Xiphosurids are an archaic group of aquatic chelicerate arthropods, generally known by the colloquial misnomer of 'horseshoe crabs'. Known from marine environments as far back as the early Ordovician, horseshoe crabs are generally considered 'living fossils'descendants of a bradytelic lineage exhibiting little morphological or ecological variation throughout geological time. However, xiphosurids are known from freshwater sediments in the Palaeozoic and Mesozoic; furthermore, the contention that xiphosurids show little morphological variation has never been tested empirically. Attempts to test this are hampered by the lack of a modern phylogenetic framework with which to explore different evolutionary scenarios. Here, I present a phylogenetic analysis of Xiphosurida and explore patterns of morphospace and environmental occupation of the group throughout the Phanerozoic. Xiphosurids are shown to have invaded non-marine environments independently at least five times throughout their evolutionary history, twice resulting in the radiation of major cladesbellinurines and austrolimulidsthat occupied novel regions of morphospace. These clades show a convergent ecological pattern of differentiation, speciation and subsequent extinction. Horseshoe crabs are shown to have a more dynamic and complex evolutionary history than previously supposed, with the extant species representing only a fraction of the group's past ecological and morphological diversity.

The chemical composition of fossil soft tissues is a potentially powerful and yet underutilized tool for elucidating the affinity of problematic fossil organisms. In some cases, it has proven difficult to assign a problematic fossil even to the invertebrates or vertebrates (more generally chordates) based on often incompletely preserved morphology alone, and chemical composition may help to resolve such questions. Here, we use in situ Raman microspectroscopy to investigate the chemistry of a diverse array of invertebrate and vertebrate fossils from the Pennsylvanian Mazon Creek Lagerstätte of Illinois, and we generate a ChemoSpace through principal component analysis (PCA) of the in situ Raman spectra. Invertebrate soft tissues characterized by chitin (polysaccharide) fossilization products and vertebrate soft tissues characterized by protein fossilization products plot in completely separate, non‐overlapping regions of the ChemoSpace, demonstrating the utility of certain soft tissue molecular signatures as biomarkers for the original soft tissue composition of fossil organisms. The controversial problematicum Tullimonstrum, known as the Tully Monster, groups with the vertebrates, providing strong evidence of a vertebrate rather than invertebrate affinity.

Implied weighting, a method for phylogenetic inference that actively seeks to downweight supposed homoplasy, has in recent years begun to be widely utilized in palaeontological datasets. Given the method's purported ability at handling widespread homoplasy/convergence, we investigate the effects of implied weighting on modelled phylogenetic data. We generated 100 character matrices consisting of 55 characters each using a Markov Chain morphology model of evolution based on a known phylogenetic tree. Rates of character evolution in these datasets were variable and generated by pulling from a gamma distribution for each character in the matrix. These matrices were then analysed under equal weighting and four settings of implied weights (k = 1, 3, 5, and 10). Our results show that implied weighting is inconsistent in its ability to retrieve a known phylogenetic tree. Equally weighted analyses are found to generally be more conservative, retrieving higher frequency of polytomies but being less likely to generate erroneous topologies. Implied weighting is found to generally resolve polytomies while also propagating errors, resulting in an increase in both correctly and incorrectly resolved nodes with a tendency towards higher rates of error compared to equal weighting. Our results suggest that equal weights may be a preferable method for parsimony analysis.

The monophyly of the class Xiphosura is critically re-examined. For the first time a phylogenetic analysis of a number of synziphosurine and xiphosurid taxa is performed together with representatives of the other chelicerate orders also included as ingroup taxa. Xiphosura as currently defined is shown to be paraphyletic, and a revised classification is presented. Previous characteristics used to unite the xiphosurids (possessing a fused thoracetron) and a paraphyletic grade of synziphosurines (retaining freely articulating opisthosomal tergites) include the presence of a cardiac lobe, ophthalmic ridges, an axial region of the opisthosoma, and a reduced first opisthosomal segment. All of these characteristics are, however, here shown to be present in other chelicerate groups, leaving Xiphosura without any defining synapomorphies. A number of other characters, including the form of the chelicerae and appendage VII, indicate that xiphosurans may be paraphyletic with respect to a clade consisting of chasmataspidids, eurypterids, and arachnids. What ramifications this has for the evolution of basal chelicerates is briefly discussed, and it is recognized that most of the currently known 'synziphosurine' taxa represent offshoots from the main chelicerate lineage with ghost ranges extending into at least the Middle Ordovician.