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 ...

Jelínková, E.; Krechler, I.; Jurajda, Pavel; Papežíková, I.; Navrátil, S.; Marková, Z.; Kosour, D.; Palíková, M.
Ústav biologie obratlovců, 2016

Identification of parentage in chamois (Rupicapra rupicapra) from NP Gran Paradiso
Poláková, Radka
2013 - English We analysed 47 faecal samples of chamois (32 samples of kids and 15 samples of females). The remaining DNA samples comprised 28 tissue samples of males and other females. Tissue samples were stored in 96% ethanol and faecal samples were placed straight into silicagel. DNA from faecal and tissue samples was extracted using commercial kits. Parentage was determined using the likelihood-based approach in CERVUS 3.0 and these results were confirmed by the program ML-Relate. We found parentage in the case of seven males that sired ten kids. Keywords: paternity analysis; microsatellites; Rupicapra rupicapra; conservation genetic Available at various institutes of the ASCR Identification of parentage in chamois (Rupicapra rupicapra) from NP Gran Paradiso

We analysed 47 faecal samples of chamois (32 samples of kids and 15 samples of females). The remaining DNA samples comprised 28 tissue samples of males and other females. Tissue samples were stored in ...

Poláková, Radka
Ústav biologie obratlovců, 2013

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 ...

Pečnerová, P.; Martínková, Natália
Ústav biologie obratlovců, 2012

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 ...

Martínková, Natália; Moravec, J.
Ústav biologie obratlovců, 2012

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 ...

Martínková, Natália
Ústav biologie obratlovců, 2012

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 ...

Martínková, Natália; Zemanová, Barbora
Ústav biologie obratlovců, 2011

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 ...

Nowak, M.; Mendel, Jan; Szczerbik, P.; Koščo, J.; Klaczak, A.; Popek, W.
Ústav biologie obratlovců, 2009

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 ...

Vallo, Peter
Ústav biologie obratlovců, 2008

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 ...

Martínková, Natália
Ústav biologie obratlovců, 2008

Proceedings of the 4th International Summer School on Computational Biology
Dušek, L.; Haruštiaková, D.; Martínková, Natália
2008 - English Keywords: International Summer School; Computational Biology Available at various institutes of the ASCR Proceedings of the 4th International Summer School on Computational Biology

Dušek, L.; Haruštiaková, D.; Martínková, Natália
Ústav biologie obratlovců, 2008