How directed is a directed network?

The trophic levels of nodes in directed networks can reveal their functional properties. Moreover, the trophic coherence of a network, defined in terms of trophic levels, is related to properties such as cycle structure, stability and percolation. The standard definition of trophic levels, however, borrowed from ecology, suffers from drawbacks such as requiring basal nodes, which limit its applicability. Here we propose simple improved definitions of trophic levels and coherence that can be computed on any directed network. We demonstrate how the method can identify node function in examples including ecosystems, supply chain networks, gene expression and global language networks. We also explore how trophic levels and coherence relate to other topological properties, such as non-normality and cycle structure, and show that our method reveals the extent to which the edges in a directed network are aligned in a global direction

Ichnofacies of the Stairway Sandstone fish-fossil beds (Middle Ordovician, Northern Territory, Australia)

The Stairway Sandstone is a 30-560 m thick succession of Middle Ordovician siliciclastic sedimentary rocks within the Amadeus Basin of central Australia, deposited in the epeiric Larapintine Sea of northern peri-Gondwana. The Stairway Sandstone is significant as one of only two known Gondwanan successions to yield articulated arandaspid (pteraspidomorph agnathan) fish. Herein we use the ichnology of the Stairway Sandstone to reveal insights into the shallow marine habitat of these early vertebrates, and compare it with that of other known pteraspidomorph-bearing localities from across Gondwana. The Stairway Sandstone contains a diverse Ordovician ichnofauna including 22 ichnotaxa of Arenicolites, Arthrophycus, Asterosoma, Cruziana, Didymaulichnus, Diplichnites, Diplocraterion,? Gordia, Lockeia, Monocraterion, Monomorphichnus, Phycodes, Planolites, Rusophycus, Skolithos and Uchirites. These ichnofauna provide a well-preserved example of a typical Ordovician epeiric sea assemblage, recording the diverse ethologies of tracemakers in a very shallow marine environment of flashy sediment accumulation and regularly shifting sandy substrates. New conodont data refine the age of the Stairway Sandstone to the early Darriwilian, with ichnostratigraphic implications for the Cruziana rugosa group and Arthrophycus alleghaniensis

Atomistic mechanism of transmembrane helix association

Transmembrane helix association is a fundamental step in the folding of helical membrane proteins. The prototypical example of this association is formation of the glycophorin dimer. While its structure and stability have been well-characterized experimentally, the detailed assembly mechanism is harder to obtain. Here, we use all-atom simulations within phospholipid membrane to study glycophorin association. We find that initial association results in the formation of a non-native intermediate, separated by a significant free energy barrier from the dimer with a native binding interface. We have used transition-path sampling to determine the association mechanism. We find that the mechanism of the initial bimolecular association to form the intermediate state can be mediated by many possible contacts, but seems to be particularly favoured by formation of non-native contacts between the C-termini of the two helices. On the other hand, the contacts which are key to determining progression from the intermediate to the native state are those which define the native binding interface, reminiscent of the role played by native contacts in determining folding of globular proteins. As a check on the simulations, we have computed association and dissociation rates from the transition-path sampling. We obtain results in reasonable accord with available experimental data, after correcting for differences in native state stability. Our results yield an atomistic description of the mechanism for a simple prototype of helical membrane protein folding

Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees

Fossils are vital for calibrating rates of molecular and morphological change through geological time, and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and invertebrate morphological datasets resulted in significant changes to phylogenetic signal; it caused individual taxa to drift from their original position, predominately downward toward the root of their respective trees. This last bias could systematically inflate evolutionary rates inferred from molecular data because first fossil occurrences will not be recognised as such. Stem-ward slippage, whereby fundamental taphonomic biases cause fossils to be interpreted as erroneously primitive, is therefore a ubiquitous problem for all biologists attempting to infer macroevolutionary rates or sequences

Dental data perform relatively poorly in reconstructing mammal phylogenies: Morphological partitions evaluated with molecular benchmarks

Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. They are inferred from both molecular and morphological data, yet the relative value of morphology has been questioned in this context due to perceived homoplasy, developmental linkage, and nonindependence of characters. Nevertheless, fossil data are limited to incomplete subsets of preserved morphology, and different regions are treated as equivalent. Through meta-analysis of 40 data sets, we show here that the dental and osteological characters of mammals convey significantly different phylogenetic signals, and that osteological characters are significantly more compatible with molecular trees. Furthermore, the application of simplified paleontological filters (retaining only dental data) results in significantly greater loss of phylogenetic signal than random character ablation. Although the mammal fossil record is largely comprised of teeth, dental data alone are generally found to be less reliable for phylogenetic reconstruction given their incongruence with osteological and molecular data. These findings highlight the need for rigorous meta-analyses of distributions of homoplasy in morphological data. These tests, and consequent refinements to phylogenetic analyses that they permit, promise to improve the quality of all macroevolutionary studies that hinge on accurate trees

A well-preserved ‘placoderm’ (stem-group Gnathostomata) upper jaw from the Early Devonian of Mongolia clarifies jaw evolution

The origin of jaws and teeth remains contentious in vertebrate evolution. ‘Placoderms’ (Silurian-Devonian armoured jawed fishes) are central to debates on the origins of these anatomical structures. ‘Acanthothoracids’ are generally considered the most primitive ‘placoderms’. However, they are so far known mainly from disarticulated skeletal elements that are typically incomplete. The structure of the jaws—particularly the jaw hinge—is poorly known, leaving open questions about their jaw function and comparison with other placoderms and modern gnathostomes. Here we describe a near-complete ‘acanthothoracid’ upper jaw, allowing us to reconstruct the likely orientation and angle of the bite and compare its morphology with that of other known ‘placoderm’ groups. We clarify that the bite position is located on the upper jaw cartilage rather than on the dermal cheek and thus show that there is a highly conserved bite morphology among most groups of ‘placoderms’, regardless of their overall cranial geometry. Incorporation of the dermal skeleton appears to provide a sound biomechanical basis for jaw origins. It appears that ‘acanthothoracid’ dentitions were fundamentally similar in location to that of arthrodire ‘placoderms’, rather than resembling bony fishes. Irrespective of current phylogenetic uncertainty, the new data here resolve the likely general condition for ‘placoderms’ as a whole, and as such, ancestral morphology of known jawed vertebrates

Systematic analysis of exceptionally preserved fossils: correlated patterns of decay and preservation

From Wiley via Jisc Publications RouterHistory: received 2020-12-18, accepted 2021-06-29, pub-electronic 2021-08-24Article version: VoRPublication status: PublishedFunder: Natural Environmental Research Council; Grant(s): NE/E015336/1, NE/K004557/1Abstract: The fossil record of non‐biomineralized animals and tissues provides important insight into deep‐time evolutionary events. Interpretation of these highly variable remains requires an understanding of how both decay and preservation lead to fossilization. Here we establish a quantitative approach that unites data from decay experiments of extant taxa with preservation mode of fossils, allowing evaluation of both information loss and information retention, and their interaction, in non‐biomineralized fossils. We illustrate our approach using fossil data from two Lagerstätten with distinct taphonomic regimes, one characterized by phosphatization, and the other by pyritization of non‐biomineralized tissues. This demonstrates that frequency of occurrence of characters in fossil taxa is significantly correlated with sequences of character decay observed in extant comparator organisms, and that decay prone and decay resistant characters have distinct preservation modes; the former are mineralized and the latter are organically preserved. The methods and principles applied here to non‐biomineralized vertebrates are applicable to other exceptionally‐preserved fossils and allow for identification of systematic biases in fossil specimen completeness, character retention and the mode of their preservation. Furthermore, our analyses validates experimental decay in supporting the interpretation of anatomy in non‐biomineralized fossils