74 Works

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)...

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...

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...

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: 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...

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...

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: 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: 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...

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: Protein-encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera, Calyptratae)

Eliana Buenaventura, Michael W. Lloyd, Juan Manuel Perilla López, Vanessa L. González, Arianna Thomas-Cabianca & Torsten Dikow
The diverse superfamily Oestroidea with more than 15,000 known species includes among others, blow flies, flesh flies, bot flies, and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems...

Historical isolation facilitates species radiation by sexual selection: insights from Chorthippus grasshoppers

Zachary Nolen, Burcin Yildirim, Iker Irisarri, Shanlin Liu, Clara Groot Crego, Daniel Amby, Frieder Mayer, M. Gilbert & Ricardo Pereira
Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address this question using sympatric grasshopper species of the genus Chorthippus, which have evolved strong behavioral isolation while lacking noticeable eco-morphological divergence. Mitochondrial genomes suggest...

Data from: A population genomic scan in Chorthippus grasshoppers unveils previously unknown phenotypic divergence

Emma L. Berdan, Camilla J. Mazzoni, Isabelle Waurick, Johannes T. Roehr & Frieder Mayer
Understanding the genetics of speciation and the processes that drive it is a central goal of evolutionary biology. Grasshoppers of the Chorthippus species group differ strongly in calling song (and corresponding female preferences) but are exceedingly similar in other characteristics such as morphology. Here, we performed a population genomic scan on three Chorthippus species (Chorthippus biguttulus, C. mollis and C. brunneus) to gain insight into the genes and processes involved in divergence and speciation in...

Data from: Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection

Daniel M. Portik, Adam D. Leaché, Danielle Rivera, Michael F. Barej, Marius Burger, Mareike Hirschfeld, Mark-Oliver Rödel, David C. Blackburn & Matthew K. Fujita
The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and...

Data from: Selective regimes and functional anatomy in the mustelid forelimb: diversification toward specializations for climbing, digging, and swimming

Brandon M. Kilbourne
Anatomical traits associated with locomotion often exhibit specializations for ecological niche, suggesting that locomotor specializations may constitute selective regimes acting on limb skeletal traits. To test this, I sampled 42 species of Mustelidae, encompassing climbing, digging, and swimming specialists, and determined whether trait variation reflects locomotor specialization by performing a principal components analysis on 14 forelimb traits. In addition to Brownian motion models, three Ornstein–Uhlenbeck models of selective regimes were applied to PC scores describing...

Data from: No ecological opportunity signal on a continental scale? Diversification and life-history evolution of African true toads (Anura: Bufonidae)

H. Christoph Liedtke, Hendrik Müller, Mark-Oliver Rödel, Michele Menegon, LeGrand Nono Gonwouo, Michael F. Barej, Václav Gvoždík, Andreas Schmitz, Alan Channing, Peter Nagel & Simon P. Loader
The niche-filling process predicted by the “ecological opportunity” (EO) model is an often-invoked mechanism for generating exceptional diversity in island colonizers. Whether the same process governs lineage accumulation and trait disparity during continental colonization events is less clear. Here, we test this prediction by investigating the rate dynamics and trait evolution of one of Africa's most widespread amphibian colonizers, the true toads (Bufonidae). By reconstructing the most complete molecular phylogeny of African Bufonidae to date,...

Data from: A new taxon of cynodont from the Tropidostoma Assemblage Zone (upper Permian) of South Africa, and the early evolution of Cynodontia

Christian F. Kammerer
A new taxon of early cynodont, Abdalodon diastematicus gen. et sp. nov., is described. The new taxon is represented by a single skull from the upper Permian Tropidostoma Assemblage Zone (AZ) of the Beaufort Group (Karoo Basin, South Africa), which was previously referred to Procynosuchus delaharpeae. Abdalodon is distinguished from Procynosuchus by the presence of only four upper and three lower incisors, fewer postcanines, a well-developed depression on the lateral surface of the maxilla posterior...

Data from: Multivariate female preference tests reveal latent perceptual biases

David A. Gray, Eileen Gabel, Thomas Blankers & R. Matthias Hennig
The question of why males of many species produce elaborate mating displays has now been largely resolved: females prefer to mate with males that produce such displays. However, the question of why females prefer such displays has been controversial, with an emerging consensus that such displays often provide information to females about the direct fitness benefits that males provide to females and/or the indirect fitness benefits provided to offspring. Alternative explanations, such as production of...

Data from: Ontogenetic and stratigraphic influence on observed phenotypic integration in the limb skeleton of a fossil tetrapod

Erin E. Maxwell & T. Alexander Dececchi
Understanding morphological integration is one of the central goals of evolutionary developmental biology. Despite its applicability to questions of paleontological interest, there are few studies on integration in fossil vertebrates. In this study, we examine limb integration in the Lower Jurassic ichthyosaur Stenopterygius quadriscissus, with the aim of examining the effect of ontogeny and anagenetic changes over short geological time spans on metrics of limb integration. Both ontogenetic and stratigraphic effects had a significant influence...

Data from: Marine invertebrate migrations trace climate change over 450 million years

Carl J Reddin, Ádám T Kocsis & Wolfgang Kiessling
Aim: Poleward migration is a clear response of marine organisms to current global warming but the generality and geographical uniformity of this response are unclear. Marine fossils are expected to record the range shift responses of taxa and ecosystems to past climate change. However, unequal sampling (natural and human) in time and space biases the fossil record, restricting previous studies of ancient migrations to individual taxa and events. We expect that temporal changes in the...

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

Laurent A. F. Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K. Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen Van Den Hurk, Sharron Ogle, Cristina Atofanei, Mark G. Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti … & Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions...

Data from: Matriline effects on metamorphic traits in a natural system in the European common frog (Rana temporaria)

Carolin Dittrich, Juliane Huster, Mark-Oliver Rödel & Heike Feldhaar
Successful reproduction is an important determinant of the fitness of an individual and of the dynamics of populations. Offspring of the European common frog (Rana temporaria) exhibit a high degree of variability in metamorphic traits. However, environmental factors alone cannot explain this phenotypic variability, and the influence of genetic factors remains to be determined. Here, we tested whether the maternal genotype influences developmental time, body size, and body condition of offspring in a forest pond...

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: 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...

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