70 Works

Genomické ddRAD datasety etiopských Lophuromys

Josef Bryja
(1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals. (2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci...

Anchored phylogenomics data used for phylogenomic analysis of Arvicanthini rodents

Josef Bryja
The files represent datasets used in the paper: Mikula et al.: Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Molecular Phylogenetics and Evolution, under review. Arvicanthini_40sp_377loci.nex = alignments of 377 nuclear loci obtained by anchored phylogenomic approach in 40 species of Arvicanthini rodents (partitioned nexus format) Arvicanthini_40sp_377loci_genetrees.nwk = Bayesian gene trees (for 377 genes) used as input for the ASTRAL analysis (newick format).

Bite force in the strictly subterranean rodent family of African mole-rats (Bathyergidae): the role of digging mode, social organisation, and ecology

Radim Šumbera, Andrea Kraus, Matěj Lövy, Ondřej Mikula, Jan Okrouhlík, Nigel Bennett, Radim Šumbera & Anthony Herrel
Bite force is an ecologically relevant performance trait that has been measured to better understand the adaptations to diet and habitat use. Moreover, bite force is relevant in understanding reproductive success, as well as inter- and intraspecific competition. African mole-rats (Bathyergidae, Rodentia) are a unique clade of mammals that use different digging strategies, show different types of social organisation, and occur in ecologically diverse savannah habitats in Sub-Saharan Africa. Whereas previous studies have suggested these...

Data from: Patterns of MHC-dependent mate selection in humans and non-human primates: a meta-analysis

Jamie Winternitz, Jessica Abbate, Elise Huchard, Jan Havlíček & Laszlo Z. Garamszegi
Genes of the major histocompatibility complex (MHC) in vertebrates are integral for effective adaptive immune response and are associated with sexual selection. Evidence from a range of vertebrates supports MHC-based preference for diverse and dissimilar mating partners, but evidence from human mate choice studies has been disparate and controversial. Methodologies and sampling peculiarities specific to human studies make it difficult to know whether wide discrepancies in results among human populations are real or artefact. To...

Data from: Postcopulatory sexual selection is associated with accelerated evolution of sperm morphology

Melissah Rowe, Tomas Albrecht, Emily Rebecca Alison Cramer, Arild Johnsen, Terje Laskemoen, Jason T. Weir & Jan T. Lifjeld
Rapid diversification of sexual traits is frequently attributed to sexual selection, though explicit tests of this hypothesis remain limited. Spermatozoa exhibit remarkable variability in size and shape, and studies report a correlation between sperm morphology (sperm length and shape) and sperm competition risk or female reproductive tract morphology. However, whether postcopulatory processes (e.g. sperm competition and cryptic female choice) influence the speed of evolutionary diversification in sperm form is unknown. Using passerine birds, we quantified...

Data from: Multilocus phylogeography of a widespread savanna-woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa’s Zambezi region

Molly M. McDonough, Radim Šumbera, Vladimír Mazoch, Adam W. Ferguson, Caleb D. Phillips & Josef Bryja
Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during...

Data from: Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing

Jakub Kreisinger, Dagmar Čížková & Jaroslav Piálek
The effects of gastrointestinal tract microbiota (GTM) on host physiology and health has been the subject of considerable interest in recent years. While a variety of captive bred species have been used in experiments, the extent to which GTM of captive and/or inbred individuals resembles natural composition and variation in wild populations is poorly understood. Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain...

Data from: Evaluation of two approaches to genotyping MHC class I in a passerine – CE-SSCP and 454 pyrosequencing

Marta Promerová, Wiesław Babik, Josef Bryja, Tomáš Albrecht, Michał Stuglik & Jacek Radwan
Genes of the highly dynamic major histocompatibility complex (MHC) are directly linked to individual fitness and are of high interest in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high levels of polymorphism in the MHC region, making genotyping of MHC a challenging task. Here, we compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: capillary electrophoresis single...

Data from: In the foothill zone - Sabanejewia balcanica (Karaman 1922), in the lowland zone - Sabanejewia bulgarica (Drensky 1928): myth or reality?

Jakub Fedorčák, Peter Križek, Jan Mendel & Jan Koščo
The status of golden loaches (genus Sabanejewia) in the region of Central Europe and Balkans is still ambiguous. The greatest controversy is caused by species Sabanejewia balcanica and S. bulgarica, whose distinguishing features are often difficult to prove and their occurrence in some river sections is often mentioned as sympatric. Previous phylogenetic studies aimed at the resolving of their taxonomic status did not include samples from their type localities and so led to a lack...

Data from: Active farmsteads are year-round strongholds for farmland birds

Martin Šálek, Miroslav Bažant & Michał Żmihorski
1. Farmland birds have experienced substantial declines over recent decades and various conservation measures have been designed to halt their massive decrease. The effectiveness of these measures is however limited, due to inappropriate identification of crucial breeding and wintering habitats. Identification of appropriate habitats, like farmsteads, and understanding seasonal changes in species richness and abundance of farmland birds within these habitats may therefore be key for farmland bird conservation. 2. We investigated the effect of...

Data from: Strategic exploitation of fluctuating asymmetry in male Endler's guppy courtship displays is modulated by social environment

Radomil Rezucha & Martin Reichard
Lateral asymmetry in signalling traits enables males to strategically exploit their best side. In many animals, both body colouration and fluctuating asymmetry are signals of male attractiveness. We demonstrated experimentally that even sexually naïve male Poecilia wingei were able to identify their most attractive side (i.e. that with a higher proportion of carotenoid pigmentation) and use it preferentially during courtship. Notably, males retained their strategic signalling in a male-biased social environment, whereas they ceased to...

Data from: Chemical defence in avian brood parasites: production and function of repulsive secretions in common cuckoo chicks

Alfréd Trnka, Milica Požgayová, Petr Procházka, Miroslav Capek & Marcel Honza
The use of active chemical defence against predators is relatively rare in birds. Among others, it has been reported for some members of family Cuculidae whose chicks, when threatened, expel dark foul-smelling liquid from their cloaca. Apart from the brood parasitic great spotted cuckoo Clamator glandarius, however, this phenomenon has not yet been systematically studied in any other cuckoo species. Here we investigated the repellent behaviour in the evicting brood parasite, the common cuckoo Cuculus...

Data from: Metazoan parasites of African annual killifish (Nothobranchiidae): abundance, diversity, and their environmental correlates

Veronika Nezhybová, Martin Reichard, Radim Blažek & Markéta Ondračková.
Estimates of biodiversity and its global patterns are affected by parasite richness and specificity. Despite this, parasite communities are largely neglected in biodiversity estimates, especially in the tropics. We studied the parasites of annual killifish of the genus Nothobranchius that inhabit annually desiccating pools across the African savannah and survive the dry period as developmentally arrested embryos. Their discontinuous, non-overlapping generations make them a unique organism in which to study natural parasite fauna. We investigated...

Data from: Repeated intraspecific divergence in life span and aging of African annual fishes along an aridity gradient

Radim Blažek, Matej Polacik, Petr Kacer, Alessandro Cellerino, Radomil Řežucha, Caroline Methling, Oldrich Tomasek, Kaila Syslova, Eva Terzibasi-Tozzini, Tomas Albrecht, Milan Vrtílek & Martin Reichard
Life span and aging are substantially modified by natural selection. Across species, higher extrinsic (environmentally related) mortality (and hence shorter life expectancy) selects for the evolution of more rapid aging. However, among populations within species, high extrinsic mortality can lead to extended life span and slower aging as a consequence of condition-dependent survival. Using within-species contrasts of eight natural populations of Nothobranchius fishes in common garden experiments, we demonstrate that populations originating from dry regions...

Data from: No evidence for host specialization or host-race formation in the European bitterling (Rhodeus amarus), a fish that parasitizes freshwater mussels

Martin Reichard, Josef Bryja, Matej Polačik & Carl Smith
Coevolutionary relationships between parasites and hosts can elevate the rate of evolutionary changes due to reciprocal adaptations between coevolving partners. Such relationships can result in the evolution of host specificity. Recent methodological advances have permitted the recognition of cryptic lineages, with important consequences for our understanding of biological diversity. We used the European bitterling (Rhodeus amarus), a freshwater fish that parasitizes unionid mussels, to investigate host specialization across regions of recent and ancient sympatry between...

Data from: Body size, swimming speed, or thermal sensitivity? Predator-imposed selection on amphibian larvae

Lumír Gvoždík & Radovan Smolinský
Background: Many animals rely on their escape performance during predator encounters. Because of its dependence on body size and temperature, escape velocity is fully characterized by three measures, absolute value, size-corrected value, and its response to temperature (thermal sensitivity). The primary target of the selection imposed by predators is poorly understood. We examined predator (dragonfly larva)-imposed selection on prey (newt larvae) body size and characteristics of escape velocity using replicated and controlled predation experiments under...

Data from: PCR-based isolation of multigene families: lessons from the avian MHC class IIB

Reto Burri, Marta Promerová, Julien Goebel & Luca Fumagalli
The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multigene families, PCR-based approaches bear the often ignored risk of incomplete isolation of family members. This problem is most prominent in gene...

GPS data of little owls

Martin Mayer, Martin Šálek, Anthony Fox, Frej Juhl Lindhøj, Lars Bo Jacobsen & Peter Sunde
Advances in bio-logging technology for wildlife monitoring have expanded our ability to study space use and behavior of many animal species at increasingly detailed scales. However, such data can be challenging to analyze due to autocorrelation of GPS positions. As a case study, we investigated spatiotemporal movements and habitat selection in the little owl (Athene noctua), a bird species that is declining in central Europe and verges on extinction in Denmark. We equipped 6 Danish...

Data from: Admixture of eastern and western European red deer lineages as a result of postglacial re-colonisation of the Czech Republic (Central Europe)

Jarmila Krojerová-Prokešová, Miroslava Barančeková & Petr Koubek
Due to a restriction of the distributional range of European red deer (Cervus elaphus L.) during the Quaternary and subsequent recolonization of Europe from different refugia, a clear phylogeographical pattern in genetic structure has been revealed using mitochondrial DNA markers. In Central Europe, 2 distinct, eastern and western, lineages of European red deer are present; however, admixture between them has not yet been studied in detail. We used mitochondrial DNA (control region and cytochrome b...

Data from: Does developmental acclimatization reduce the susceptibility to predation in newt larvae?

Radovan Smolinsky & Lumir Gvozdik
Many organisms respond to the heterogeneity of abiotic environmental conditions by plastic modifications of their phenotypes (acclimation or acclimatization). Despite considerable research efforts in this area, the beneficial (adaptive) effect of acclimation or acclimatization is still debated. We examined whether development of newt larvae (Ichthyosaura alpestris) in different natural light and thermal conditions subsequently altered their susceptibility to predation in sun-exposed versus shaded tanks in nature. During predation trials in various light and temperature conditions,...

Data from: Sperm is a sexual ornament in rose bitterling

Carl Smith, Rowena Spence & Martin Reichard
In many taxa, odour cues mediate mating decisions. A key question is what these odours comprise, where they are produced, and what they signal. Using rose bitterling, fish that spawn in the gills of freshwater mussels, we investigated the role of sperm cues on female oviposition decisions using individuals of known MHC genotype. Male bitterling frequently released sperm prior to female oviposition and females responded with an increased probability of oviposition and released a greater...

Data from: Genetics, morphology, advertisement calls, and historical records distinguish six new polyploid species of African clawed frog (Xenopus, Pipidae) from West and Central Africa

Ben J. Evans, Timothy F. Carter, Eli Greenbaum, Václav Gvoždík, Darcy B. Kelley, Patrick J. McLaughlin, Olivier S. G. Pauwels, Daniel M. Portik, Edward L. Stanley, Richard C. Tinsley, Martha L. Tobias & David C. Blackburn
African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolutionary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecular variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness...

Data from: Around the Mediterranean: an extreme example of loop migration in a long-distance migratory passerine

Petr Klvaňa, Jaroslav Cepák, Pavel Munclinger, Romana Michálková, Oldřich Tomášek & Tomas Albrecht
An important issue in migration research is how small-bodied passerines pass over vast geographical barriers; in European-African avian migration, these are represented by the Mediterranean Sea and the Sahara Desert. Eastern (passing Eastern Mediterranean), central (passing Apennine Peninsula) and western (via western Mediterranean) major migration flyways are distinguished for European migratory birds. The autumn and spring migration routes may differ (loop migration) and there could be a certain level of individual flexibility in how individuals...

Data from: Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): inference from transcriptome-wide coalescence analyses

Beate Nürnberger, Konrad Lohse, Anna Fijarczyk, Jacek M. Szymura & Mark L. Blaxter
Ancient origins, profound ecological divergence, and extensive hybridization make the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of...

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