No (20)
Used filters
(4)
Number of found documents:
20
Published from
to
Seasonal dynamics of ergasilosis in reservoir fish
Jelínková, E.; Krechler, I.; Jurajda, Pavel; Papežíková, I.; Navrátil, S.; Marková, Z.; Kosour, D.; Palíková, M.
2016 - English
We evaluated ergasilosis seasonal dynamics at two reservoirs (Hubenov, Korycany) in the Morava River Basin (Czech Republic). Samples of fish were obtained at monthly intervals between April and October 2014. In total, 189 fish of 11 species were caught using electrofishing and seine nets. Highest overall values for E. sieboldi infection intensity and abundance were recorded at Hubenov in June and September. Prevalence ranged between 80 and 100%. Two highest peaks of infection intensity and abundance were recorded at Korycany in May and the second around September and October, prevalence ranging between 33 and 100%. As the nauplius and copepod stages of arthropods form part of the zooplankton assemblage, they will be found at highest numbers in reservoirs with low predatory pressure, i.e. where predatory fish suppress zooplanktonophagic fish species.
Keywords:
Copepoda; parasite; Ergasilus sieboldi; arthropods; predatory pressure; biomanipulation
Available at various institutes of the ASCR
Seasonal dynamics of ergasilosis in reservoir fish
We evaluated ergasilosis seasonal dynamics at two reservoirs (Hubenov, Korycany) in the Morava River Basin (Czech Republic). Samples of fish were obtained at monthly intervals between April and ...
Multilocus phylogeny of Sciurini tree squirrels
Pečnerová, P.; Martínková, Natália
2012 - English
Phylogenetic relationships inside the tribe Sciurini produce conflict between older morphological research and modern molecular studies. We provided a detailed phylogenetic analysis by incorporating eight loci and various methods of data processing. We used prevailing and user-friendly software packages (Geneious, BioEdit, MrBayes, ModelTest). Evolutionary history of Sciurini squirrels was examined by means of Bayesian inference of concatenated data set and six supertree construction methods. The concatenated data and supertrees generated by SuperTriplets, modified MinCut, standard MRP and veto supertree (without source tree correction) yielded similar results with taxa grouped according to their zoogeographic distribution. The genus Tamiasciurus formed a separate evolutionary lineage at the base of our trees and the other taxa gradually diverged into Palaearctic/Indomalayan, Nearctic and Neotropical groups. The other used methods, MinCut, Purvis-MRP and veto (with source tree correction) showed deviations from this pattern.
Keywords:
phylogeny; supermatrix; supertree; squirrels
Available at various institutes of the ASCR
Multilocus phylogeny of Sciurini tree squirrels
Phylogenetic relationships inside the tribe Sciurini produce conflict between older morphological research and modern molecular studies. We provided a detailed phylogenetic analysis by incorporating ...
Reconstructing phylogeny from patchy data of rodents
Martínková, Natália; Moravec, J.
2012 - English
To reveal phylogeny of sparsely sequenced taxa, standard methods could not be successfully used due to patchy character of data and new methods had to be developed. We summarize such methods and present their funcionality on phylogeny of Arvicolini voles. Analyzing tree space with terraces, we have found that supermatrix approach is superior to supertree approach in extracting signal from data and determining a resolved and well-supported phylogeny. The most widely used program from Bayesian phylogeny inference fails to determine the correct lengths of branches in a large supermatrix with a lot of missing data, it still successfully determines the true tree topology.
Keywords:
phylogeny; supermatrix; supertree; arvicolini; Bayesian inference
Available at various institutes of the ASCR
Reconstructing phylogeny from patchy data of rodents
To reveal phylogeny of sparsely sequenced taxa, standard methods could not be successfully used due to patchy character of data and new methods had to be developed. We summarize such methods and ...
Tree of life in a gappy genomic era
Martínková, Natália
2012 - English
Increasing volume of publicly available DNA sequence data enables comprehensive studies that address integrative questions. For these projects, bioinformatic analysis requires advanced methods and computational infrestructure. I present the character of DNA sequence matrices for multilocus datasets, which contain large portions of missing data. A condition critical for analysis of multilocus data is that datasets for all loci or genes need to have partially overlapping taxon sets. The work-flow for analysing such data differs between supermatrix and supertree estimation of species trees. In the supermatrix approach, aligned sequences for all genes are concatenated and the species tree is estimated directly from a partitioned matrix. In the supertree approach, gene sequence alignments are used for inference of gene trees. Those are then combined into a species supertree. Smaller projects could benefit from utilising all available information in the supermatrix. Larger projects should rely on supertree methods for computational optimisation.
Keywords:
DNA sequence evolution; phylogeny; multilocus genotyping; supermatrix; supertree
Available at various institutes of the ASCR
Tree of life in a gappy genomic era
Increasing volume of publicly available DNA sequence data enables comprehensive studies that address integrative questions. For these projects, bioinformatic analysis requires advanced methods and ...
Genetic diversity in populations
Martínková, Natália; Zemanová, Barbora
2011 - English
Genetic diversity accumulates over time on the level of DNA sequence with accumulation of mutations. It is additionally increased with population admixture, and the decrease in genetic diversity is often the first indication of detrimental processes affecting populations, such as reduction in the number of breeding individuals or breeding of close relatives. Nucleotide diversity shows how different the sequences of a given gene are in a population. Gene diversity estimates how likely two individuals are to share the same sequence of a gene. Number of alleles is the count of different versions of a gene with differing sequences, and this is corrected for sample size in estimation of allelic richness. Heterozygosity is the average frequency that an individual will have two different copies of a gene.
Keywords:
nucleotide diversity; haplotype diversity; heterozygosity; Hardy-Weinberg equilibrium
Available at various institutes of the ASCR
Genetic diversity in populations
Genetic diversity accumulates over time on the level of DNA sequence with accumulation of mutations. It is additionally increased with population admixture, and the decrease in genetic diversity is ...
First record of the Danube whitefin gudgeon (Romanogobio vladykovi) in the Nida River drainage, Poland
Nowak, M.; Mendel, Jan; Szczerbik, P.; Koščo, J.; Klaczak, A.; Popek, W.
2009 - English
The Danube whitefin gudgeon Romanogobio vladykovi Fang, 1943 belongs to the R. albipinnatus (Lukasch, 1933) species group. In the territory of Poland so-called whitefin gudgeon was recorded for the first time in the middle stretches of Vistula River (1965). Since then the species has been found in some 20 localities in the Vistula and Odra River drainages. In May and July 2009 two specimens identified initially as belonging to the R. albipinnatus species group were caught in the main course of Nida River. Molecular approach based on combination of both mitochondrial and nuclear markers confirmed occurrence of R. vladykovi on Polish territory. This conclusion alters the knowledge about the distribution of the species of the R. albipinnatus species group. Kottelat and Freyhof (2007) considered that the territory of Poland is inhabited by R. belingi, whereas R. vladykovi is restricted only to the drainage area of Danube River. Hrouzek běloploutvý z Dunaje, Romanogobio vladykovi Fang, 1943 patří do skupiny druhů R. albipinnatus (Lukasch, 1933). Poprvé byl na území Polska zaznamenán ve středním úseku řeky Vistula v roce 1965. Od té doby byl pak nalezen na 20 lokalitách v povodí řek Vistula a Odra. V květnu a červenci 2009 byli odchyceni dva jedinci patřící do skupiny R. albipinnatus v hlavním toku řeky Nidy. Molekulární přístup založený na kombinaci mitochondriálního a jaderného markeru potvrdil výskyt R. vladykovi na polském území. Tento závěr mění informace o distribuci druhů hrouzka běloploutvého. Kottelat a Freyhof (2007) uváděli, že území Polska je obývané R. belingi, kdežto R. vladykovi je vyhrazený jen pro povodí Dunaje.
Keywords:
fish; Poland
Available at various institutes of the ASCR
First record of the Danube whitefin gudgeon (Romanogobio vladykovi) in the Nida River drainage, Poland
The Danube whitefin gudgeon Romanogobio vladykovi Fang, 1943 belongs to the R. albipinnatus (Lukasch, 1933) species group. In the territory of Poland so-called whitefin gudgeon was recorded for the ...
Basic phylogenetic methods
Vallo, Peter
2008 - English
This volume comprises contributions of a team of lecturers, who held their speeches at a course for undergraduate students on computational biology. The particular topic of phylogenetic methods is briefly introduced, covering basics of DNA sequence evolution and tree nomenclature. Methods of tree reconstructions are further explained; both general tree searching algorithms and particular reconstruction methods i.e. distance, parsimony, likelihood and Bayesian approaches. Tento svazek zahrnuje příspěvky týmu autorů, kteří přednášeli na kurzu výpočetní biologie pro pregraduální studenty. Téma fylogenetických metod je stručne uvedeno, pokrývajíc základy evoluce sekvencí DNA a názvosloví stromů. Dále jsou vysvětlovány metody rekonstrukce stromů; jak obecné algoritmy pro hledání stromů, tak i jednotlivé metody rekonstrukce t.j. distanční, parsimonický, věrohodnostní a Bayesiánský přístup.
Keywords:
molecular phylogeny; distance methods; maximum parsimony; maximum likelihood; Bayesian analysis
Available at various institutes of the ASCR
Basic phylogenetic methods
This volume comprises contributions of a team of lecturers, who held their speeches at a course for undergraduate students on computational biology. The particular topic of phylogenetic methods is ...
Tutorial in phylogenetic analyses
Martínková, Natália
2008 - English
Reconstruction of phylogeny plays an important role in presentday science. Aim of this paper is to introduce basic methods of phylogenetic analysis using DNA sequences. In a brief manner, approaches to phylogenetic inference, commonly used methods of tree reconstruction, and models of DNA evolution are presented. This compendium may serve as an introduction to this exciting discipline of biological science. Fylogenetické analýzy se rychle vyvíjejí a často se objevují nové metody nebo pokročilá vylepšení stávajících metod. Školení poskytne návod, jak určit důležité kroky ve fylogenetické analýze sekvencí DNA, které mohou být aplikovány na další výpočtové techniky. Tyto kroky zahrnují alignment sekvencí, identifikace alel a haplotypů, výběr substitučního modelu a rekonstrukce fylogenetických stromů.
Keywords:
phylogenetic DNA sequence analysis
Available at various institutes of the ASCR
Tutorial in phylogenetic analyses
Reconstruction of phylogeny plays an important role in presentday science. Aim of this paper is to introduce basic methods of phylogenetic analysis using DNA sequences. In a brief manner, approaches ...
Perch (Perca fluviatilis L.) diet during the flooding period of the Chabařovice coal mining pit (North-West Bohemia, Czech Republic)
Adámek, Zdeněk; Jurajda, Pavel; Musil, J.; Janáč, Michal; Kabilka, P.; Polačik, Matej; Ťuk, J.; Valová, Zdenka; Zeman, J.
2006 - English
The Chabařovice coal mining pit (Chabařovice lake) is currently still under the process of continuous flooding and its area increased up to 174 ha since 2001. The inflow water originates from surface waterbodies and hence the penetration of fish species, undesirable with respect to biomanipulation efforts, makes a serious problem in fisheries management of the lake. Adult perch have been the most numerous fish of the lake until 2004. Current perch population consists of one cohort (7+ - 8+) originating from the recruitment of two subsequent year classes. The food bulk of adult perch consisted of benthic animals and zooplankton in both years under study, however their proportion differed significantly. In 2004, dragon fly nymphs were the dominant food items with 58.80% proportion, followed by cladocerans Daphnia sp., which made up 23.82% of food ingested. In 2005, chironomid larvae prevailed in the food bulk with 41.95% and the diversity of ingested food items was obviously wider. Důlní propadlina Chabařovice je v současné době postupně napouštěna a její plocha se od roku 2001 trvale zvyšuje na stávajících 174 ha. Voda přítoku pochází z povrchových zdrojů a vnikání některých druhů ryb, nežádoucích s ohledem na biomanipulační snahy, se tak stává závažným problémem pro rybářský management nádrže. Adultní okoun byl nejpočetnější rybou nádrže až do roku 2004 a jeho současná populace je tvořena v podstatě pouze dvěma věkovými kohortami (7+ - 8+), které pocházejí ze dvou následných úspěšných výtěrů. Potravu okouna na nádrži tvoří především bentičtí (fytofilní) bezobratlí a zooplankton (Daphnia), ale jejich zastoupení se v průběhu dvou period sledování lišilo. V roce 2004 převládaly larvy vážek (Libellula quadrilineata a Coenagrion puella) s podílem 58.80%, následované perloočkami Daphnia sp., které tvořily až 23.82% přijaté potravy. V roce 2005 byly hlavními potravními organismy larvy pakomárů (41.95%) a diverzita konzumovaných organizmů se významně zvýšila.
Keywords:
perch; Chabařovice lake; biomanipulation; food
Available at various institutes of the ASCR
Perch (Perca fluviatilis L.) diet during the flooding period of the Chabařovice coal mining pit (North-West Bohemia, Czech Republic)
The Chabařovice coal mining pit (Chabařovice lake) is currently still under the process of continuous flooding and its area increased up to 174 ha since 2001. The inflow water originates from surface ...
New approach to phytophilous macroinvertebrates sampling in emergent littoral vegetation
Sychra, Jan; Adámek, Zdeněk
2006 - English
The aim of the study was to design the sampling method for collection of phytophilous macroinvertebrates associated with submersed parts of hard emergent littoral vegetation in still waters, which will join technical sampler unpretentiousness, sampling simplicity and maximal quantitative accuracy. For these purposes, we developed a modified Gerking´s frame box sampler with movable cutter for sampling of animals in the littoral macrophyte beds and a new type of core sampler for collection of animals inhabiting the root zone of emergent plant beds. Both sampling devices are suitable for studies targeted on macroinvertebrates monitoring. The comparative sampling using frame box sampler and benthos handnet was performed in the littoral of three carp ponds. The sampling procedure utilizing the frame sampler was more labour demanding however it enabled significantly (P < 0.05) more efficient collection of slowly moving or sedentary animals. Cílem studie bylo vyvinout takovou metodu vzorkování fytofilních bezobratlých kolonizujících ponořené části tvrdé vynořené flóry litorálu stojatých vod, která by splňovala nároky na jednoduchost a přesnost odběru. Nejvhodnější se ukázala kombinace modifikovaného Gerkingova rámového vzorkovače s pohyblivým nožem pro odběry v litorálních porostech a nový typ sondy pro odběry zoobentosu v jejich kořenové zóně. Srovnání účinnosti rámového vzorkovače a ruční síťky bylo provedeno v litorálu tří kaprových rybníků. Vzorkování s použitím rámového vzorkovače bylo sice pracnější avšak umožnilo významně (P < 0.05) efektivnější odběr pomalu se pohybujících nebo přisedlých živočichů jako jsou plži, máloštětinatí červi, pijavky, vodní roztoči a larvy pakomárů. Naproti tomu však rychleji pohybliví bezobratlí (vodní ploštice, larvy koreter) byly významně (P < 0.05) méně přítomni ve vzorcích z rámového vzorkovače v porovnání s ruční síťkou.
Keywords:
littoral vegetation; phytophilous macroinvertebrates; pond macrozoobenthos; sampling
Available at various institutes of the ASCR
New approach to phytophilous macroinvertebrates sampling in emergent littoral vegetation
The aim of the study was to design the sampling method for collection of phytophilous macroinvertebrates associated with submersed parts of hard emergent littoral vegetation in still waters, which ...
NRGL provides central access to information on grey literature produced in the Czech Republic in the fields of science, research and education. You can find more information about grey literature and NRGL at service web
Send your suggestions and comments to nusl@techlib.cz
Provider
Other bases