The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogues for phylogenetic reconstruction. We developed a novel approach of detecting paralogues and utilizing them for phylogenetic tree inference, by retrieving both ortho- and paralogous copies and creating orthologous alignments, from which the gene trees are built. We implemented this approach in ParalogWizard and demonstrate its performance in plant groups that underwent a whole genome duplication relatively recently: the subtribe Malinae (family Rosaceae), using Angiosperms353 as well as Malinae481 probes, the genus Oritrophium (family Asteraceae), using Compositae1061 probes, and the genus Amomum (family Zingiberaceae), using Zingiberaceae1180 probes. Discriminating between orthologues and paralogues reduced gene tree discordance and increased the species tree support in the case of the Malinae, but not for Oritrophium and Amomum. This may relate to the difference in the proportion of paralogous loci between the data sets, which was highest for the Malinae. Overall, retrieving paralogues for phylogenetic reconstruction following ParalogWizard has the potential to increase the species tree support and reduce gene tree discordance in target enrichment data, particularly if the proportion of paralogous loci is high.

• Klíčová slova
• angiosperms, bioinfomatics/phyloinfomatics, paralogy, species tree,
• MeSH
• fylogeneze MeSH
• genom * MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. RESULTS: Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. The program can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). CONCLUSION: The Physcraper workflow showcases the benefits of doing open science for phylogenetics, encouraging researchers to strive for better scientific sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and usage are available at https://physcraper.readthedocs.io.

• Klíčová slova
• DNA alignment, Gene phylogeny, Gene tree, Interoperability, Multilocus, Open Tree of Life, Open science, Otol, Public database, Reproducibility,
• MeSH
• fylogeneze * MeSH
• Publikační typ
• časopisecké články MeSH

The Win95 program for computation of distance matrixes and construction of phylogenetic or phenetic trees on the basis of RAPD, RFLP and allozyme data was presented. In contrast with other presently available software, the program FreeTree can also assess the robustness of the tree topology by bootstrap, jackknife or OTU-jackknife analysis. Moreover, the program can be used also for an analysis of data obtained in several independent experiments performed with nonidentical subsets of taxa. The function of the program was demonstrated by an analysis of RAPD data from 22 strains of Frenkelia. The program is available as an autoextractive archive containing the installation files of FreeTree and TreeView, manual in MS Word format and a sample of the input file at http://www.natur.cuni.cz/flegr/programs/+ ++freetree.

• MeSH
• Coccidia genetika   MeSH
• druhová specificita MeSH
• Eimeriida genetika   MeSH
• fylogeneze * MeSH
• software * MeSH
• technika náhodné amplifikace polymorfní DNA * MeSH
• Toxoplasma genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Sixteen isolates of Claviceps spp. were analyzed for the production of polysaccharides, oligosaccharides, and sucrose metabolism under conditions of submerged fermentation. Physiological markers calculated by the Verhulst-Pearl law were used for hierarchical cluster analysis. Low correlation was found between physiologically based dendrogram and phylogenetic analysis constructed from an alignment of rDNA sequences. To confirm the intraspecific uniformity of physiological markers three isolates of C. africana from different hosts and locations were included. The influence of genotype, physiological variability, environmental location and habitat on metabolite production is discussed.

• MeSH
• Claviceps klasifikace   genetika   metabolismus   fyziologie   MeSH
• fermentace MeSH
• fylogeneze * MeSH
• kultivační média MeSH
• molekulární sekvence - údaje MeSH
• polysacharidy metabolismus   MeSH
• sacharosa metabolismus   MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kultivační média MeSH
• polysacharidy MeSH
• sacharosa MeSH

A comparison of random amplified polymorphic DNA (RAPD) was used to investigate genetic polymorphisms among 25 isolates of Giardia intestinalis and to assess the utility of RAPD for subtype detection and genealogical analysis. Using data obtained for six human and 19 animal-derived isolates in polymerase chain reactions using 13 different primers, phylogenetic trees were constructed and bootstrap values computed by the program FreeTree. Three major clades were distinguished, corresponding to previously defined genetic assemblages A, B, and E. The purported specificity of assemblage E genotypes for artiodactyl hosts was supported. Assemblages A and B showed wide host spectra, including human and animal hosts. No correlation was found between the genotype of analyzed isolates and the presence or absence of the double-stranded RNA Giardiavirus. The results indicate that RAPD data provide reliable genetic information that can be used for both "fingerprinting" and genealogical purposes.

• MeSH
• druhová specificita MeSH
• fylogeneze * MeSH
• Giardia lamblia klasifikace   genetika   izolace a purifikace   MeSH
• giardiáza klasifikace   genetika   MeSH
• kočky MeSH
• krysa rodu Rattus MeSH
• lidé MeSH
• polymerázová řetězová reakce metody   MeSH
• psi MeSH
• savci parazitologie   MeSH
• technika náhodné amplifikace polymorfní DNA * MeSH
• zvířata MeSH
• Check Tag
• kočky MeSH
• krysa rodu Rattus MeSH
• lidé MeSH
• psi MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH

BACKGROUND: Despite the excellent fossil record of cephalopods, their early evolution is poorly understood. Different, partly incompatible phylogenetic hypotheses have been proposed in the past, which reflected individual author's opinions on the importance of certain characters but were not based on thorough cladistic analyses. At the same time, methods of phylogenetic inference have undergone substantial improvements. For fossil datasets, which typically only include morphological data, Bayesian inference and in particular the introduction of the fossilized birth-death model have opened new possibilities. Nevertheless, many tree topologies recovered from these new methods reflect large uncertainties, which have led to discussions on how to best summarize the information contained in the posterior set of trees. RESULTS: We present a large, newly compiled morphological character matrix of Cambrian and Ordovician cephalopods to conduct a comprehensive phylogenetic analysis and resolve existing controversies. Our results recover three major monophyletic groups, which correspond to the previously recognized Endoceratoidea, Multiceratoidea, and Orthoceratoidea, though comprising slightly different taxa. In addition, many Cambrian and Early Ordovician representatives of the Ellesmerocerida and Plectronocerida were recovered near the root. The Ellesmerocerida is para- and polyphyletic, with some of its members recovered among the Multiceratoidea and early Endoceratoidea. These relationships are robust against modifications of the dataset. While our trees initially seem to reflect large uncertainties, these are mainly a consequence of the way clade support is measured. We show that clade posterior probabilities and tree similarity metrics often underestimate congruence between trees, especially if wildcard taxa are involved. CONCLUSIONS: Our results provide important insights into the earliest evolution of cephalopods and clarify evolutionary pathways. We provide a classification scheme that is based on a robust phylogenetic analysis. Moreover, we provide some general insights on the application of Bayesian phylogenetic inference on morphological datasets. We support earlier findings that quartet similarity metrics should be preferred over the Robinson-Foulds distance when higher-level phylogenetic relationships are of interest and propose that using a posteriori pruned maximum clade credibility trees help in assessing support for phylogenetic relationships among a set of relevant taxa, because they provide clade support values that better reflect the phylogenetic signal.

• Klíčová slova
• Bayesian phylogenetics, Cephalopoda, Endoceratoidea, Fossilized birth-death process, Multiceratoidea, Nautiloidea, Orthoceratoidea, Phylogeny, Posterior clade probabilities, Tree similarities,
• MeSH
• Bayesova věta MeSH
• fylogeneze MeSH
• hlavonožci * genetika   MeSH
• pravděpodobnost MeSH
• zkameněliny MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5-7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.

• MeSH
• biodiverzita * MeSH
• databáze faktografické MeSH
• déšť MeSH
• fylogeneze MeSH
• lidské činnosti MeSH
• stromy * klasifikace   fyziologie   MeSH
• teplota MeSH
• zavlečené druhy * statistika a číselné údaje   trendy   MeSH
• životní prostředí * MeSH
• Publikační typ
• časopisecké články MeSH

The prediction of vegetation responses to climate requires a knowledge of how climate-sensitive plant traits mediate not only the responses of individual plants, but also shifts in the species and functional compositions of whole communities. The emission of isoprene gas - a trait shared by one-third of tree species - is known to protect leaf biochemistry under climatic stress. Here, we test the hypothesis that isoprene emission shapes tree species compositions in tropical forests by enhancing the tolerance of emitting trees to heat and drought. Using forest inventory data, we estimated the proportional abundance of isoprene-emitting trees (pIE) at 103 lowland tropical sites. We also quantified the temporal composition shifts in three tropical forests - two natural and one artificial - subjected to either anomalous warming or drought. Across the landscape, pIE increased with site mean annual temperature, but decreased with dry season length. Through time, pIE strongly increased under high temperatures, and moderately increased following drought. Our analysis shows that isoprene emission is a key plant trait determining species responses to climate. For species adapted to seasonal dry periods, isoprene emission may tradeoff with alternative strategies, such as leaf deciduousness. Community selection for isoprene-emitting species is a potential mechanism for enhanced forest resilience to climatic change.

• Klíčová slova
• climate feedback, drought, plant functional traits, plant secondary metabolism, thermotolerance, tree physiology, tropical forest, volatile organic compounds,
• MeSH
• butadieny analýza   MeSH
• časové faktory MeSH
• fylogeneze * MeSH
• hemiterpeny analýza   MeSH
• klimatické změny * MeSH
• lesy MeSH
• stromy fyziologie   MeSH
• tropické klima * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• butadieny MeSH
• hemiterpeny MeSH
• isoprene MeSH Prohlížeč

Phylogenetic distances of coexisting species differ greatly within plant communities, but their consequences for decomposers and decomposition remain unknown. We hypothesized that large phylogenetic distance of leaf litter mixtures increases differences of their litter traits, which may, in turn, result in increased resource complementarity or decreased resource concentration for decomposers and hence increased or decreased chemical transformation and reduction of litter. We conducted a litter mixture experiment including 12 common temperate tree species (evolutionarily separated by up to 106 Myr), and sampled after seven months, at which average mass loss was more than 50%. We found no effect of increased phylogenetic distance on litter mass loss or on abundance and diversity of invertebrate decomposers. However, phylogenetic distance decreased microbial biomass and increased carbon/nitrogen (C/N) ratios of litter mixtures. Consistently, four litter traits showed (marginally) significant phylogenetic signal and in three of these traits increasing trait difference decreased microbial biomass and increased C/N. We suggest that phylogenetic proximity of litter favours microbial decomposers and chemical transformation of litter owing to a resource concentration effect. This leads to a new hypothesis: closely related plant species occurring in the same niche should promote and profit from increased nutrient availability.

• Klíčová slova
• complementarity versus resource concentration hypotheses, decomposer, litter degradation, niche, phylogenetic biodiversity ecosystem functioning, phylogenetic signal of functional traits,
• MeSH
• bezobratlí fyziologie   MeSH
• biodegradace MeSH
• biomasa MeSH
• dusík analýza   MeSH
• fylogeneze MeSH
• lesy MeSH
• listy rostlin chemie   klasifikace   MeSH
• Magnoliopsida klasifikace   fyziologie   MeSH
• mikrobiota fyziologie   MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• stromy klasifikace   fyziologie   MeSH
• uhlík analýza   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Francie MeSH
• Názvy látek
• dusík MeSH
• půda MeSH
• uhlík MeSH

Biological age is typically estimated using biomarkers whose states have been observed to correlate with chronological age. A persistent limitation of such aging clocks is that it is difficult to establish how the biomarker states are related to the mechanisms of aging. Somatic mutations could potentially form the basis for a more fundamental aging clock since the mutations are both markers and drivers of aging and have a natural timescale. Cell lineage trees inferred from these mutations reflect the somatic evolutionary process, and thus, it has been conjectured, the aging status of the body. Such a timer has been impractical thus far, however, because detection of somatic variants in single cells presents a significant technological challenge. Here, we show that somatic mutations detected using single-cell RNA sequencing (scRNA-seq) from thousands of cells can be used to construct a cell lineage tree whose structure correlates with chronological age. De novo single-nucleotide variants (SNVs) are detected in human peripheral blood mononuclear cells using a modified protocol. A default model based on penalized multiple regression of chronological age on 31 metrics characterizing the phylogenetic tree gives a Pearson correlation of 0.81 and a median absolute error of ~4 years between predicted and chronological ages. Testing of the model on a public scRNA-seq dataset yields a Pearson correlation of 0.85. In addition, cell tree age predictions are found to be better predictors of certain clinical biomarkers than chronological age alone, for instance glucose, albumin levels, and leukocyte count. The geometry of the cell lineage tree records the structure of somatic evolution in the individual and represents a new modality of aging timer. In addition to providing a numerical estimate of "cell tree age," it unveils a temporal history of the aging process, revealing how clonal structure evolves over life span. Cell Tree Rings complements existing aging clocks and may help reduce the current uncertainty in the assessment of geroprotective trials.

• Klíčová slova
• Biological age, Cell Tree Rings, Geroprotective trials,
• MeSH
• biologické markery MeSH
• dlouhověkost MeSH
• fylogeneze MeSH
• leukocyty mononukleární * MeSH
• lidé MeSH
• stárnutí * genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• biologické markery MeSH