineages at the onset of their evolutionary diversification. Polyploidization led to the occurrence of hexaploids, which expanded and changed their ecological niche.

• MeSH
• Aster genetika   MeSH
• biologická evoluce * MeSH
• biologické modely MeSH
• DNA chloroplastová analýza   MeSH
• fylogeneze * MeSH
• fylogeografie MeSH
• genetické markery MeSH
• mezerníky ribozomální DNA analýza   MeSH
• polyploidie * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

All 100+ bedbug species (Cimicidae) are obligate blood-sucking parasites [1, 2]. In general, blood sucking (hematophagy) is thought to have evolved in generalist feeders adventitiously taking blood meals [3, 4], but those cimicid taxa currently considered ancestral are putative host specialists [1, 5]. Bats are believed to be the ancestral hosts of cimicids [1], but a cimicid fossil [6] predates the oldest known bat fossil [7] by >30 million years (Ma). The bedbugs that parasitize humans [1, 8] are host generalists, so their evolution from specialist ancestors is incompatible with the "resource efficiency" hypothesis and only partially consistent with the "oscillation" hypothesis [9-16]. Because quantifying host shift frequencies of hematophagous specialists and generalists may help to predict host associations when vertebrate ranges expand by climate change [17], livestock, and pet trade in general and because of the previously proposed role of human pre-history in parasite speciation [18-20], we constructed a fossil-dated, molecular phylogeny of the Cimicidae. This phylogeny places ancestral Cimicidae to 115 mya as hematophagous specialists with lineages that later frequently populated bat and bird lineages. We also found that the clades, including the two major current urban pests, Cimex lectularius and C. hemipterus, separated 47 mya, rejecting the notion that the evolutionary trajectories of Homo caused their divergence [18-21]. VIDEO ABSTRACT.

• MeSH
• Chiroptera genetika   parazitologie   MeSH
• Cimicidae genetika   fyziologie   MeSH
• fylogeneze * MeSH
• interakce hostitele a parazita * MeSH
• koevoluce * MeSH
• lidé MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.

• MeSH
• biodiverzita MeSH
• DNA bakterií MeSH
• fylogeneze * MeSH
• genotyp MeSH
• ledový příkrov mikrobiologie   MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• RNA ribozomální 16S genetika   MeSH
• sinice klasifikace   genetika   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Arktida MeSH
• Svalbard MeSH

Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.

• MeSH
• etnicita * MeSH
• fylogeografie MeSH
• genetická variace * MeSH
• lidé MeSH
• mitochondriální DNA chemie   genetika   MeSH
• populační genetika * MeSH
• rasové skupiny * MeSH
• sekvenční analýza DNA * MeSH
• starobylá DNA chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Asie MeSH
• Černé moře MeSH
• Evropa MeSH

Východiska: Nádorové onemocnění se vyvíjí na základě vzniklé somatické mutace evolučním procesem podle Darwinovských pravidel. Vývoj nádoru je proces dynamické klonální expanze a následné selekce vedoucí ke vzniku geneticky odlišných subpopulací přizpůsobených odlišným podmínkám nádorového mikroprostředí konkrétního hostitele. Genom jednotlivých nádorových buněk je utvářen různými selekčními tlaky. Evoluční dráha vývoje nádoru má ve většině případů rozvětvený charakter a jednotlivé nádorové subklony se tak vyvíjejí paralelně. Diverzita klonů v rámci jediné nádorové tkáně vede ke vzniku genetické, epigenetické a fenotypové variability, což současně představuje hlavní překážku exaktní diagnostiky a účinné personalizované léčby konkrétního nádorového onemocnění u konkrétního jedince. Pokroky v sekvenačních technikách nám v současnosti umožňují odpovědět na otázky ohledně růstu a progrese heterogenních nádorů a také jejich schopnosti odpovídat na léčbu. Porozumění mechanizmu vzniku a sledování změn na úrovni nádorových klonů v průběhu progrese nádorového onemocnění může pomoci zlepšit účinnost protinádorové léčby. Cíl: Tento přehledový článek se zabývá nádorovou heterogenitou a ukazuje, jak klonální diverzita ovlivňuje nádorovou heterogenitu na úrovni genetické, epigenetické i proteinové. Dále popisuje, jak fylogenetika, efektivní nástroj systémové biologie, může pomoci při sledování klonální evoluce nádoru v průběhu jeho progrese a tvorbě metastáz. Na závěr také hodnotí, jakým způsobem přispívá nádorová heterogenita k problémům v diagnostice nádorových onemocnění a jejich léčbě.

Background: Cancer develops as a result of somatic mutations and evolutionary processes with a Darwinian character. Tumors evolve by dynamic clonal expansion and selection to form genetically diverse cell subpopulations adapted to different tumor microenvironmental conditions. Within cancer cells, the genome is shaped by various selective pressures. Cancer evolution often follows a branched trajectory with divergent subclones evolving simultaneously. Clonal diversity within the same tumor results in genetic, epigenetic and phenotypic variability in tumor mass, which represents a major obstacle for the development of efficient diagnostics and personalized treatment. Advances in sequencing techniques have enabled a better understanding of the growth, progression and response to cancer treatment in heterogeneous cancers. Concurrently, understanding the mechanisms involved and monitoring changes in cancer clones during disease progression may improve the efficiency of cancer therapy. Aim: In this review, we summarize available data on intratumor heterogeneity. We show how intratumor heterogeneity, arising from clonal diversity, manifests itself at various levels, including at the genetic, epigenetic, and protein levels. We describe how phylogenetics, a powerful systems biology approach, can help trace clonal evolution during cancer progression and metastasis formation. We also highlight the main problems caused by intratumor heterogeneity, which hinders the development of novel diagnostics and therapies.

• Klíčová slova
• evoluce nádorová, nádorová fylogenetika, nádorová heterogenita,
• MeSH
• genetická heterogenita MeSH
• karcinogeneze * MeSH
• klonální evoluce MeSH
• lidé MeSH
• nádory * genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• přehledy MeSH