Sea dragons of Avalon

Tourists driving through the village2 of Street on their way to Glastonbury might well wonder at the representation of a skeleton on the road sign. Could this perhaps be a warning that this stretch of the A39 is a roadkill hotspot? I (Stig Walsh, once a local inhabitant) suspect that the skeleton’s true identity may be far from what most outsiders expect of this part of Somerset (and most locals too). Cider, cheddar cheese, sheepskins, sensible shoes and scratched vinyl LPs of ‘The Best of the Wurzels’ probably rank highly in a top ten list of ‘objects found on and around the Somerset Levels’; Mesozoic ichthyosaurs probably wouldn’t make the top 40. Street nonetheless has an important place in the history of vertebrate palaeontology, and the PalAss review seminar held in late July was organised to look at what can be said about those fossils today

A more comprehensive habitable zone for finding life on other planets

The habitable zone (HZ) is the circular region around a star(s) where standing bodies of water could exist on the surface of a rocky planet. Space missions employ the HZ to select promising targets for follow-up habitability assessment. The classical HZ definition assumes that the most important greenhouse gases for habitable planets orbiting main-sequence stars are CO2 and H2O. Although the classical HZ is an effective navigational tool, recent HZ formulations demonstrate that it cannot thoroughly capture the diversity of habitable exoplanets. Here, I review the planetary and stellar processes considered in both classical and newer HZ formulations. Supplementing the classical HZ with additional considerations from these newer formulations improves our capability to filter out worlds that are unlikely to host life. Such improved HZ tools will be necessary for current and upcoming missions aiming to detect and characterize potentially habitable exoplanets.Comment: Published in Geosciences. Invited review for the "Planetary Evolution and Search for Life on Habitable Planets" Special Issue (58 pages, 15 Figures, 1 Table). Fixed a typo in Table 1 and updated acknowledgements (was not fixed in v2). http://www.mdpi.com/2076-3263/8/8/280/ht

The Deep Evolution of Ecdysozoa

Ecdysozoa (moulting animals) comprises the protostome Phyla Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Priapulida and Tardigrada, but our precise understanding of the phylogenetic relationships between these is disputed. Ecdysozoa is an extremely ancient clade that originated in the oceans, and ecdysozoans remain major components of modern marine and terrestrial ecosystems, including the most diverse and abundant of all animal Phyla (Arthropoda and Nematoda respectively). In this thesis, I explore the phylogenetic relationships and divergence times of fossil and extant ecdysozoans in order to address several outstanding issues in the early evolutionary history and palaeobiology of Ecdysozoa, employing data from fossils and molecular sequences. First, the phylogenetic relationships of the eight ecdysozoan phyla was tested using Bayesian models from a molecular matrix containing newly sequenced taxa from Nematomorpha, Priapulida and Tardigrada. Analyses retrieved a monophyletic Scalidophora (Kinorhyncha, Loricifera and Priapulida) which in turn is sister-group to a clade comprising Nematoida (Nematoda and Nematomorpha) and Panarthropoda (Arthropoda, Onychophora and Tardigrada) – this is named Cryptovermes nov. An improved set of fossil calibrations was compiled and used to infer the divergence times of ecdysozoans under a range of alternative parameters. Crown-group Ecdysozoa diverged in the Ediacaran Period between 636 – 578 Ma, at least 23 million years before the oldest potential fossil evidence of ecdysozoans in the late Ediacaran (<556 Ma). Arthropods show more precision and less incongruence with the fossil record compared to other ecdysozoan phyla. Several vermiform (worm-like) fossils from the exceptionally preserved Cambrian Stage 3 Chengjiang Biota of Yunnan Province, south-western China were investigated to address the origin of Ecdysozoa and Panarthropoda in a morphological phylogenetic context. Phylogenetic analyses placed Acosmia maotiania in stem-group Ecdysozoa. Ancestral character state reconstructions revealed the similarities and contrasts between the stem-group ecdysozoan A. maotiania and a reconstruction of the common ancestor of crown-group Ecdysozoa. This reveals that pharyngeal teeth and circumoral armament are likely to be derived traits of the ecdysozoan crown-group, and may have 3 influenced the diversification of crown-group ecdysozoans – perhaps facilitating a change in feeding style (e.g. predation). The cycloneuralians Tabelliscolex hexagonus, Cricocosmia jinningensis and Mafangscolex yunnanensis (=Palaeoscolecidomorpha nov.) share several characters in common with lobopodian panarthropods. This includes paired, seriated ventral trunk structures, corresponding (in T. hexagonus and C. jinningensis) to seriated lateral/dorsolateral trunk sclerites with a net-like microstructure. However, phylogenetic analyses did not retrieve a relationship between palaeoscolecidomorphs and panarthropods, indicating that this style of morphological seriation may have multiple origins within Ecdysozoa. The lobopodian Facivermis yunnanicus is rejected as a model system to understand the acquisition a segmental bodyplan with paired appendages in Panarthropoda. Phylogenies generated here indicate that F. yunnanicus’ worm-like appearance is secondarily adapted from more typical lobopodian ancestors, as a result of adaptation to a specialised tube-dwelling suspension-feeding ecology. Finally, the phylogenetic relationships and divergence times of chelicerate arthropod groups were inferred, and interpreted in the context of arthropod terrestrialization. Phylogenetic analysis of a highly complete matrix of slowly evolving genes supports the monophyly of arachnids. Furthermore, it is parsimonious that the common ancestor of scorpions and other air-breathing arachnids was terrestrial – or at least amphibious – if arachnids are a monophyletic group. Molecular clocks estimate that arachnids diverged in the Cambrian or Early Ordovician, though body fossils of these arthropods are absent until the Silurian which supports the hypothesis of paleontologically cryptic early terrestrial biosphere – mirrored by the molecular and fossil records of myriapods and land plants. Scorpions are the oldest extant terrestrial chelicerate lineage in the fossil record, but is unclear whether the earliest Silurian examples were marine, terrestrial, or even secondarily marine in life

Integrating genomics with the fossil record to explore the evolutionary history of Echinoidea

Echinoidea constitutes one of five major clades of living echinoderms, marine animals uniquely characterized by a pentaradial symmetry. Approximately 1,000 living and 10,000 extinct species have been described, including many commonly known as sea urchins, heart urchins and sand dollars. Today, echinoids are ubiquitous in benthic marine environments, where they strongly affect the functioning of biodiverse communities such as coral reefs and kelp forests. Given the quality of their fossil record, their remarkable morphological complexity and our thorough understanding of their development, echinoids provide unparalleled opportunities to explore evolutionary questions in deep-time, providing access to the developmental and morphological underpinnings of evolutionary innovation. These questions cannot be addressed without first resolving the phylogenetic relationships among living and extinct lineages. The goal of this dissertation is to advance our understanding of echinoid relationships and evolutionary history, as well as to explore more broadly the integration of phylogenomic, morphological and paleontological data in phylogenetic reconstruction and macroevolutionary inference.In Chapter 1, I report the results of the first phylogenomic analysis of echinoids based on the sequencing of 17 novel echinoid transcriptomes. Phylogenetic analyses of this data resolve the position of several clades—including the sand dollars—in disagreement with traditional morphological hypotheses. I demonstrate the presence of a strong phylogenetic signal for these novel resolutions, and explore scenarios to reconcile these findings with morphological evidence. In Chapter 7, I extend this approach with a more thorough taxon sampling, resulting in a robust topology with a near-complete sampling of major echinoid lineages. This effort reveals that apatopygids, a clade of three species with previously unclear affinities, represent the only living descendants of a once diverse Mesozoic clade. I also perform a thorough time calibration analysis, quantifying the relative effects of choosing among alternative models of molecular evolution, gene samples and clock priors. I introduce the concept of a chronospace and use it to reveal that only the last among the aforementioned choices affects significantly our understanding of echinoid diversification. Molecular clocks unambiguously support late Permian and late Cretaceous origins for crown group echinoids and sand dollars, respectively, implying long ghost ranges for both. Fossils have been shown to improve the accuracy of phylogenetic comparative methods, warranting their inclusion alongside extant terminals when exploring evolutionary processes across deep timescales. However, their impact on topological inference remains controversial. I explore this topic in Chapter 3 with the use of simulations, which show that morphological phylogenies are more accurate when fossil taxa are incorporated. I also show that tip-dated Bayesian inference, which takes stratigraphic information from fossils into account, outperforms uncalibrated methods. This approach is complemented in Chapter 2 with the analysis of empirical datasets, confirming that incorporating fossils reshapes phylogenies in a manner that is entirely distinct from increased sampling of extant taxa, a result largely attributable to the occurrence of distinctive character combinations among fossils. Even though phylogenomic and paleontological data are complementary resources for unraveling the relationships and divergence times of lineages, few studies have attempted to fully integrate them. Chapter 4 revisits the phylogeny of crown group Echinoidea using a total-evidence dating approach combining phylogenomic, morphological and stratigraphic information. To this end, I develop a method (genesortR) for subsampling molecular datasets that selects loci with high phylogenetic signal and low systematic biases. The results demonstrate that combining different data sources increases topological accuracy and helps resolve phylogenetic conflicts. Notably, I present a new hypothesis for the origin and early morphological evolution of the sand dollars and close allies. In Chapter 6, I compare the behavior of genesortR against alternative subsampling strategies across a sample of phylogenomic matrices. I find this method to systematically outperform random loci selection, unlike commonly-used approaches that target specific evolutionary rates or minimize sources of systematic error. I conclude that these methods should not be used indiscriminately, and that multivariate methods of phylogenomic subsampling should be favored. Finally, in Chapter 5, I explore the macroevolutionary dynamics of echinoid body size across 270 million years using data for more than 5,000 specimens in a phylogenetically explicit context. I also develop a method (extendedSurface) for parameterizing adaptive landscapes that overcomes issues with existing approaches and finds better fitting models. While echinoid body size has been largely constrained to evolve within a single adaptive peak, the disparity of the clade was generated by regime shifts driving the repeated evolution of miniaturized and gigantic forms. Most innovations occurred during the latter half of the Mesozoic, and were followed by a drastic slowdown in the aftermath of the Cretaceous-Paleogene mass extinction

What CIOs and CTOs Need to Know About Big Data and Data-Intensive Computing

This paper was completed as part of the final research component in the University of Oregon Applied Information Management Master's Degree Program [see htpp://aim.uoregon.edu].The nature of business computing is changing due to the proliferation of massive data sets referred to as big data, that can be used to produce business analytics (Borkar, Carey, & Li, 2012). This annotated bibliography presents literature published between 2000 and 2012. It provides information to CIOs and CTOs about big data by: (a) identifying business examples, (b) describing the relationship to data-intensive computing, (c) exploring opportunities and limitations, and (d) identifying cost factors