Martin R. Smith
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View article: StratoBayes: a Bayesian method for automated stratigraphic correlation and age modelling
StratoBayes: a Bayesian method for automated stratigraphic correlation and age modelling Open
Stratigraphic correlation and age modelling are fundamental to reconstructing Earth's history, biological evolution, and palaeoclimate, and underpin the exploration for subsurface resources. Correlations are produced by integrating diverse…
View article: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies Open
Evolutionary rate covariation (ERC) is an established comparative genomics method that identifies sets of genes sharing patterns of sequence evolution, which suggests shared function. Whereas many functional predictions of ERC have been em…
View article: Reply to Comment on: <i>Omnidens</i> appendages and the origin of radiodont mouthparts
Reply to Comment on: <i>Omnidens</i> appendages and the origin of radiodont mouthparts Open
National Natural Science Foundation of China https://doi.org/10.13039/501100001809
View article: StratoBayes: A Bayesian method for automated stratigraphic correlation and age modelling
StratoBayes: A Bayesian method for automated stratigraphic correlation and age modelling Open
Stratigraphic correlation and age modelling are fundamental to reconstructing Earth’s history, biological evolution, and palaeoclimate, and underpin the exploration for subsurface resources. Correlations are produced by integrating diverse…
View article: ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies
ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies Open
Evolutionary Rate Covariation (ERC) is an established comparative genomics method that identifies sets of genes sharing patterns of sequence evolution, which suggests shared function. Whereas many functional predictions of ERC have been em…
View article: Responsibilizing the Net-Zero Hero? Creation and Implications of a Tragic Subject Position
Responsibilizing the Net-Zero Hero? Creation and Implications of a Tragic Subject Position Open
The energy sector is the largest contributor to global carbon dioxide emissions. To address the current climate emergency, however, energy market actors (e.g., energy providers, nongovernmental organizations, policy makers) try to make ind…
View article: <i>Omnidens</i> appendages and the origin of radiodont mouthparts
<i>Omnidens</i> appendages and the origin of radiodont mouthparts Open
The sophisticated, modular and adaptable body plan of arthropods underpins their dominance in marine invertebrate communities. The origin of this body plan from legged lobopodian worms can be inferred from Cambrian Konservat‐Lagerstätten, …
View article: Organ systems of a Cambrian euarthropod larva
Organ systems of a Cambrian euarthropod larva Open
The Cambrian radiation of euarthropods can be attributed to an adaptable body plan. Sophisticated brains and specialized feeding appendages, which are elaborations of serially repeated organ systems and jointed appendages, underpin the dom…
View article: A Bayesian astrochronology for the Cambrian first occurrence of trilobites in West Gondwana (Morocco)
A Bayesian astrochronology for the Cambrian first occurrence of trilobites in West Gondwana (Morocco) Open
The first occurrence of trilobites at ca. 520 Ma is an iconic feature of the Cambrian Explosion. Developing a robust evolutionary view on early Cambrian life is generally hindered by large uncertainties in the ages of fossil finds and thei…
View article: <i>climenv</i>: Download, extract and visualise climatic and elevation data
<i>climenv</i>: Download, extract and visualise climatic and elevation data Open
Understanding the relationship between climate and vegetation requires climate data to be linked with ecological data, including habitat types and vegetation mapping. Our new R package climenv allows researchers to efficiently acquire, ext…
View article: Protomelission is an early dasyclad alga and not a Cambrian bryozoan
Protomelission is an early dasyclad alga and not a Cambrian bryozoan Open
The animal phyla and their associated body plans originate from a singular burst of evolution occurring during the Cambrian period, over 500 million years ago1. The phylum Bryozoa, the colonial 'moss animals', have been the exception: conv…
View article: Dating the first Siberian trilobites with a Bayesian, stratigraphic age model
Dating the first Siberian trilobites with a Bayesian, stratigraphic age model Open
Trilobites are the most diverse animal phylum in the Cambrian, and are critical stratigraphic markers. Despite their significance, the exact sequence of trilobite appearances across the globe, and their respective ages, are difficult to re…
View article: TreeSearch: Morphological Phylogenetic Analysis in R
TreeSearch: Morphological Phylogenetic Analysis in R Open
TreeSearch is an R package for phylogenetic analysis, optimized for discrete character data. Tree search may be conducted using equal or implied step weights with an explicit (albeit inexact) allowance for inapplicable character entries, a…
View article: The Cambrian cirratuliform <i>Iotuba</i> denotes an early annelid radiation
The Cambrian cirratuliform <i>Iotuba</i> denotes an early annelid radiation Open
The principal animal lineages (phyla) diverged in the Cambrian, but most diversity at lower taxonomic ranks arose more gradually over the subsequent 500 Myr. Annelid worms seem to exemplify this pattern, based on molecular analyses and the…
View article: ZIP archive containing details of phylogenetic analysis from The Cambrian cirratuliform <i>Iotuba</i> denotes an early annelid radiation
ZIP archive containing details of phylogenetic analysis from The Cambrian cirratuliform <i>Iotuba</i> denotes an early annelid radiation Open
Character descriptions, phylogenetic matrices, summary of results, and character mapping on a most parsimonious tree
View article: Robust Analysis of Phylogenetic Tree Space
Robust Analysis of Phylogenetic Tree Space Open
Phylogenetic analyses often produce large numbers of trees. Mapping trees’ distribution in “tree space” can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences bet…
View article: Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees
Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees Open
“Rogue” taxa of uncertain affinity can confound attempts to summarize the results of phylogenetic analyses. Rogues reduce resolution and support values in consensus trees, potentially obscuring strong evidence for relationships between oth…
View article: Discussion on ‘ <i>Tabelliscolex</i> (Cricocosmiidae: Palaeoscolecidomorpha) from the early Cambrian Chengjiang Biota and the evolution of seriation in Ecdysozoa’ by Shi <i>et al.</i> 2021 ( <i>JGS</i> , jgs2021-060)
Discussion on ‘ <i>Tabelliscolex</i> (Cricocosmiidae: Palaeoscolecidomorpha) from the early Cambrian Chengjiang Biota and the evolution of seriation in Ecdysozoa’ by Shi <i>et al.</i> 2021 ( <i>JGS</i> , jgs2021-060) Open
Supplementary material: Code necessary to reproduce analyses from the paper is available at https://doi.org/10.6084/m9.figshare.16419522
View article: TreeSearch: morphological phylogenetic analysis in R
TreeSearch: morphological phylogenetic analysis in R Open
TreeSearch is an R package for phylogenetic analysis, optimized for morphological datasets. Tree search may be conducted using equal or implied step weights with an explicit (albeit inexact) allowance for inapplicable character entries, av…
View article: TreeDist: Distances Between Phylogenetic Trees
TreeDist: Distances Between Phylogenetic Trees Open
An R package that implements a suite of metrics that quantify the topological distance between pairs of unweighted phylogenetic trees.
View article: Phylogenetic Signal and Bias in Paleontology
Phylogenetic Signal and Bias in Paleontology Open
An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data typically used in paleontology (bones and teeth) from six data se…
View article: An integrated Bayesian stratigraphic correlation approach for the Cambrian Explosion
An integrated Bayesian stratigraphic correlation approach for the Cambrian Explosion Open
<p>The Cambrian Explosion is characterised by a large diversification of life. The precise nature of this major evolutionary event is heavily debated, featuring anomalously fast versus more gradual evolutionary scenarios. Our ability…
View article: Astrochronology for the oldest Cambrian trilobites in Moroccan West Gondwana
Astrochronology for the oldest Cambrian trilobites in Moroccan West Gondwana Open
<p>The lower Cambrian successions of Southern Morocco (West Gondwana) feature some of the oldest trilobites and archaeocyaths fossil remains in the world, as well as some of the largest carbon isotope excursions of the Phanerozoic. C…
View article: TBRDist: Calculate Rearrangement Distances Between Unrooted Phylogenetic Trees
TBRDist: Calculate Rearrangement Distances Between Unrooted Phylogenetic Trees Open
An R package to calculate exact and approximage TBR, SPR and Replug rearrangement distances between unrooted phylogenetic trees.