88 Works

Data from: Machine learning identifies ecological selectivity patterns across the end-Permian mass extinction

William Foster, Georgy Ayzel, Jannes Münchmeyer, Tabea Rettelbach, Niklas Kitzmann, Terry Isson, Maria Mutti & Martin Aberhan
The end-Permian mass extinction occurred alongside a large swathe of environmental changes that are often invoked as extinction mechanisms, even when a direct link is lacking. One way to elucidate the cause(s) of a mass extinction is to investigate extinction selectivity as it can reveal critical information on organismic traits as key determinants of extinction and survival. Here we show that machine learning algorithms, specifically gradient boosted decision trees, can be used to identify determinants...

D1.1 Report on life sciences use cases and user stories

Heli Fitzgerald, Aino Juslén, Sabine von Mering, Mareike Petersen, Niels Raes, Sharif Islam, Frederik Berger, Tea Katharina von Bonsdorff-Salminen, Rui Figueira, Elspeth Haston, Eva Häffner, Laurence Livermore, Veljo Runnel, Sofie De Smedt, Sarah Vincent & Claus Weiland

D1.2 Report on Earth sciences use cases and user stories

Sabine von Mering, Mareike Petersen, Heli Fitzgerald, Aino Juslén, Niels Raes, Sharif Islam, Frederik Berger, Tea Katharina von Bonsdorff-Salminen, Rui Figueira, Elspeth Haston, Eva Häffner, Laurence Livermore, Veljo Runnel, Sofie De Smedt, Sarah Vincent & Claus Weiland

Data from: Decoupling of taxonomic diversity and morphological disparity during decline of the Cambrian trilobite family Pterocephaliidae

Melanie J. Hopkins
Though discordance between taxonomic diversity and morphological disparity is common, little is known about the underlying dynamics that drive this decoupling. Early in the history of the Cambrian trilobite family Pterocephaliidae, there was an increase in taxonomic diversity and morphological diversity. As taxonomic diversity declined in the later history of the clade, range of variation stayed high, and disparity continued to increase. However, per-branch rates of morphological evolution estimated from a recent phylogeny decreased with...

Data from: Relationships of the Indian phytosaur Parasuchus hislopi Lydekker, 1885

Christian F. Kammerer, Richard J. Butler, Saswati Bandyopadhyay & Michelle R. Stocker
The neotype skull of the Indian phytosaur Parasuchus hislopi Lydekker, 1885 (ISI R42) is re-evaluated and compared with the type material of other basal phytosaurs. Parasuchus hislopi is extremely similar to species previously placed in Paleorhinus (P. bransoni and P. angustifrons), sharing with them such characters as a series of nodes on the lateral surface of the jugal, paired ridges on the squamosal and a frontal depression. Parasuchus hislopi represents a valid species: it can...

Do meristic characters used in phylogenetic analysis evolve in an ordered manner?

Neil Brocklehurst & Yara Haridy
The use of ordered characters in phylogenetic analysis has been inconsistent through research history. It has become more widespread in recent years, and some have advocated that all characters representing continuous or meristic traits should be ordered as a matter of course. Here, using the example of dental evolution, we examine two factors that may impact on whether meristic characters actually evolve in an ordered manner: the regulatory hierarchy governing the development of teeth that...

Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)

Adam Leache, Daniel Portik, Danielle Rivera, Mark-Oliver Rodel, Johannes Penner, Václav Gvoždík, Eli Greenbaum, Gregory Jongsma, Caleb Ofori-Boateng, Marius Burger, Edem Eniang, Rayna Bell & Matthew Fujita
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA)...

Temperature-related body size change of marine benthic macroinvertebrates across the early Toarcian Anoxic Event

Veronica Piazza, Clemens V. Ullmann & Martin Aberhan
The Toarcian Oceanic Anoxic Event (TOAE, Early Jurassic, ~182 Ma ago) was characterised by severe environmental perturbations which led to habitat degradation and extinction of marine species. Warming-induced anoxia is usually identified as main driver, but because marine life was also affected in oxygenated environments the role of raised temperature and its effects on marine life need to be addressed. Body size is a fundamental characteristic of organisms and is expected to decrease as a...

Data from: Evolutionary diversification of reef corals: a comparison of the molecular and fossil records

Carl Simpson, Wolfgang Kiessling, Heike Mewis, Rosemarie C. Baron-Szabo & Johannes Müller
Understanding historical patterns of diversity dynamics is of paramount importance for many evolutionary questions. The fossil record has long been the only source of information on patterns of diversification, but the molecular record, derived from time-calibrated phylogenies, is becoming an important additional resource. Both fossil and molecular approaches have shortcomings and biases. These have been well studied for fossil data but much less so for molecular data and empirical comparisons between approaches are lacking. Here...

Data from: The cranial morphology, phylogenetic position and biogeography of the upper Permian dicynodont Compsodon helmoedi van Hoepen (Therapsida, Anomodontia)

Kenneth D. Angielczyk & Christian F. Kammerer
Compsodon helmoedi is an obscure dicynodont originally described based on a single specimen from the upper Permian of the Karoo Basin. The discovery of three new specimens of Compsodon from the Luangwa Basin of Zambia and two additional specimens from South African museum collections facilitates a reassessment of its cranial morphology and phylogenetic position. Compsodon is diagnosed by an autapomorphic secondary palate morphology: medial depression at anterior end of premaxillary secondary palate; medial anterior palatal...

Data from: On formation-based sampling proxies and why they should not be used to correct the fossil record

Alexander M. Dunhill, Bjarte Hannisdal, Neil Brocklehurst & Michael J. Benton
The fossil record is a unique resource on the history of life, but it is well known to be incomplete. In a series of high-profile papers, a residual modelling technique has been applied to correct the raw palaeodiversity signal for this bias and incompleteness, and the claim is made that the processed time series are more accurate than the raw data. We apply empirical and simulation approaches to test for correlation and directionality of any...

Data from: Female-biased dispersal in a bat with a female-defence mating strategy

Martina Nagy, Linus Günther, Mirjam Knörnschild & Frieder Mayer
The ultimate causes for predominant male-biased dispersal (MBD) in mammals and female-biased dispersal (FBD) in birds are still subject to much debate. Studying exceptions to general patterns of dispersal, for example, FBD in mammals, provides a valuable opportunity to test the validity of proposed evolutionary pressures. We used long-term behavioural and genetic data on individually banded Proboscis bats (Rhynchonycteris naso) to show that this species is one of the rare mammalian exceptions with FBD. Our...

DiSSCo Prepare Milestone report MS3.4 \"Proposed Content for a DiSSCo Digital Maturity Tool\"

Helen Hardy, Laurence Livermore, Anne Koivunen, Quentin Groom, Patricia Mergen, Frederik Berger, Peter Giere, Sabine von Mering, Rui Figueira, Pedro Arsénio & Alexandra Cartaxana

DiSSCo Prepare Deliverable D3.1 \"Summary Insights and Recommendations on DiSSCo Competencies and Digital Maturity\"

Helen Hardy, Anne Koivunen, Quentin Groom, Patricia Mergen, Frederik Berger, Peter Giere, Sabine von Mering, Rui Figueira, Pedro Arsénio & Alexandra Cartaxana

DiSSCo Prepare Milestone Report MS5.5 \"Compilation of relevant data standards\"

Mareike Petersen, Sabine von Mering & Falko Glöckler

Data from: Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’

Emma M. Dunne, Roger A. Close, David J. Button, Neil Brocklehurst, Daniel D. Cashmore, Graeme T. Lloyd & Richard J. Butler
The Carboniferous and early Permian were critical intervals in the diversification of early four-limbed vertebrates (tetrapods), yet the major patterns of diversity and biogeography during this time remain unresolved. Previous estimates suggest that global tetrapod diversity rose continuously across this interval and that habitat fragmentation following the ‘Carboniferous rainforest collapse’ (CRC) drove increased endemism among communities. However, previous work failed to adequately account for spatial and temporal biases in sampling. Here, we reassess early tetrapod...

Data from: Using molecular phylogenies in island biogeography: it’s about time

Luis Valente, Albert B. Phillimore & Rampal S. Etienne
Island biogeography aims at inferring the processes that govern the assembly of communities in space and time. Molecular phylogenies can tell us about the timings of island colonisations and diversification, but have rarely been used for the estimation of colonisation, speciation and extinction rates on islands. In this study we illustrate the effects of including phylogenetic information with the Galápagos avifauna. We find that by including colonisation times we obtain much more precise and accurate...

Data from: Iterative ontogenetic development of ammonoid conch shapes from the Devonian through to the Jurassic

Sonny A. Walton & Dieter Korn
We measured longitudinal growth in conch cross-sections of 177 Devonian to Jurassic ammonoid species to test whether conch ontogenetic development parallels the iterative evolution of pachyconic or globular conch shapes. Ontogenetic trajectories of two cardinal conch parameters, conch width index and umbilical width index, show a few common recurring ontogenetic pathways in terms of the number of ontogenetic phases. The most common, with three phases in the conch width index (decrease–increase–decrease) and umbilical width index...

Data from: Whole-body photoreceptor networks are independent of ‘lenses’ in brittle stars

Lauren Sumner-Rooney, Imran A. Rahman, Julia D. Sigwart & Esther Ullrich-Lüter
Photoreception and vision are fundamental aspects of animal sensory biology and ecology, but important gaps remain in our understanding of these processes in many species. The colour-changing brittle star Ophiocoma wendtii is iconic in vision research, speculatively possessing a unique whole-body visual system that incorporates information from nerve bundles underlying thousands of crystalline ‘microlenses’. The hypothesis that these form a sophisticated compound eye-like system regulated by chromatophore movement has been extensively reiterated, with consequent investigations...

Data from: Skeletal microstructure of Stenopterygius quadriscissus (Reptilia, Ichthyosauria) from the Posidonienschiefer (Posidonia Shale, Lower Jurassic) of Germany

Katherine L. Anderson, Patrick S. Druckenmiller, Gregory M. Erickson & Erin E. Maxwell
Ichthyosaurians (Ichthyosauria) are a major clade of secondarily aquatic marine tetrapods that occupied several major predatory niches during the Mesozoic Era. Multiple lines of evidence including isotopic, body shape and swimming modality analyses suggest they exhibited elevated growth and metabolic rates, and body temperatures. However, applications of osteohistological methods to test hypotheses regarding their physiology are few. Previous studies focused on the humeri, vertebrae and ribs from a small number of taxa. Here, we use...

Data from: The early evolution of synapsids, and the influence of sampling on their fossil record

Neil Brocklehurst, Christian F. Kammerer & Jörg Fröbisch
Synapsids dominated the terrestrial realm between the late Pennsylvanian and the Triassic. Their early evolution includes some of the first amniotes to evolve large size, herbivory, and macro-predators. However, little research has focused on the changes in diversity occurring during this early phase in their evolutionary history, with more effort concentrating on later events such the Permo-Triassic extinction. Here we assess synapsid diversity, at both the species and genus levels, between the Carboniferous (Moscovian) and...

Data from: Anatomy and relationships of the South African gorgonopsian Arctops (Therapsida, Theriodontia)

Christian F. Kammerer
The gorgonopsian genus Arctops from the late Permian of South Africa is revised and redescribed. The nominal species Arctops kitchingi and Arctops watsoni are found to be junior synonyms of the type species Arctops willistoni. A well-prepared specimen previously referred to Lycaenops angusticeps and additional, previously undescribed specimens are also referred to A. willistoni. The vomerine morphology of Arctops is highly distinctive, supporting previous work highlighting the taxonomic importance of this element. Arctops is restricted...

Data from: Principal component analysis as an alternative treatment for morphometric characters: phylogeny of caseids as a case study

Neil Brocklehurst, Marco Romano & Jörg Fröbisch
In a recent study, the phylogeny of Caseidae (a herbivorous family of Palaeozoic synapsids belonging to the paraphyletic grade known as pelycosaurs) was analysed with a dataset employing more than three hundred continuous morphological characters in an effort to follow the principles of total evidence. Continuous characters are a source of great debate, with disagreements surrounding their suitability for and treatment in phylogenetic analysis. A number of shortcomings were identified in the handling of continuous...

Data from: Developmental dynamics of ecomorphological convergence in a transcontinental lizard radiation

Christy A. Hipsley & Johannes Müller
Phenotypic convergence has confounded evolutionary biologists for centuries, explained as adaptations to shared selective pressures, or alternatively, the result of limited developmental pathways. We tested the relative roles of adaptation and constraint in generating convergent cranial morphologies across a large lizard radiation, the Lacertidae, whose members inhabit diverse environments throughout the Old World and display high amounts of homoplasy associated with ecological niche. Using three-dimensional X-ray computed tomography, we quantified cranial shape variation associated with...

Data from: Divergence of cuticular hydrocarbons in two sympatric grasshopper species and the evolution of fatty acid synthases and elongases across insects

Jonas Finck, Emma L. Berdan, Frieder Mayer, Bernhard Ronacher & Sven Geiselhardt
Cuticular hydrocarbons (CHCs) play a major role in the evolution of reproductive isolation between insect species. The CHC profiles of two closely related sympatric grasshopper species, Chorthippus biguttulus and C. mollis, differ mainly in the position of the first methyl group in major methyl-branched CHCs. The position of methyl branches is determined either by a fatty acid synthase (FAS) or by elongases. Both protein families showed an expansion in insects. Interestingly, the FAS family showed...

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  • Museum für Naturkunde
  • Humboldt University of Berlin
  • Meise Botanic Garden
  • Natural History Museum
  • Botanischer Garten und Botanisches Museum Berlin
  • University of Lisbon
  • Smithsonian Institution
  • Berlin Brandenburg Institute of Advanced Biodiversity Research
  • Senckenberg Nature Research Society
  • University of Cambridge