82 results found
Furness EN, Garwood RJ, Sutton MD, 2023, REvoSim v3: A fast evolutionary simulation tool withecological processes, Journal of Open Source Software, Vol: 8, Pages: 5284-5284
Briggs DEG, Siveter DJ, Siveter DJ, et al., 2023, A vicissicaudatan arthropod from the Silurian Herefordshire Lagerstätte, UK., R Soc Open Sci, Vol: 10, ISSN: 2054-5703
A new arthropod, Carimersa neptuni gen. et sp. nov., is described from the Silurian (Wenlock Series) Herefordshire Konservat-Lagerstätte, UK. The head bears pedunculate eyes and five pairs of appendages. Triflagellate antennae are followed by two pairs of uniramous limbs each with an endopod bearing a pronounced gnathobasic basipod. The posterior two pairs of head limbs and all trunk limbs bear an endopod, exopod and filamentous exite. The trunk consists of 10 appendage-bearing segments followed by an apodous abdomen of four segments. The arthropod resolves as sister taxon to Kodymirus and Eozetetes + Aglaspidida. It is the first representative of Vicissicaudata reported from the Herefordshire Lagerstätte and the first Silurian example with well-preserved appendages. The preservation of a cluster of radiolarians apparently captured by the trunk appendages is the first direct association of predator and prey discovered in the Herefordshire fauna, and suggests that Carimersa was a nektobenthic form that used its gnathobasic basipods in microdurophagy.
Furness EN, Saupe EE, Garwood RJ, et al., 2023, The jigsaw model: a biogeographic model that partitions habitat heterogeneity from area, Frontiers of Biogeography, Vol: 15
Species–area models now frequently include habitat heterogeneity. These models often fit real-world data better than those that exclude this factor. However, such models usually link the effects of habitat heterogeneity and study area. Critically, we show that difficulties in quantifying habitat heterogeneity within these models can lead to distortions of the apparent effect of area on species richness. Here, we derive a model that minimises these distortions by partitioning the influence of habitat heterogeneity from that of area, without compromising ease of application. This ‘jigsaw model’ achieves this by assuming that different habitats within an area can support similar numbers of species. We compare the behaviour of this model to that of existing models of similar complexity using both simulated island ecosystems and 40 published empirical datasets. The effects of habitat heterogeneity and area on species richness vary independently in our simulations, and these independent effects are recovered by the jigsaw model. This flexibility, however, is not present when the same data are analysed using other models of similar complexity. When applied to real-world data, the jigsaw model demonstrates that the relative importance of area and habitat heterogeneity varies depending on the study system. The jigsaw model provides the best fit to real-world data (according to AICc) of all tested models in logarithmic form, and the second best fit, after the choros model, in power-law form. Our results demonstrate the importance of partitioning the effects of habitat heterogeneity and area on species richness in biogeographic models. The jigsaw model is a simple but powerful tool for such partitioning. It has the potential to elucidate the underlying drivers of species richness patterns, and to be used as a tool in biological conservation projects, where data are often incomplete
Carter R, Sutton M, Briggs D, et al., 2021, A Silurian ophiuroid with soft tissue preservation, Papers in Palaeontology, Vol: 7, Pages: 2041-2047, ISSN: 2056-2802
Most Palaeozoic brittle stars lack the fused arm ossicles (vertebrae) that facilitate the remarkable mode of walking that characterizes living forms. Here we describe a stem ophiuroid from the Herefordshire Lagerstätte (Silurian, Wenlock Series) which is remarkable in preserving the body cavity uncompacted and long tube feet. We assign the specimen to the order Oegophiurida. The morphology of the arms and attitude of the specimen suggest that locomotion may have been achieved by arm propulsion combined with podial walking. This ophiuroid increases the diversity of echinoderm higher taxa with preserved soft parts represented in the Herefordshire Lagerstätte.
Siveter DJ, Fortey RA, Briggs DEG, et al., 2021, The first Silurian trilobite with three-dimensionally preserved soft parts reveals novel appendage morphology, PAPERS IN PALAEONTOLOGY, Vol: 7, Pages: 2245-2253, ISSN: 2056-2799
Furness EN, Garwood RJ, Mannion PD, et al., 2021, Productivity, niche availability, species richness, and extinction risk: Untangling relationships using individual-based simulations, Ecology and Evolution, Vol: 11, Pages: 8923-8940, ISSN: 2045-7758
It has often been suggested that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the “more individuals” hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual-based eco-evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual-based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: Rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species population size, apparently due to increased competition when total community abundance is higher. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems in which niche partitioning has not been halted by species saturation. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favor of neutral explanations, as has historically been the case with the MIH. Our simulations de
Furness EN, Garwood RJ, Mannion PD, et al., 2021, Evolutionary simulations clarify and reconcile biodiversity-disturbance models, Proceedings of the Royal Society B: Biological Sciences, Vol: 288, Pages: 1-9, ISSN: 0962-8452
There is significant geographic variation in species richness. However, the nature of the underlying relationships, such as that between species richness and environmental stability, remains unclear. The stability-time hypothesis suggests that environmental instability reduces species richness by suppressing speciation and increasing extinction risk. By contrast, the patch-mosaic hypothesis suggests that small-scale environmental instability can increase species richness by providing a steady supply of non-equilibrium environments. Although these hypotheses are often applied to different time scales, their core mechanisms are in conflict. Reconciling these apparently competing hypotheses is key to understanding how environmental conditions shape the distribution of biodiversity. Here, we use REvoSim, an individual-based, eco-evolutionary system, to model the evolution of sessile organisms in environments with varying magnitudes and scales of environmental instability. We demonstrate that when environments have substantial permanent heterogeneity, a high level of localized environmental instability reduces biodiversity, whereas in environments lacking permanent heterogeneity, high levels of localized instability increase biodiversity. By contrast, broad-scale environmental instability, acting on the same time scale, invariably reduces biodiversity. Our results provide a new view of the biodiversity–disturbance relationship that reconciles contrasting hypotheses within a single model and implies constraints on the environmental conditions under which those hypotheses apply. These constraints can inform attempts to conserve adaptive potential in different environments during the current biodiversity crisis.
Keating JN, Sansom RS, Sutton MD, et al., 2020, Morphological phylogenetics evaluated using novel evolutionary simulations, Systematic Biology, Vol: 69, Pages: 897-912, ISSN: 1063-5157
Evolutionary inferences require reliable phylogenies. Morphological data has traditionally been analysed using maximum parsimony, but recent simulation studies have suggested that Bayesian analyses yield more accurate trees. This debate is ongoing, in part, because of ambiguity over modes of morphological evolution and a lack of appropriate models. Here we investigate phylogenetic methods using two novel simulation models - one in which morphological characters evolve stochastically along lineages and another in which individuals undergo selection. Both models generate character data and lineage splitting simultaneously: the resulting trees are an emergent property, rather than a fixed parameter. Standard consensus methods for Bayesian searches (Mki) yield fewer incorrect nodes and quartets than the standard consensus trees recovered using equal weighting and implied weighting parsimony searches. Distances between the pool of derived trees (most parsimonious or posterior distribution) and the true trees - measured using Robinson-Foulds (RF), subtree prune and regraft (SPR), and tree bisection reconnection (TBR) metrics - demonstrate that this is related to the search strategy and consensus method of each technique. The amount and structure of homoplasy in character data differs between models. Morphological coherence, which has previously not been considered in this context, proves to be a more important factor for phylogenetic accuracy than homoplasy. Selection-based models exhibit relatively lower homoplasy, lower morphological coherence, and higher inaccuracy in inferred trees. Selection is a dominant driver of morphological evolution, but we demonstrate that it has a confounding effect on numerous character properties which are fundamental to phylogenetic inference. We suggest that the current debate should move beyond considerations of parsimony versus Bayesian, towards identifying modes of morphological evolution and using these to build models for probabilist
Spencer A, Garwood R, Sutton MD, 2020, palaeoware/SPIERS: SPIERS v3.1.1
This is a patch release containing fixes for the macOS release. The following has been changed since the last v3.1.0 release. This is now the recommended version.
Siveter DJ, Briggs DEG, Siveter DJ, et al., 2020, The Herefordshire Lagerstätte: fleshing out Silurian marine life, Journal of the Geological Society, Vol: 177, Pages: 1-13, ISSN: 0016-7649
Bennett D, Sutton M, Turvey S, 2019, How the past impacts the future: modelling the performance of evolutionarily distinct mammals through time, Philosophical Transactions B: Biological Sciences, Vol: 374, ISSN: 0962-8436
How does past evolutionary performance impact future evolutionary performance? This is an important question not just for macroevolutionary biologists who wish to chart the phenomena that describe deep-time changes in biodiversity but also for conservation biologists, as evolutionarily distinct species – which may be deemed “low-performing” in our current era – are increasingly the focus of conservation efforts. Contrasting hypotheses exist to account for the history and future of evolutionarily distinct species: on the one hand they may be relicts of large radiations, potentially “doomed” to extinction; or they may be slow-evolving, “living fossils”, likely neither to speciate nor go extinct; or they may be seeds of future radiations. Here we attempt to test these hypotheses in Mammalia by combining a molecular phylogenetic supertree with fossil record occurrences and measuring change in evolutionary distinctness (ED) at different time slices. With these time slices, we modelled future ED as a function of past ED. We find that past evolutionary performance does indeed have an impact on future evolutionary performance: the most evolutionarily isolated clades tend to become more evolutionarily distinct with time, indicating that low-performing clades tend to remain low-performing throughout their evolutionary history.
Nadhira A, Sutton M, Botting J, et al., 2019, Three-dimensionally preserved soft-tissues and calcareous hexactins in a Silurian sponge: implications for early sponge evolution, Royal Society Open Science, Vol: 6, Pages: 1-13, ISSN: 2054-5703
Sponges (Porifera), as one of the earliest-branching animal phyla, are crucial for understanding early metazoan phylogeny. Recent studies of Lower Palaeozoic sponges have revealed a variety of character states and combinations unknown in extant taxa, challenging our views of early sponge morphology. The Herefordshire Konservat-Lagerstätte yields an abundant, diverse sponge fauna with three-dimensional preservation of spicules and soft tissue. Carduispongia pedicula gen. et sp. nov. possesses a single layer of hexactine spicules arranged in a regular orthogonal network. This spicule type and arrangement is characteristic of the reticulosans, which have traditionally been interpreted as early members of the extant siliceous class Hexactinellida. However, the unusual preservation of the spicules of C. pedicula reveals an originally calcareous composition, which would be diagnostic of the living class Calcarea. The soft tissue architecture closely resembles the complex sylleibid or leuconid structure seen in some modern calcareans and homoscleromorphs. This combination of features strongly supports a skeletal continuum between primitive calcareans and hexactinellid siliceans, indicating that the last common ancestor of Porifera was a spiculate, solitary, vasiform animal with a thin skeletal wall.
Garwood RJ, Spencer ART, Sutton MD, 2019, REvoSim: Organism-level simulation of macro and microevolution, Palaeontology, Vol: 62, Pages: 339-355, ISSN: 0031-0239
Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth–life system in deep time. Model-based approaches can reveal important macroevolutionary patterns and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License) and as distributables for a variety of operating systems. REvoSim is an individual-based model with a strong focus on computational efficiency. It can simulate populations of 10 5 –10 7 digital organisms over geological timescales on a typical desktop computer, and incorporates spatial and temporal environmental variation, recombinant reproduction, mutation and dispersal. Whilst microevolutionary processes drive the model, macroevolutionary phenomena such as speciation and extinction emerge. We present results and analysis of the model focusing on validation, and note a number potential applications. REvoSim can serve as a multipurpose platform for studying both macro and microevolution, and bridges this divide. It will be continually developed by the authors to expand its capabilities and hence its utility.
Rahman IA, Thompson JR, Briggs DEG, et al., 2019, A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan, Proceedings of the Royal Society B: Biological Sciences, Vol: 286, ISSN: 0962-8452
Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, Sollasina cthulhu, from the Silurian Herefordshire Lagerstätte, UK. Sollasina cthulhu belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical-optical tomography and computer reconstruction, we visualize the internal anatomy of S. cthulhu in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that Sollasina and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
Spencer A, Sutton M, Garwood R, 2019, palaeoware/revosim: REvoSim and EnviroGen v2.0.1
This is a patch release of the REvoSim and EnviroGen software containing minor bug fixes and code improvements. This release and the underlying model has been described in detail in the following paper:Garwood, R.J., Spencer A.R.T. and Sutton, M.D. 2019. REvoSim: Organism-level simulation of macro- and microevolution. Palaeontology.The code is archived on zenodo.org:Documentation:REvoSim Online DocumentationEnviroGen Online DocumentationChange log:The following has been changed since the last release.REvoSimUpdate in copyright notice datesMoved licence text to a resource fileEnviroGenUpdate in copyright notice datesMoved licence text to a resource fileGeneralUpdated README file with compile instructions.Updated conditional defines to ensure that the program compiles with pre QT 5.6Updated icons for all operating systemsRelease information: WindowsA zip containing all required binaries can be downloaded from the assets above. Alternatively an installer is provided. See notes below:Note 1: The .zip archive contains all REvoSim programs (REvoSim and EnviroGen). The .zip can be extracted and the programs run by double clicking the .exe files in the ./bin folder. All the required libraries have been included and are found in the ./bin folder.Note 2: The windows installer will not overwrite any pre-existing REvoSim installations. However, it will set the default program for all REvoSim files (.revosim) to to use the newly installed version.MacA zip containing the REvoSim programs (REvoSim and EnviroGen) can be downloaded from the assets above. To install the software, drag and drop the required .app folder(s) into the Applications folder. You may be required to the approve the software in security and privacy settings before it will launch.LinuxAny Linux users willing to test a Linux build should contact firstname.lastname@example.org. A Linux package is planned for release during Q1 2019.
Spencer A, Garwood R, Sutton M, 2019, palaeoware/revosim: REvoSim and EnviroGen v2.0.0
This is the first public release of the REvoSim and EnviroGen software. This release and the underlying model has been described in detail in the following paper:Garwood, R.J., Spencer A.R.T. and Sutton, M.D. 2019. REvoSim: Organism-level simulation of macro- and microevolution. Palaeontology.Change log:The following has been changed since the last release.REvoSimInitial public release.EnviroGen:Initial public release.Release information: LinuxAny Linux users willing to test a Linux build should contact email@example.com.WindowsA zip containing all required binaries can be downloaded from the assets above. Alternatively an installer is provided. See notes below:Note 1: the .zip archive contains all REvoSim programs (REvoSim and EnviroGen). The .zip can be extracted and the programs run by double clicking the .exe files in the ./bin folder. All the required libraries have been included and are found in the ./bin folder.Note 2: The windows installer will not overwrite any pre-existing REvoSim installations. However, it will set the default program for all REvoSim files (.revosim) to to use the newly installed version.MacWe are working on a Mac release and hope to have it released soon.
Siveter D, Briggs D, Siveter D, et al., 2018, A well-preserved respiratory system in a Silurian ostracod, Biology Letters, Vol: 14, ISSN: 1744-957X
Ostracod crustaceans are diverse and ubiquitous in aqueous environments today but relatively few known species have gills. Ostracods are the most abundant fossil arthropods but examples of soft-part preservation, especially of gills, are exceptionally rare. A new ostracod, Spiricopia aurita (Myodocopa), from the marine Silurian Herefordshire Lagerstätte (430 Mya), UK, preserves appendages, lateral eyes and gills. The respiratory system includes five pairs of gill lamellae with hypobranchial and epibranchial canals that conveyed haemolymph. A heart and associated vessels had likely evolved in ostracods by the Mid-Silurian.
Siveter D, Briggs D, Siveter D, et al., 2018, A three-dimensionally preserved lobopodian from the Herefordshire (Silurian) Lagerstätte, UK, Royal Society Open Science, Vol: 5, ISSN: 2054-5703
The Herefordshire (Silurian) Lagerstätte (approx. 430 Myr BP) has yielded, among many exceptionally preserved invertebrates, a wide range of new genera belonging to crown-group Panarthropoda. Here, we increase this panarthropod diversity with the lobopodian Thanahita distos, a new total-group panarthropod genus and species. This new lobopodian preserves at least nine paired, long, slender appendages, the anterior two in the head region and the posterior seven representing trunk lobopods. The body ends in a short post-appendicular extension. Some of the trunk lobopods bear two claws, others a single claw. The body is covered by paired, tuft-like papillae. Thanahita distos joins only seven other known three-dimensionally preserved lobopodian or onychophoran (velvet worm) fossil specimens and is the first lobopodian to be formally described from the Silurian. Phylogenetic analysis recovered it, together with all described Hallucigenia species, in a sister-clade to crown-group panarthropods. Its placement in a redefined Hallucigeniidae, an iconic Cambrian clade, indicates the survival of this clade to Silurian times.
Sigwart JD, Sutton MD, Bennett K, 2018, How big is a genus? Towards a nomothetic systematics, Zoological Journal of the Linnean Society, Vol: 183, Pages: 237-252, ISSN: 1096-3642
A genus is a taxonomic unit that may contain one species (monotypic) or thousands. Yet counts of genera or families are used to quantify diversity where species-level data are not available. High frequencies of monotypic genera (~30% of animals) have previously been scrutinized as an artefact of human classification. To test whether Linnean taxonomy conflicts with phylogeny, we compared idealized phylogenetic systematics in silico with real-world data. We generated highly replicated, simulated phylogenies under a variety of fixed speciation/extinction rates, imposed three independent taxonomic sorting algorithms on these clades (2.65 × 108 simulated species) and compared the resulting genus size data with quality-controlled taxonomy of animal groups (2.8 × 105 species). ‘Perfect’ phylogenetic systematics arrives at similar distributions to real-world taxonomy, regardless of the taxonomic algorithm. Rapid radiations occasionally produce a large genus when speciation rates are favourable; however, small genera can arise in many different ways, from individual lineage persistence and/or extinctions creating subdivisions within a clade. The consistency of this skew distribution in simulation and real-world data, at sufficiently large samples, indicates that specific aspects of its mathematical behaviour could be developed into generalized or nomothetic principles of the global frequency distributions of higher taxa. Importantly, Linnean taxonomy is a better-than-expected reflection of underlying evolutionary patterns.
Bennett DJ, Sutton MD, Turvey ST, 2018, Quantifying the living fossil concept, Palaeontologia Electronica, Vol: 21, ISSN: 1094-8074
“Living fossil” is a contentious label, often used to identify clades that have experienced particularly little evolutionary change. Many of the problems associated with the term are due to a lack of a clear definition. To date, most work on the phenomenon has been primarily qualitative, leading to a list of living fossils each selected for different sets of reasons. This non-uniformity in living fossil identification makes the ubiquity, clarity and potential causes of the phenomenon difficult to assess. An alternative approach is to use a quantitative metric that matches the most common interpretations of “living fossil” to generate a less subjective listing. Here, we present the Evolutionary Performance Index (EPI); this metric is calculable across the entire tree of life and allows for fair comparisons between taxonomic groups. With this index, we calculated the performance scores for over 24,000 clades within Metazoa and Embryophyta. Many well-known living fossils featured among the lowest performing clades, e.g., coelacanths, gingko, tuatara as well as groups that have previously been overlooked. By grounding the definition in a strictly quantitative framework, future researchers will be better able to test the causes and relevance of the phenomenon.
Briggs DEG, Siveter DJ, Siveter DJ, et al., 2017, An edrioasteroid from the Silurian Herefordshire Lagerstatte of England reveals the nature of the water vascular system in an extinct echinoderm, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 284, ISSN: 0962-8452
Echinoderms are unique in having a water vascular system with tube feet, which perform a variety of functions in living forms. Here, we report the first example of preserved tube feet in an extinct group of echinoderms. The material, from the Silurian Herefordshire Lagerstätte, UK, is assigned to a new genus and species of rhenopyrgid edrioasteroid, Heropyrgus disterminus. The tube feet attach to the inner surface of compound interradial plates and form two sets, an upper and a lower, an arrangement never reported previously in an extant or extinct echinoderm. Cover plates are absent and floor plates are separated creating a large permanent entrance to the interior of the oral area. The tube feet may have captured food particles that entered the oral area and/or enhanced respiration. The pentameral symmetry of the oral surface transitions to eight columns in which the plates are vertically offset resulting in a spiral appearance. This change in symmetry may reflect flexibility in the evolutionary development of the axial and extraxial zones in early echinoderm evolution.
Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.
Siveter DJ, Briggs DEG, Siveter DJ, et al., 2017, A new crustacean from the Herefordshire (Silurian) Lagerstätte, UK, and its significance in malacostracan evolution, Proceedings of the Royal Society B: Biological Sciences, Vol: 284, ISSN: 0962-8452
Cascolus ravitis gen. et sp. nov. is a three-dimensionally preserved fossil crustacean with soft parts from the Herefordshire (Silurian) Lagerstätte, UK. It is characterized by a head with a head shield and five limb pairs, and a thorax (pereon) with nine appendage-bearing segments followed by an apodous abdomen (pleon). All the appendages except the first are biramous and have a gnathobase. The post-mandibular appendages are similar one to another, and bear petal-shaped epipods that probably functioned as a part of the respiratory–circulatory system. Cladistic analysis resolves the new taxon as a stem-group leptostracan (Malacostraca). This well-preserved arthropod provides novel insights into the evolution of appendage morphology, tagmosis and the possible respiratory–circulatory physiology of a basal malacostracan.
Parry LA, Legg DA, Sutton MD, 2017, Enalikter is not an annelid: homology, autapomorphies and the interpretation of problematic fossils, Lethaia, Vol: 50, Pages: 222-226, ISSN: 0024-1164
A megacheiran arthropod, Enalikter aphson, was recently described by Siveter et al. (2014) from the mid-Silurian (late Wenlock) of Herefordshire. Previously, megacheirans had only been recognized from the Cambrian. Struck et al. (2015) considered the body plan of Enalikter to be incompatible with this affinity, arguing that many of the arthropod features were either not present or misinterpreted. Instead, they compared Enalikter to polychaete annelids, identifying characters from numerous polychaete lineages which they considered to be present in Enalikter. A reply to this critique by Siveter et al. (2015) reaffirmed arthropod affinities for Enalikter by presenting additional evidence for key arthropod features, such as arthropodized appendages. Here, we augment Siveter et al. by critically addressing the putative annelid characters of Enalikter presented by Struck et al. and additionally explore the morphological and phylogenetic implications of their hypothesis. We conclude that similarities between Enalikter and polychaetes are superficial and that character combinations proposed by Struck et al. are not present in any annelid, living or extinct. This taxon highlights the importance of using a phylogenetic framework for interpreting fossils that present unusual morphologies, such that proposed shared characters are hypotheses of homology rather than merely phenotypic similarities. Crucially, we argue that autapomorphic characters of subgroups of large taxa (like families or classes within phyla) should not be used to diagnose problematic fossils.
Bennett DJ, Sutton MD, Turvey ST, 2017, treeman: an R package for efficient and intuitive manipulation of phylogenetic trees, BMC Research Notes, Vol: 10, Pages: 30-30, ISSN: 1756-0500
BACKGROUND: Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. RESULTS: We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. CONCLUSIONS: We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.
Bennett, Sutton MD, Turvey ST, 2016, Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates, Paleobiology, Vol: 43, Pages: 34-48, ISSN: 0094-8373
As a label for a distinct category of life, ‘living fossil’ is controversial. The term has multiple definitions and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective where a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that speciation rates must have been unequally distributed between species in the past to produce the shape of the tree of life. Although an uneven distribution of speciation rates may create the possibility for a distinct group of living fossil lineages, such a grouping could only be considered genuine if extinction rates also show a consistent pattern, be it indicative of dead-end or panchronic lineages. To determine whether extinction rates also show an unequal distribution, we developed a tree-growth model where the probability of speciation and extinction is a function of a tip’s ED. We simulated 1,000s of trees where the ED function for a tip is randomly and independently determined for speciation and extinction rates. We find that simulations where the most evolutionarily distinct tips have lower rates of speciation and extinction produce phylogenetic trees closest in shape to empirical trees. This implies that a distinct set of lineages with reduced rates of diversification, indicative of a panchronic definition, is required to create the shape of the tree of life.
Briggs DEG, Siveter DJ, Siveter DJ, et al., 2016, Reply to Piper: aquilonifer’s kites are not mites, Proceedings of the National Academy of Sciences of the United States of America, Vol: 113, Pages: E3320-E3321, ISSN: 1091-6490
Piper (1) offers the fascinating observation that the attachment of small arthropods by threads to the Silurian arthropod Aquilonifer (2) is similar to that of the nymphs of Uropodina mites to larger arthropods (e.g., beetles) to facilitate their dispersal in patchy habitats (phoresy). Clearly these two examples are profoundly separated by time (∼430 Mya) and ecology (the one fully marine, the other terrestrial), but it is worth considering the possibility that the adherence of tiny arthropods to Aquilonifer represents the behavior of some sort of marine mite ancestor.
Briggs DEG, Siveter DJ, Siveter DJ, et al., 2016, Tiny individuals attached to a new Silurian arthropod suggest a unique mode of brood care, Proceedings of the National Academy of Sciences of the United States of America, Vol: 113, Pages: 4410-4415, ISSN: 0027-8424
The ∼430-My-old Herefordshire, United Kingdom, Lagerstätte has yielded a diversity of remarkably preserved invertebrates, many of which provide fundamental insights into the evolutionary history and ecology of particular taxa. Here we report a new arthropod with 10 tiny arthropods tethered to its tergites by long individual threads. The head of the host, which is covered by a shield that projects anteriorly, bears a long stout uniramous antenna and a chelate limb followed by two biramous appendages. The trunk comprises 11 segments, all bearing limbs and covered by tergites with long slender lateral spines. A short telson bears long parallel cerci. Our phylogenetic analysis resolves the new arthropod as a stem-group mandibulate. The evidence suggests that the tethered individuals are juveniles and the association represents a complex brooding behavior. Alternative possibilities—that the tethered individuals represent a different epizoic or parasitic arthropod—appear less likely.
Sutton MD, Rahman IA, Garwood RJ, 2016, VIRTUAL PALEONTOLOGY – AN OVERVIEW, Journal of Paleontology, ISSN: 1937-2337
Virtual paleontology is the study of fossils through three-dimensional digital visualizations; it represents a powerful and well-established set of tools for the analysis and dissemination of fossil-data. Techniques are divisible into tomographic (i.e. slice-based) and surface-based types. Tomography has a long pre-digital history, but the recent explosion of virtual paleontology has resulted primarily from developments in X-ray computed tomography (CT), and of surface-based technologies such as laser scanning. Destructive tomographic methods include forms of physical-optical tomography (e.g. serial grinding); these are powerful but problematic techniques. Focused Ion Beam (FIB) tomography is a modern alternative for microfossils, also destructive but capable of extremely high resolutions. Non-destructive tomographic methods include the many forms of CT; these are the most widely used data-capture techniques at present, but are not universally applicable. Where CT is inappropriate, other non-destructive technologies (neutron tomography, magnetic resonance imaging, optical tomography) may prove suitable. Surface-based methods provide portable and convenient data capture for surface topography and texture, and may be appropriate when internal morphology is not of interest; technologies include laser scanning, photogrammetry, and mechanical digitization. Reconstruction methods that produce visualizations from raw data are many and various; selection of an appropriate workflow will depend on many factors, but is an important consideration that should be addressed prior to any study. The vast majority of three-dimensional fossils can now be studied using some form of virtual paleontology, and barriers to broader uptake are being eroded. Technical issues regarding data-sharing, however, remain problematic. Technological developments continue; those promising tomographic recovery of compositional data are of particular relevance to paleontology.
Tennant JP, Mannion PD, Upchurch P, et al., 2016, Biotic and environmental dynamics through the Late Jurassic–Early Cretaceous transition: evidence for protracted faunal and ecological turnover, Biological Reviews, Vol: 92, Pages: 776-814, ISSN: 1469-185X
The Late Jurassic to Early Cretaceous interval represents a time of environmental upheaval and cataclysmic events, combined with disruptions to terrestrial and marine ecosystems. Historically, the Jurassic/Cretaceous (J/K) boundary was classified as one of eight mass extinctions. However, more recent research has largely overturned this view, revealing a much more complex pattern of biotic and abiotic dynamics than has previously been appreciated. Here, we present a synthesis of our current knowledge of Late Jurassic–Early Cretaceous events, focusing particularly on events closest to the J/K boundary. We find evidence for a combination of short-term catastrophic events, large-scale tectonic processes and environmental perturbations, and major clade interactions that led to a seemingly dramatic faunal and ecological turnover in both the marine and terrestrial realms. This is coupled with a great reduction in global biodiversity which might in part be explained by poor sampling. Very few groups appear to have been entirely resilient to this J/K boundary ‘event’, which hints at a ‘cascade model’ of ecosystem changes driving faunal dynamics. Within terrestrial ecosystems, larger, more-specialised organisms, such as saurischian dinosaurs, appear to have suffered the most. Medium-sized tetanuran theropods declined, and were replaced by larger-bodied groups, and basal eusauropods were replaced by neosauropod faunas. The ascent of paravian theropods is emphasised by escalated competition with contemporary pterosaur groups, culminating in the explosive radiation of birds, although the timing of this is obfuscated by biases in sampling. Smaller, more ecologically diverse terrestrial non-archosaurs, such as lissamphibians and mammaliaforms, were comparatively resilient to extinctions, instead documenting the origination of many extant groups around the J/K boundary. In the marine realm, extinctions were focused on low-latitude, shallow marine shel
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