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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 ...
Ichthyofauna of the lower reaches of the Dyje River and the adjacent floodplain with floodplain forests
Lusk, Stanislav; Lusková, Věra; Halačka, Karel; Horák, Václav; Pražák, O.
2001 - English
The lower reaches of the Dyje River with adjacent floodplain constitute an unique territory fragment in the Czech Republic. Its hydrological system is prominent with a high diversity of aquatic habitats including natural floodings over the floodplain part. During last 50 years, the occurrence of 49 species fish was found there in total. Of them, 41 species are assessed to be autochtonous, i.e. 75% of the native ichthyofauna structure of the Czech Republic. As strategically significant, the direct barrier-free connection of the lower Dyje River through the Morava River with the Danube has been manifested. In such way during recent years, the occurrence has been renewed of naturally immigrating Pelecus cultratus, Gymnocephalus schraetser and Zingel zingel, which had disappeared in the past. Sporadically, also the occurrence of Acipenser ruthenus and the wild form Cyprinus carpio is renewed. Naturally in the territory of the Czech Republic, new species such as Carassius auratus, Proterorhinus marmoratus, Sander volgense and Gymnocephalus baloni have penetrated. This unique territory is intended to be proclaimed for the Biospherical reserve and as protected territory for selected fish species within the NATURA 2000 system.
Keywords:
River Dyje; floodplain; ichthyofauna
Available at various institutes of the ASCR
Ichthyofauna of the lower reaches of the Dyje River and the adjacent floodplain with floodplain forests
The lower reaches of the Dyje River with adjacent floodplain constitute an unique territory fragment in the Czech Republic. Its hydrological system is prominent with a high diversity of aquatic ...
Fish assemblages of the artificially made water habitats in floodplain forests
Horák, Václav
2001 - English
In the alluvium of the Dyje River (r. kms 0.0-35.00) the original biotops and the artificially made biotops (created as a part of revitalisation activities) were studied in two floodplain forest complexes (the Kančí obora and the Soutok floodplain forests). Within the Kančí obora floodplain forest the most diversified assemblage was found in the new made complex of three pools, the Palachy (16 species) because of its permanent connection with hydrological systém. The species Rutilus rutilus, Scardinius erythrophthalmus, Blicca bjoerkna occured most. In the original pool U svaleného dubu (14 species) were the R. rutilus, S. erythrophthalmus species most frequent. Within the Soutok area in the artificially made complex of two pools, the Kesle, 9 fish species were found. The species Abramis ballerus occured most. In the original pool, the Krumpava, 10 fish species were found with A. ballerus occuring most as well. The artificially made habitats (pools) provide the same conditions for fish if permanently connected with the hydrological system of the floodplain forest.
Keywords:
floodplain forest; fish communities; druhy; mosty
Available at various institutes of the ASCR
Fish assemblages of the artificially made water habitats in floodplain forests
In the alluvium of the Dyje River (r. kms 0.0-35.00) the original biotops and the artificially made biotops (created as a part of revitalisation activities) were studied in two floodplain forest ...
Revitalisation and fishes in the inundation area and the floodplain forests along the lower reaches of the River Dyje
Lusk, Stanislav; Halačka, Karel; Lusková, Věra; Horák, Václav
2001 - English
The hydroeconomical modifications during 1968-1986 have changed fundamentally the natural hydrological regime of the lower Dyje River and adjacted floodplain. The proper stream channel was straightened and erected flood-oreventing leeves stopped natural floodings over the original floodplain substantial part. Elaborated and successively realised were specific rehabilitation projects that should eliminate negative impact of the modifications performed on the fish biota there. Concerned in the rehabilitation of the longitudinal and lateral migration permeability of the respective hydrological system for fish. That means to achieve the increase of aquatic habitat diversity by revitalisation of vanishing or by creation of new beckwater, pools and lagoons. The controlled inundation over a part of alluvial meadows has improved conditions for reproduction of phytophilous fish species. The rehabilitation of permanent connection in oxbows cut off (original river meanders) with the Dyje River will increase significantly the diversity of hydrological and geomorphological characteristics of the river bed channelised. The final goal is to create conditions for the ichthyofauna stabilisation and development in the respective area.
Keywords:
River Dyje; floodplain; fish biota
Available at various institutes of the ASCR
Revitalisation and fishes in the inundation area and the floodplain forests along the lower reaches of the River Dyje
The hydroeconomical modifications during 1968-1986 have changed fundamentally the natural hydrological regime of the lower Dyje River and adjacted floodplain. The proper stream channel was ...
Ultrastructure of spirochetes isolated from culicine mosquitoes
Sanogo, Yibayiri Osée; Reipert, S.; Halouzka, Jiří; Hubálek, Zdeněk; Němec, M.
2000 - English
We report the morphological studies of six spirochetal strains. In transmission electron microscopy (thin sections and negative staining), with both blunt and tapered ends, a three-layered outer membrane and variable number of endoflagella.
Keywords:
were observed. The strains were heterogenous in their lengths, widths and the number of their flagella.
Available at various institutes of the ASCR
Ultrastructure of spirochetes isolated from culicine mosquitoes
We report the morphological studies of six spirochetal strains. In transmission electron microscopy (thin sections and negative staining), with both blunt and tapered ends, a three-layered outer ...
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