427 Works

Data from: Synchrotron X-ray tomographic microscopy of fossil embryos

Philip C. J. Donoghue, Stefan Bengtson, Xi-Ping Dong, Neil J. Gostling, Therese Huldtgren, John A. Cunningham, Chongyu Yin, Zhao Yue, Fan Peng & Marco Stampanoni
Fossilized embryos from the late Neoproterozoic and earliest Phanerozoic have caused much excitement because they preserve the earliest stages of embryology of animals that represent the initial diversification of metazoans. However, the potential of this material has not been fully realized because of reliance on traditional, non-destructive methods that allow analysis of exposed surfaces only, and destructive methods that preserve only a single two-dimensional view of the interior of the specimen. Here, we have applied...

Data from: microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

Alysha M. Heimberg, Richard Cowper-Sal·Lari, Marie Sémon, Philip C. J. Donoghue, Kevin J. Peterson & R. Cowper-Sal{Middle Dot}Lari
Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing...

Data from: Recent ecological selection on regulatory divergence is shaping clinal variation in Senecio on Mount Etna

Graham Muir, Owen G. Osborne, Jonas Sarasa, Simon J. Hiscock & Dmitry A. Filatov
The hybrid zone on Mount Etna (Sicily) between Senecio aethnensis and Senecio chrysanthemifolius (two morphologically and physiologically distinct species) is a classic example of an altitudinal cline. Hybridization at intermediate altitudes and gradients in phenotypic and life-history traits occur along altitudinal transects of the volcano. The cline is considered to be a good example of ecological selection with species differences arising by divergent selection opposing gene flow. However, the possibility that the cline formed from...

Data from: Multiple cases of asymmetric introgression among horseshoe bats detected by phylogenetic conflicts across loci

Xiuguang Mao, Vu D. Thong, Paul J. J. Bates, Gareth Jones, Shuyi Zhang & Stephen J. Rossiter
Phylogenetic discordance among taxa can provide powerful insights into past episodes of introgressive hybridization, as well as lineage sorting. Previously, we showed that the taxonomically distinct taxon Rhinolophus sinicus septentrionalis has undergone historical introgression with its sympatric sister subspecies Rhinolophus sinicus sinicus. To examine in more detail the extent of gene flow between these two taxa, and also between these and their sister species Rhinolophus thomasi, we obtained new samples from China, Myanmar, and Vietnam,...

Data from: A giant pliosaurid skull from the Late Jurassic of England

Roger B. J. Benson, Mark Evans, Adam S. Smith, Judyth Sassoon, Scott Moore-Faye, Hilary F. Ketchum & Richard Forrest
Pliosaurids were a long-lived and cosmopolitan group of marine predators that spanned 110 million years and occupied the upper tiers of marine ecosystems from the Middle Jurassic until the early Late Cretaceous. A well-preserved giant pliosaurid skull from the Late Jurassic Kimmeridge Clay Formation of Dorset, United Kingdom, represents a new species, Pliosaurus kevani. This specimen is described in detail, and the taxonomy and systematics of Late Jurassic pliosaurids is revised. We name two additional...

Data from: Hierarchical polygyny in multiparous lesser flat-headed bats

Panyu Hua, Libiao Zhang, Guangjian Zhu, Gareth Jones, Shuyi Zhang & Stephen James Rossiter
How males gain access to mates and the potential for female choice will determine whether polygyny can operate at several levels, from within litters and groups to the wider population. Female lesser flat-headed bats (Tylonycteris pachypus) form maternity groups in bamboo stems. Unusually for bats, they are multiparous, providing the opportunity to test whether multi-level polygyny differs among males depending on whether they roost with females, with males, or are solitary. We genotyped 662 individuals...

Data from: Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae)

Matthew J Hegarty, Tom Batstone, Gary L Barker, Keith J Edwards, Richard J Abbott & Simon J Hiscock
The merger of two or more divergent genomes within an allopolyploid nucleus can facilitate speciation and adaptive evolution in flowering plants. Widespread changes to gene expression have been shown to result from interspecific hybridisation and polyploidy in a number of plant species, and attention has now shifted to determining the epigenetic processes which drive these changes. We present here an analysis of cytosine methylation patterns in triploid F1 Senecio (ragwort) hybrids and their allohexaploid derivatives....

Data from: Masquerade is associated with polyphagy and larval overwintering in the Lepidoptera

Andrew D. Higginson, Leoni De Wert, Hannah M. Rowland, Michael P. Speed & Graeme D. Ruxton
Masquerading animals benefit from the difficulty that predators have in differentiating them from the inedible objects, such as twigs, that they resemble. The function of masquerade has been demonstrated, but how it interacts with the life history of organisms has not been studied. Here, we report the use of comparative analyses to test hypotheses linking masquerade to life-history parameters. We constructed a phylogenetic tree of the British species of the lepidoptera families Geometridae and Drepanidae...

Data from: Year-round sexual harassment as a behavioral mediator of vertebrate population dynamics

Victoria Wearmouth, Emily Southall, David Morritt, Richard C. Thompson, Innes C. Cuthill, Julian Partridge, David W. Sims & Julian C. Partridge
Within-species sexual segregation is a widespread phenomenon among vertebrates but its causes remain a topic of much debate. Female avoidance of male coercive mating attempts has the potential to influence the social structure of animal populations, yet it has been largely overlooked as a driver of sexual separation. Indeed, its potential role in long-term structuring of natural populations has not been studied. Here we use a comparative approach to examine the suitability of multiple hypotheses...

Data from: Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils

Bettina E. Schirrmeister, Muriel Gugger & Philip C. J. Donoghue
NOTE: PLEASE ALSO SEE THE CORRIGENDUM TO THE ORIGINAL ARTICLE, PUBLISHED AT http://dx.doi.org/10.1111/pala.12193. Cyanobacteria are among the most ancient of evolutionary lineages, oxygenic photosynthesizers that may have originated before 3.0 Ga, as evidenced by free oxygen levels. Throughout the Precambrian, cyanobacteria were one of the most important drivers of biological innovations, strongly impacting early Earth's environments. At the end of the Archean Eon, they were responsible for the rapid oxygenation of Earth's atmosphere during an...

Data from: Beyond the print - virtual paleontology in science publishing, outreach and education

Stephan Lautenschlager & Martin Rücklin
Virtual paleontology unites a variety of computational techniques and methods for the visualization and analysis of fossils. Due to their great potential and increasing availability, these methods have become immensely popular in the last decade. However, communicating the wealth of digital information and results produced by the various techniques is still exacerbated by traditional methods of publication. Transferring and processing three-dimensional information, such as interactive models or animations, into scientific publications still poses a challenge....

Data from: Feeding ecology of the deep-bodied fish Dapedium (Actinopterygii, Neopterygii) from the Sinemurian of Dorset, England

Fiann M. Smithwick
Reconstructing the feeding ecology of fossil fishes can be difficult, but new mechanical approaches enable reasonably reliable inferences by comparison with living forms. Here, the feeding ecology of one of the most iconic and abundant actinopterygians of the Early Jurassic, Dapedium, is explored through detailed anatomical study and functional analyses of jaw mechanics. Mathematical models derived from modern teleost functional morphology are applied, to ascertain the transmission of force through the jaws of Dapedium. A...

Data from: Tag jumps illuminated – reducing sequence-to-sample misidentifications in metabarcoding studies

Ida Bærholm Schnell, Kristine Bohmann, M. Thomas P. Gilbert & Ida Baerholm Schnell
Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps...

Data from: A dynamic framework for the study of optimal birth intervals reveals the importance of sibling competition and mortality risks

Matthew G. Thomas, Daryl P. Shanley, Alasdair I. Houston, John M. McNamara, Ruth Mace & Tom B. L. Kirkwood
Human reproductive patterns have been well studied, but the mechanisms by which physiology, ecology and existing kin interact to affect the life history need quantification. Here, we create a model to investigate how age-specific interbirth intervals adapt to environmental and intrinsic mortality, and how birth patterns can be shaped by competition and help between siblings. The model provides a flexible framework for studying the processes underlying human reproductive scheduling. We developed a state-based optimality model...

Data from: Early Pennsylvanian (Langsettian) fish assemblages from the Joggins Formation, Canada, and their implications for palaeoecology and palaeogeography

David K. Carpenter, Howard J. Falcon-Lang, Michael J. Benton & Melissa Grey
A review of all available specimens of fossil fishes from the classic Pennsylvanian Joggins locality of Nova Scotia, Canada, reveals the existence of a diverse community of chondrichthyans (xenacanthids, ctenacanthids and the enigmatic Ageleodus), acanthodians (gyracanthids), sarcopterygians (rhizodontids, megalichthyids, rhizodopsids and dipnoans) and actinopterygians (haplolepids). Reassessment of supposed endemic species (Ctenoptychius cristatus, Sagenodus plicatus, Gyracanthus duplicatus) indicates they are invalid, and overall, the assemblage comprises cosmopolitan taxa that were widespread around the coasts of tropical...

Data from: The fossil record of ichthyosaurs, completeness metrics and sampling biases

Terri J. Cleary, Benjamin C. Moon, Alexander M. Dunhill & Michael J. Benton
Ichthyosaurs were highly successful marine reptiles with an abundant and well-studied fossil record. However, their occurrences through geological time and space are sporadic, and it is important to understand whether times of apparent species richness and rarity are real or the result of sampling bias. Here, we explore the skeletal completeness of 351 dated and identified ichthyosaur specimens, belonging to all 102 species, the first time that such a study has been carried out on...

Data from: Computed tomography, anatomical description and three-dimensional reconstruction of the lower jaw of Eusthenopteron foordi Whiteaves, 1881 from the Upper Devonian of Canada

Laura B. Porro, Emily J. Rayfield & Jennifer A. Clack
The cranial anatomy of the iconic early tetrapod Eusthenopteron foordi is probably the best understood of all fossil fishes. In contrast, the anatomy of the lower jaw – crucial for both phylogenetics and biomechanical analyses – has been only superficially described. Computed tomography data of three Eusthenopteron skulls were segmented using visualization software to digitally separate bone from matrix and individual bones from each other. Here, we present a new description of the lower jaw...

Data from: Herbivorous dinosaur jaw disparity and its relationship to extrinsic evolutionary drivers

Jamie A. MacLaren, Philip S. L. Anderson, Paul Barrett & Emily J. Rayfield
Morphological responses of nonmammalian herbivores to external ecological drivers have not been quantified over extended timescales. Herbivorous nonavian dinosaurs are an ideal group to test for such responses, because they dominated terrestrial ecosystems for more than 155 Myr and included the largest herbivores that ever existed. The radiation of dinosaurs was punctuated by several ecologically important events, including extinctions at the Triassic/Jurassic (Tr/J) and Jurassic/Cretaceous (J/K) boundaries, the decline of cycadophytes, and the origin of...

Data from: Cranial biomechanics underpins high sauropod diversity in resource-poor environments

David J. Button, Emily J. Rayfield & Paul M. Barrett
High megaherbivore species richness is documented in both fossil and contemporary ecosystems despite their high individual energy requirements. An extreme example of this is the Late Jurassic Morrison Formation, which was dominated by sauropod dinosaurs, the largest known terrestrial vertebrates. High sauropod diversity within the resource-limited Morrison is paradoxical, but might be explicable through sophisticated resource partitioning. This hypothesis was tested through finite-element analysis of the crania of the Morrison taxa Camarasaurus andDiplodocus. Results demonstrate...

Data from: Lifespan and reproductive cost explain interspecific variation in the optimal onset of reproduction

Emeline Mourocq, Pierre Bize, Sandra Bouwhuis, Russell Bradley, Anne Charmantier, Carlos De La Cruz, Szymon Marian Obniak, Richard H. M. Espie, Márton Herenyi, Hermann Hötker, Oliver Kruger, John Marzluff, Anders P. Møller, Shinichi Nakagawa, Richard A. Phillips, Andrew N. Radford, Alexandre Roulin, János Török, Juliana Valencia, Martijn Van De Pol, Ian G. Warkentin, Isabel S. Winney, Andrew G. Wood, Michael Griesser & Szymon M. Drobniak
Fitness can be profoundly influenced by the age at first reproduction (AFR), but to date the AFR-fitness relationship only has been investigated intraspecifically. Here we investigated the relationship between AFR and average lifetime reproductive success (LRS) across 34 bird species. We assessed differences in the deviation of the Optimal AFR (i.e., the species-specific AFR associated with the highest LRS) from the age at sexual maturity, considering potential effects of life-history as well as social and...

Data from: Violence in the prehistoric period of Japan: the spatiotemporal pattern of skeletal evidence for violence in the Jomon period

Hisashi Nakao, Kohei Tamura, Yui Arimatsu, Tomomi Nakagawa, Naoko Matsumoto & Takehiko Matsugi
Whether man is predisposed to lethal violence, ranging from homicide to warfare, and how that may have impacted human evolution, are among the most controversial topics of debate on human evolution. Although recent studies on the evolution of warfare have been based on various archaeological and ethnographic data, they have reported mixed results: it is unclear whether or not warfare among prehistoric hunter–gatherers was common enough to be a component of human nature and a...

Data from: Aposematism: balancing salience and camouflage

James B. Barnett, Nicholas E. Scott-Samuel & Innes C. Cuthill
Aposematic signals are often characterized by high conspicuousness. Larger and brighter signals reinforce avoidance learning, distinguish defended from palatable prey and are more easily memorized by predators. Conspicuous signalling, however, has costs: encounter rates with naive, specialized or nutritionally stressed predators are likely to increase. It has been suggested that intermediate levels of aposematic conspicuousness can evolve to balance deterrence and detectability, especially for moderately defended species. The effectiveness of such signals, however, has not...

Data from: Fish and tetrapod communities across a marine to brackish salinity gradient in the Pennsylvanian (early Moscovian) Minto Formation of New Brunswick, Canada, and their palaeoecological and palaeogeographical implications

Aodhán Ó Gogáin, Howard J. Falcon-Lang, David K. Carpenter, Randall F. Miller, Michael J. Benton, Peir K. Pufahl, Marcello Ruta, Thomas G. Davies, Steven J. Hinds & Matthew R. Stimson
Euryhaline adaptations in Pennsylvanian vertebrates allowed them to inhabit the marine to freshwater spectrum. This is illustrated by new assemblages of fish and tetrapods from the early Moscovian Minto Formation of New Brunswick, Canada. Fish include chondrichthyans (xenacanthids and the enigmatic Ageleodus), acanthodians (gyracanthids and acanthodiforms), sarcopterygians (rhizodontids, megalichthyids and dipnoans), and actinopterygians (eurynotiforms). Tetrapods include small- to medium-sized, and largely aquatic, stem tetrapods (colosteids) and anthracosaurs (embolomeres). A key finding is that the parautochthonous...

Data from: Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye

Sarah E. Gabbott, Philip C.J. Donoghue, Robert S. Sansom, Jakob Vinther, Andrei Dolocan, Mark A. Purnell & Philip C. J. Donoghue
The success of vertebrates is linked to the evolution of a camera-style eye and sophisticated visual system. In the absence of useful data from fossils, scenarios for evolutionary assembly of the vertebrate eye have been based necessarily on evidence from development, molecular genetics and comparative anatomy in living vertebrates. Unfortunately, steps in the transition from a light-sensitive ‘eye spot’ in invertebrate chordates to an image-forming camera-style eye in jawed vertebrates are constrained only by hagfish...

Data from: Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

Milan Malinsky, Richard J. Challis, Alexandra M. Tyers, Stephan Schiffels, Yohey Terai, Benjamin P. Ngatunga, Eric A. Miska, Richard Durbin, Martin J. Genner & George F. Turner
The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic “islands” of high differentiation...

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