114 Works

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

Jessen Bredeson, Jessica Lyons, Ibukun Oniyinde, Nneka Okereke, Olufisayo Kolade, Ikenna Nnabue, Nneka Okereke, Christian Nwadili, Eva Hribova, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey Barton, Anna Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie Egesi, Jonathan Featherston … & Daniel Rokhsar
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an ‘orphan crop.’ Here we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive...

Effects of biases in adult sex ratio and male body condition on the alternative reproductive tactics of a gift-giving spider

Cristina Tuni, Daniel Heimerl, Pavla Dudová, Karoline Wacker, Elisa Schenkel & Garance Despréaux
This dataset contains raw data from the manuscript entitled "Adult sex ratio and male body condition affect alternative reproductive tactics in a spider", from Daniel Heimerl, Pavla Dudová, Karoline Wacker, Elisa Schenkel, Garance Despréaux, Cristina Tuni, accepted for publication in the journal Behavioral Ecology, The study investigates how biases in adult sex ratios can affect mating tactics in a spider. Sex ratio variation can alter the intensity of sexual selection by enhancing competition for mates....

Nest microhabitats and tree size mediate shifts in ant community structure across elevation in tropical rainforest canopies

Nichola Plowman, Ondrej Mottl, Vojtech Novotny, Clifson Idigel, Frank Jurgen Philip & Petr Klimes
Declines or mid-elevation peaks in invertebrate diversity with elevation are often attributed to climate and geometric constraints. However, vegetation structure may also drive diversity patterns, especially for tree-dwelling species, via its effects on microhabitat use and competitive interactions. Here we investigate these effects on the diversity and community structure of tree-nesting ants over elevation. We exhaustively sampled ant nests in 1254 trees within continuous plots of primary rainforest at low (200 m a.s.l.), mid (900...

Data from: Facultative asexual reproduction and genetic diversity of populations in the humivorous termite Cavitermes tuberosus

Denis Fournier, Simon Hellemans, Robert Hanus & Yves Roisin
Termite colonies are typically founded by a pair of sexually reproducing dispersers, which can sometimes be replaced by some of their offspring. Some Reticulitermes and Embiratermes species routinely practice asexual queen succession (AQS): the queen is replaced by neotenic daughters produced by parthenogenesis, which mate with the primary king. Here, to cast light on the evolution of AQS, we investigated another candidate species, Cavitermes tuberosus (Termitinae). Of 95 nests, 39 contained a primary queen and...

Data from: Population-specific responses to an invasive species

Martin Reichard, Karel Douda, Mirosław Przybyłski, Oana P. Popa, Eva Karbanová, Klára Matasová, Kateřina Rylková, Matej Polačik, Radim Blažek & Carl Smith
Predicting the impacts of non-native species remains a challenge. As populations of a species are genetically and phenotypically variable, the impact of non-native species on local taxa could crucially depend on population-specific traits and adaptations of both native and non-native species. Bitterling fishes are brood parasites of unionid mussels and unionid mussels produce larvae that parasitize fishes. We used common garden experiments to measure three key elements in the bitterling–mussel association among two populations of...

Data from: Morphological and molecular characterization within 26 strains of the genus Cylindrospermum (Nostocaceae, Cyanobacteria), with descriptions of three new species

Jeffrey R. Johansen, Marketa Bohunicka, Alena Lukesova, Kristyna Hreckova, Melissa A. Vaccarino & Nicholas M. Chesarino
Twenty-six strains morphologically identified as Cylindrospermum as well as the closely related taxon Cronbergia siamensis were examined microscopically as well as phylogenetically using sequence data for the 16S rRNA gene and the 16S-23S ITS region. Phylogenetic analysis of the 16S rRNA revealed three distinct clades. The clade we designate as Cylindrospermum sensu stricto had all five of the foundational species, C. maius, C. stagnale, C. licheniforme, C. muscicola, and C. catenatum. In addition to these...

Data from: Seasonality promotes grassland diversity: interactions with mowing, fertilization and removal of dominant species

Jiri Dolezal, Vojtech Lanta, Ondrej Mudrak & Jan Leps
1. Current biodiversity declines in species-rich grasslands are connected with the cessation of management, eutrophication and the expansion of dominant grass species. One of the theoretical mechanisms limiting biodiversity loss is the ability of subordinate species to avoid competitive exclusion by seasonal niche separation from dominant species. Here we explore how seasonality underpins the maintenance of diversity in temperate meadows under different management regimes and competition intensities in relation to species functional traits. 2. We...

Data from: Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov.

Vit Hubka, Alena Nováková, Željko Jurjević, František Sklenář, Jens C. Frisvad, Jos Houbraken, Maiken C. Arendrup, João P. Z. Siqueira, Josepa Gené & Miroslav Kolařík
Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves...

Data from: Alternative intrapopulation life history strategies and their trade-offs in an African annual fish

Matej Polačik, Radim Blažek, Radomil Řežucha, Milan Vrtílek, Eva Terzibasi-Tozzini & Martin Reichard
In ephemeral habitats, the same genotypes cope with unpredictable environmental conditions, favouring the evolution of developmental plasticity and alternative life-history strategies (ALHS). We tested the existence of intrapopulation ALHS in an annual killifish, Nothobranchius furzeri, inhabiting temporary pools. The pools are either primary (persisting throughout the whole rainy season) or secondary (refilled after desiccation of the initial pool), representing alternative niches. The unpredictable conditions led to the evolution of reproductive bet-hedging with asynchronous embryonic development....

High parasite diversity in the amphipod Gammarus lacustris in a subarctic lake

Jenny Shaw, Eirik Henriksen, Rune Knudsen, Jesper Kuhn, Armand Kuris, Kevin Lafferty, Anna Siwertsson, Miroslava Soldánová & Per-Arne Amundsen
Amphipods are often key species in aquatic food webs due to their functional roles in the ecosystem and as intermediate hosts for trophically transmitted parasites. Amphipods can also host many parasite species, yet few studies address the entire parasite community of a gammarid population, precluding a more dynamic understanding of the food web. We set out to identify and quantify the parasite community of Gammarus lacustris to understand the contributions of the amphipod and its...

Contrasting biomass allocation responses across ontogeny and stress gradients reveal plant adaptations to drought and cold

Jiri Dolezal, Veronica Jandova, Martin Macek & Pierre Liancourt
How plants allocate their biomass to different organs is essential to understand plant adaptation and distribution. Overall, biomass allocation may follow fixed rules across taxa. They are also likely to exhibit substantial departure from these rules during ontogeny and in response to particular limiting factors to optimize their growth and maximize their survival. However, how plants adjust their allocation priorities depending on size and age across stress gradients remain largely unkown in wild populations. We...

Data from: Molecular detection of trophic links in a complex insect host-parasitoid food web

Jan Hrcek, Scott E Miller, Donald L J Quicke & M. Alex Smith
Previously, host-parasitoid links have been unveiled almost exclusively by time-intensive rearing, while molecular methods were used only in simple agricultural host-parasitoid systems in the form of species specific primers. Here we present a general method for molecular detection of these links applied to a complex caterpillar-parasitoid food web from tropical rainforest of Papua New Guinea. We DNA barcoded hosts, parasitoids and their tissue remnants and matched the sequences to our extensive library of local species....

ddRAD-derived genotypes of Centaurea jacea and Betonica officinalis populations from the White Carpathians

Johannes Höfner, Theresa Klein-Raufhake, Christian Lampei, Ondrej Mudrak, Anna Bucharova & Walter Durka
Ecological restoration and plant re-introductions aim to create plant populations that are genetically similar to natural populations to preserve the regional gene pool, yet genetically diverse to allow adaptation to a changing environment. For this purpose, seeds for restoration are increasingly sourced from multiple populations in the target region. However, it has only rarely been tested whether using regional seed indeed leads to genetically diverse restored populations which are genetically similar to natural populations. We...

A new, undescribed species of Melanocharis berrypecker from western New Guinea and the evolutionary history of the family Melanocharitidae

Borja Milá, Jade Bruxaux, Guillermo Friis, Katerina Sam, Hidayat Ashari & Christophe Thébaud
Western New Guinea remains one of the last biologically underexplored regions of the world, and much remains to be learned regarding the diversity and evolutionary history of its fauna and flora. During a recent ornithological expedition to the Kumawa Mountains in West Papua, we encountered an undescribed species of Melanocharis berrypecker (Melanocharitidae) in cloud forest at an elevation of 1200 m asl. Its main characteristics are iridescent blue-black upperparts, satin-white underparts washed lemon yellow, and...

What defines insularity for plants in edaphic islands?

Francisco Emmanuel Méndez Castro, Luisa Conti, Milan Chytrý, Borja Jimenez-Alfaro, Michal Hajek, Michal Horsák, David Zeleny, Marco Malavasi & Gianluigi Ottaviani
The Theory of Island Biogeography postulates that size and isolation are key drivers of biodiversity on islands. This theory has been applied not only to true (e.g. oceanic) islands but also to terrestrial island-like systems (e.g. edaphic islands). Recently, a debate has opened as to whether terrestrial island-like systems function like true islands. However, identifying the effect of insularity in terrestrial systems is conceptually and methodologically challenging because recognizing species source(s) and measuring isolation is...

Data from: Impacts of habitat on butterfly dispersal in tropical forests, parks and grassland patches embedded in an urban landscape

Anuj Jain, Simon Kee Mun Chan, Petr Vlasanek & Edward Layman Webb
Dispersal distances of 17 species of butterflies in tropical Singapore were significantly greater in forest than in urban habitat. Butterflies in urban plots frequently moved within suitable habitat (park/grassland) patches but rarely crossed non-habitat patches suggesting potential isolation and a need for urban corridors.

Data from: Broad-scale patterns of the Afro-Palearctic landbird migration

Martins Briedis, Silke Bauer, Peter Adamík, José Alves, Joana Costa, Tamara Emmenegger, Lars Gustafsson, Jaroslav Koleček, Miloš Krist, Felix Liechti, Simeon Lisovski, Christoph Meier, Petr Procházka & Steffen Hahn
Aim: Animal migration strategies balance trade-offs between mortality and reproduction in seasonal environments. Knowledge of broad-scale biogeographical patterns of animal migration is important for understanding ecological drivers of migratory behaviours. Here we present a flyway-scale assessment of the spatial structure and seasonal dynamics of the Afro-Palearctic bird migration system and explore how phenology of the environment guides long-distance migration. Location: Europe and Africa. Time period: 2009–2017. Major taxa studied: Birds. Methods: We compiled an individual-based...

Data from: Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring

Anne-Marie Dion-Côté, Radka Symonová, Petr Ráb, Louis Bernatchez, P. Rab & R. Symonova
Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish (Coregonus clupeaformis). We examined...

Data from: Earthworms increase plant biomass more in soil with no earthworm legacy than in earthworm mediated soil, and favor late successional species in competition

Ondřej Mudrák & Jan Frouz
As ecosystem engineers, earthworms greatly affect plant communities. They create persistent soil structures enriched by nutrients that improve the conditions for plant growth and modify competition between plant species. We therefore hypothesized that earthworm activity would be more important in early stages of the primary succession, when the soil is not modified by earthworms, than in the late stages of the succession, when the soil is already improved by earthworms. On the other hand, earthworms...

Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage

Marketa Kaucka, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, Karl Annusver, Maria Kasper, Orsolya Symmons, Leslie Pan, Francois Spitz, Jozef Kaiser, Maria Hovorakova, Tomas Zikmund, Kazunori Sunadome, Michael P. Matise, Hui Wang, Ulrika Marklund, Hind Abdo, Patrik Ernfors, Pascal Maire, Maud Wurmser, Andrei S. Chagin, Kaj Fried … & Igor Adameyko
Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly,...

Data from: Metabolomic and transcriptomic data on major metabolic/biosynthetic pathways in workers and soldiers of the termite Prorhinotermes simplex (Isoptera: Rhinotermitidae) and chemical synthesis of intermediates of defensive (E)-nitropentadec-1-ene biosynthesis

Anna Jirošová, Andrej Jančařík, Riya C. Menezes, Olga Bazalová, Klára Dolejšová, Heiko Vogel, Pavel Jedlička, Aleš Buček, Jana Brabcová, Pavel Majer, Robert Hanus & Aleš Svatoš
Production of nitro compounds has only seldom been recorded in arthropods. The aliphatic nitroalkene (E)-nitropentadec-1-ene (NPD), identified in soldiers of the termite genus Prorhinotermes, was the first case documented in insects in early seventies. Yet, the biosynthetic origin of NPD has long remained unknown. We previously proposed that NPD arises through the condensation of amino acids glycine and/or l-serine with tetradecanoic acid along a biosynthetic pathway analogous to the formation of sphingolipids. Here, we provide...

Data from: No immediate or future extra costs of raising a virulent brood parasite chick

Peter Samaš, Tomas Grim, Václav Jelínek, Marek M. Abraham, Michal Šulc & Marcel Honza
Parental care is an adaptive behaviour increasing the survival of young. Virulent brood parasites, like the common cuckoo Cuculus canorus, avoid the parental care and leave the care for their nestlings to hosts. Although raising a cuckoo is always costly because it kills host’s progeny, to date it is not known whether raising of a brood parasite itself represents an extra cost affecting host’s fitness. We quantified costs of rearing a cuckoo nestling in the...

High diversity of mites (Acari: Oribatida, Mesostig-mata) supports the high conservation value of a broadleaf forest in Eastern Norway

Anna Seniczak, Stanisław Seniczak, Josef Starý, Sławomir Kaczmarek, Bjarte Jordal, Jarosław Kowalski, Steffen Roth, Per Djursvoll & Thomas Bolger
Broadleaf forests are critical habitats for biodiversity and this biodiversity is in turn essential for their proper functioning. Mites (Acari) are a numerous and functionally essential component of these forests. We report the diversity of two important groups, Oribatida and Mesostigmata, in a broadleaf forest in Eastern Norway which is considered to be a biodiversity hotspot. Eighteen samples, each 500 cm3, were collected from diverse microhabitats (moss on ground, lichens on tree twigs lying on...

The species richness-productivity relationship varies among regions and productivity estimates, but not with spatial resolution

Aleš Lisner, Gianluigi Ottaviani, Jitka Klimešová, Ondřej Mudrák, Jana Martínková & Jan Lepš
The relationship between species richness and productivity (SRPR) has been a long-studied and hotly debated topic in ecology. Different studies have reported different results with variable shapes (i.e. unimodal, linear) and directions (i.e. positive, negative) of SRPRs depending on spatial grain (i.e. size of sampling unit for species richness), productivity estimates, and study extent. In this study, we quantified the effect of multiple estimates of productivity (aboveground, belowground and total biomass, and various measures of...

Land-use and elevation interact to shape bird functional and phylogenetic diversity and structure: Implications for designing optimal agriculture landscapes

Rachakonda Sreekar, Xingfeng Si, Katerina Sam, Jiajia Liu, Salindra Dayananda, Uromi Goodale, Sarath Kotagama & Eben Goodale
Conversion of rainforests into agriculture resulted in massive changes in species diversity and community structure. Although the conservation of the remaining rainforests is of utmost importance, identifying and creating biodiversity-friendly agriculture landscape is vital for preserving biodiversity and their functions. Biodiversity studies in agriculture have often been conducted at low elevations. In this study, we compared the functional diversity (FD), phylogenetic diversity (PD), and community structure of birds along an interacting gradient of land-use (protected...

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