26 Works

Data from: Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation

Huai-Chun Wang, Bui Quang Minh, Edward Susko & Andrew J. Roger
Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum...

Data from: Evolution of brain region volumes during artificial selection for relative brain size

Alexander Kotrschal, Hong-Li Zeng, Wouter Van Der Bijl, Caroline Öhman-Mägi, Kurt Kotrschal, Kristiaan Pelckmans & Niclas Kolm
The vertebrate brain shows an extremely conserved layout across taxa. Still, the relative sizes of separate brain regions vary markedly between species. One interesting pattern is that larger brains seem associated with increased relative sizes only of certain brain regions, for instance telencephalon and cerebellum. Till now, the evolutionary association between separate brain regions and overall brain size is based on comparative evidence and remains experimentally untested. Here we test the evolutionary response of brain...

Data from: Functional trait differences and trait plasticity mediate biotic resistance to potential plant invaders

Luisa Conti, Svenja Block, Madalin Parepa, Tamara Münkemüller, Wilfried Thuiller, Alicia T.R. Acosta, Mark Van Kleunen, Stefan Dullinger, Franz Essl, Iwona Dullinger, Dietmar Moser, Günther Klonner, Oliver Bossdorf, Marta Carboni & Alicia T. R. Acosta
1. Biotic resistance represents an important natural barrier to potential invaders throughout the world, yet the underlying mechanisms that drive such resistance are still debated. In theory, native communities should repel both functionally similar invaders which compete for the same resources, and invaders which possess less competitive traits. However, environmental stress, trade-offs across vital rates and competition-induced plastic trait shifts may modify expected competitive outcomes, thereby influencing invasion dynamics. 2. In order to test these...

Data from: Bounds to parapatric speciation: A dobzhansky-muller incompatibility model involving autosomes, X chromosomes and mitochondria

Ilse Höllinger & Joachim Hermisson
We investigate the conditions for the origin and maintenance of postzygotic isolation barriers, so called (Bateson-)Dobzhansky-Muller incompatibilities or DMIs, among populations that are connected by gene flow. Specifically, we compare the relative stability of pairwise DMIs among autosomes, X chromosomes, and mitochondrial genes. In an analytical approach based on a continent-island framework, we determine how the maximum permissible migration rates depend on the genomic architecture of the DMI, on sex bias in migration rates, and...

Data from: Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids

Richard M. Bateman, Gábor Sramkó & Ovidiu Paun
Background and Aims. Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistics techniques to clarify the phylogeny of the genus. Methods. At least two accessions of each of the ten species groups previously...

Data from: Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis

Brandon K.B. Seah, Thomas Schwaha, Jean-Marie Volland, Bruno Huettel, Nicole Dubilier & Harald R. Gruber-Vodicka
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected...

Data from: The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes

Guido W. Grimm, Benjamin Bomfleur & Stephen McLoughlin
The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This...

Data from: Can hook-bending be let off the hook? Bending/unbending of pliant tools by cockatoos

Isabelle B. Laumer, Thomas Bugnyar, Stephan A. Reber & Alice M. I. Auersperg
The spontaneous crafting of hook-tools from bendable material to lift a basket out of a vertical tube in corvids has widely been used as one of the prime examples of animal tool innovation. However, it was recently suggested that the animals' solution was hardly innovative but strongly influenced by predispositions from habitual tool use and nest building. We tested Goffin's cockatoo, which is neither a specialized tool user nor a nest builder, on a similar...

Data from: Utterance-final position and pitch marking aid word learning in school-age children

Piera Filippi, Sabine Laaha & W. Tecumseh Fitch
We investigated the effects of word order and prosody on word learning in school-age children. Third graders viewed photographs belonging to one of three semantic categories while hearing four-word nonsense utterances containing a target word. In the control condition, all words had the same pitch and, across trials, the position of the target word was varied systematically within each utterance. The only cue to word–meaning mapping was the co-occurrence of target words and referents. This...

Data from: A Mesoamerican origin of cherimoya (Annona cherimola Mill.). Implications for the conservation of plant genetic resources

Nerea Larranaga, Federico J. Albertazzi, Gustavo Fontecha, Margarita Palmieri, Heimo Rainer, Maarten Van Zonneveld & Jose I Hormaza
Knowledge on the structure and distribution of genetic diversity is a key aspect in order to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the neotropics and used as a food source by pre-Columbian cultures, was collected...

Data from: Functional morphological adaptations of the bony labyrinth in marsupials (Mammalia, Theria)

Cathrin Pfaff, Stefan Czerny, Doris Nagel & Jürgen Kriwet
Diprotodontia represents the largest and ecologically most distinct order of marsupials occurring in Australasian being highly divers in size, locomotion, habitat preferences, feeding, and activity pattern. The spatial orientation in the habitat and therefore the three-dimensional space is detected by the vestibular system of the inner ear, more precisely by the three semicircular canals. In this study, we investigated the bony labyrinth of diprotodontian and selected non-diprotodontian marsupial mammals of almost all genera with noninvasive...

Data from: Induced parental care in a poison frog: a tadpole cross-fostering experiment

Andrius Pašukonis, Kristina Barbara Beck, Marie-Therese Fischer, Steffen Weinlein, Susanne Stückler & Eva Ringler
Understanding the external stimuli and natural contexts that elicit complex behaviours, such as parental care, is key in linking behavioural mechanisms to their real-life function. Poison frogs provide obligate parental care by shuttling their tadpoles from terrestrial clutches to aquatic nurseries, but little is known about the proximate mechanisms that control these behaviours. In this study, we used Allobates femoralis, a poison frog with predominantly male parental care, to investigate whether tadpole transport can be...

Data from: Test flattening in the larger foraminifer Heterostegina depressa: predicting bathymetry from axial sections

Wolfgang Eder, Johann Hohenegger & Antonino Briguglio
Previous attempts to quantify the test flattening trend in Heterostegina depressa with water depth have been rather unsuccessful. Due to its broad depth distribution, H. depressa is a perfect model species to calibrate test flattening as a bathymetric signal for fossil assemblages. This might enable us to better reconstruct palaeoenvironments of fossil larger foraminiferal communities or even provide clues on the degree of transport in allochthonous deposits. In this study we used growth-independent functions to...

Data from: Body length of bony fishes was not a selective factor during the biggest mass extinction of all time

Mark N. Puttick, Jürgen Kriwet, Wen Wen, Shixue Hu, Gavin H. Thomas & Michael J. Benton
The Permo-Triassic mass extinction devastated life on land and in the sea, but it is not clear why some species survived and others went extinct. One explanation is that lineage loss during mass extinctions is a random process in which luck determines which species survive. Alternatively, a phylogenetic signal in extinction may indicate a selection process operating on phenotypic traits. Large body size has often emerged as an extinction risk factor in studies of modern...

Data from: Socio-economic impact classification of alien taxa (SEICAT)

Sven Bacher, Tim M. Blackburn, Franz Essl, Piero Genovesi, Jaakko Heikkilä, Jonathan M. Jeschke, Glyn Jones, Reuben Keller, Marc Kenis, Christoph Kueffer, Angeliki F. Martinou, Wolfgang Nentwig, Jan Pergl, Petr Pyšek, Wolfgang Rabitsch, David M. Richardson, Helen E. Roy, Wolf-Christian Saul, Riccardo Scalera, Montserrat Vila, John R. U. Wilson, Sabina Kumschick & Sabrina Kumschick
Many alien taxa are known to cause socio-economic impacts by affecting the different constituents of human well-being (security; material and non-material assets; health; social, spiritual and cultural relations; freedom of choice and action). Attempts to quantify socio-economic impacts in monetary terms are unlikely to provide a useful basis for evaluating and comparing impacts of alien taxa because they are notoriously difficult to measure and important aspects of human well-being are ignored. Here, we propose a...

Data from: Looks matter: changes in flower form affect pollination effectiveness in a sexually-deceptive orchid

Demetra Rakosy, Monica Cuervo, Hannes Paulus & Manfred Ayasse
Many species of the sexually-deceptive genus Ophrys are characterized by insect-like flowers. Their form has been traditionally considered to play an important role in pollinator attraction and manipulation. Yet the evolution of the floral form remains insufficiently understood. We hypothesize that pollinator-mediated selection is essential for driving floral form evolution in Ophrys, but that form components are being subjected to varying selection pressures depending on their role in mediating interactions with pollinators. By using the...

Data from: Climate change and body size shift in Mediterranean bivalve assemblages: unexpected role of biological invasions

Rafał Nawrot, Paolo G. Albano, Devapriya Chattopadhyay & Martin Zuschin
Body size is a synthetic functional trait determining many key ecosystem properties. Reduction in average body size has been suggested as one of the universal responses to global warming in aquatic ecosystems. Climate change, however, coincides with human-enhanced dispersal of alien species and can facilitate their establishment. We address effects of species introductions on the size structure of recipient communities using data on Red Sea bivalves entering the Mediterranean Sea through the Suez Canal. We...

Data from: Function and flexibility of object exploration in kea and New Caledonian crows

Megan L. Lambert, Martina Schiestl, Raoul Schwing, Alex H. Taylor, Gyula K. Gajdon, Katie E. Slocombe & Amanda M. Seed
A range of nonhuman animals frequently manipulate and explore objects in their environment, which may enable them to learn about physical properties and potentially form more abstract concepts of properties such as weight and rigidity. Whether animals can apply the information learned during their exploration to solve novel problems, however, and whether they actually change their exploratory behaviour to seek functional information about objects have not been fully explored. We allowed kea (Nestor notabilis) and...

Data from: Do pet dogs (Canis familiaris) follow ostensive and non-ostensive human gaze to distant space and to objects?

Charlotte Duranton, Friederike Range & Zsófia Virányi
Dogs are renowned for being skilful at using human-given communicative cues such as pointing. Results are contradictory, however, when it comes to dogs' following human gaze, probably due to methodological discrepancies. Here we investigated whether dogs follow human gaze to one of two food locations better than into distant space even after comparable pre-training. In Experiments 1 and 2, the gazing direction of dogs was recorded in a gaze-following into distant space and in an...

Data from: Evolution of the locomotory system in eels (Teleostei: Elopomorpha)

Cathrin Pfaff, Roberto Zorzin & Jürgen Kriwet
Background Living anguilliform eels represent a distinct clade of elongated teleostean fishes inhabiting a wide range of habitats. Locomotion of these fishes is highly influenced by the elongated body shape, the anatomy of the vertebral column, and the corresponding soft tissues represented by the musculotendinous system. Up to now, the evolution of axial elongation in eels has been inferred from living taxa only, whereas the reconstruction of evolutionary patterns and functional ecology in extinct eels...

Data from: Habitat disturbance selects against both small and large species across varying climates

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Xavier Arnan, Heraldo L. Vasconcellos, David A. Donoso, Alan N. Andersen, Rogerio R. Silva, Tom R. Bishop, Crisanto Gomez, Blair F. Grossman, Kalsum M. Yusah, Sarah H. Luke, Renata Pacheco, Jessica Pearce-Duvet, Javier Retana, Melanie Tista, Catherine L. Parr & H. L. Vasconcelos
Global extinction drivers, including habitat disturbance and climate change, are thought to affect larger species more than smaller species. However, it is unclear if such drivers interact to affect assemblage body size distributions. We asked how these two key global change drivers differentially affect the interspecific size distributions of ants, one of the most abundant and ubiquitous animal groups on earth. We also asked whether there is evidence of synergistic interactions and whether effects are...

Data from: Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model

Lam-Tung Nguyen, Arndt Von Haeseler & Bui Quang Minh
The invariable site plus Γ model is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the invariable site plus continuous Γ model is identifiable (model parameters can be inferred correctly given enough data) has increased the creditability of its application to phylogeny reconstruction. However, most phylogenetic software implement the invariable site plus discrete Γ model, whose identifiability is likely but unproven. How well the...

Data from: Humans recognize emotional arousal in vocalizations across all classes of terrestrial vertebrates: evidence for acoustic universals

Piera Filippi, Jenna V. Congdon, John Hoang, Daniel Liu Bowling, Stephan A. Reber, Andrius Pašukonis, Marisa Hoeschele, Sebastian Ocklenburg, Bart De Boer, Christopher B. Sturdy, Albert Newen & Onur Gunturkun
Writing over a century ago, Darwin hypothesized that vocal expression of emotion dates back to our earliest terrestrial ancestors. If this hypothesis is true, we should expect to find cross-species acoustic universals in emotional vocalizations. Studies suggest that acoustic attributes of aroused vocalizations are shared across many mammalian species, and that humans can use these attributes to infer emotional content. But do these acoustic attributes extend to non-mammalian vertebrates? In this study, we asked human...

Data from: Population assignment in autopolyploids

David L. Field, Linda M. Broadhurst, Carole P. Elliot & Andrew G. Young
Understanding patterns of contemporary gene dispersal within and among populations is of critical importance to population genetics and in managing populations for conservation. In contrast to diploids, there are few studies of gene dispersal in autopolyploids, in part due to complex polysomic inheritance and genotype ambiguity. Here we develop a novel approach for population assignment for codominant markers for autotetraploids and autohexaploids. This method accounts for polysomic inheritance, unreduced gametes and unknown allele dosage. It...

Data from: Marker development for phylogenomics: the case of Orobanchaceae, a plant family with contrasting nutritional modes

Xi Li, Baohai Hao, Da Pan & Gerald M. Schneeweiss
Phylogenomic approaches, employing next-generation sequencing (NGS) techniques, have revolutionized systematic and evolutionary biology. Target enrichment is an efficient and cost-effective method in phylogenomics and is becoming increasingly popular. Depending on availability and quality of reference data as well as on biological features of the study system, (semi-)automated identification of suitable markers will require specific bioinformatic pipelines. Here, we established a highly flexible bioinformatic pipeline, BaitsFinder, to identify putative orthologous single copy genes (SCGs) and to...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Vienna
  • University of Veterinary Medicine Vienna
  • University of Cambridge
  • University of Veterinary Medicine
  • University of York
  • South African National Biodiversity Institute
  • Vrije Universiteit Brussel
  • Estación Biológica de Doñana
  • University of Adelaide
  • Indian Institute of Science Education and Research Kolkata