Eric J Hilton
email: ehilton@vims.edu

Nalani K Schnell
email: nschnell@mnhn.fr.

Peter Konstantinidis
email: peterk@vims.edu

When Tradition Meets Technology: Systematic Morphology of Fishes in the Early 21 st Century

Many of the primary groups of fishes currently recognized have been established through an iterative process of anatomical study and comparison of fishes that has spanned a time period approaching 500 years. In this paper we give a brief history of the systematic morphology of fishes, focusing on some of the individuals and their works from which we derive our own inspiration. We further discuss what is possible at this point in history in the anatomical study of fishes and speculate on the future of morphology used in the systematics of fishes. Beyond the collection of facts about the anatomy of fishes, morphology remains extremely relevant in the age of molecular data for at least three broad reasons: 1) new techniques for the preparation of specimens allow new data sources to be broadly compared; 2) past morphological analyses, as well as new ideas about interrelationships of fishes (based on both morphological and molecular data) provide rich sources of hypotheses to test with new morphological investigations; and 3) the use of morphological data is not limited to understanding phylogeny and evolution of fishes, but rather is of broad utility to understanding the general biology (including phenotypic adaptation, evolution, ecology, and conservation biology) of fishes. Although in some ways morphology struggles to compete with the lure of molecular data for systematic research, we see the anatomical study of fishes entering into a new and exciting phase of its history because of recent technological and methodological innovations. With each new advance of technology and with each new generation of researcher, systematic morphology becomes a new and vibrant science.

[Morphology] is one of the most interesting departments of Natural History, and may almost be said to be its very soul. What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?

Charles [START_REF] Darwin | On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life[END_REF]Darwin ( [1958:403]:403]) T HERE is something intrinsically appealing in the anatomical form of fishes that has captured the human imagination, both from a scientific perspective as well as that of a general audience. For instance, Hemingway's (1952:70) protagonist in The Old Man and the Sea, Santiago, reflects that fishes "are not as intelligent as we who kill them, although they are more noble and more able," suggesting a reverence and appreciation for fishes that is found in many works of art, literature, and other aspects of culture and human thought. From both popular and scientific perspectives, part of this appeal, perhaps, is the complexity that is inherent in the anatomy of fishes. For the scientist, there is a large source of descriptive and comparative data in the skeleton of fishes alone. [START_REF] Grande | A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history[END_REF] note that there are more than 680 individual ossified bones (excluding scales, fin rays, teeth, etc.) in the skeleton of the holostean Amia calva. Variation in each of these elements carries with it the potential for phylogenetic information. While the skeleton of teleostean fishes is generally marked with reduction in number of elements, a conservative estimate for even taxa such as Tetraodontiformes, notoriously reductive in nature, puts this figure at over 230 bones or cartilages. Therefore, even the skeleton of the most paedomorphic or otherwise anatomically reduced taxa "provides effectively an infinite number of potential characters for analysis" (Grande and Bemis, 1998:ix). With this as a starting frame of reference, coupled with their taxonomic diversity-over 30,000 extant species and an unparalleled (among vertebrates) fossil record-fishes generally, and actinopterygians in particular, offer an endless source of intrigue for the morphologist and evolutionary biologist.

The purpose of this paper is two-fold. First, we give a brief history of the morphology of fishes and its impact in comparative morphology, focusing on some of the individuals and their works from which we derive our inspiration. This is not an exhaustive discussion, as there are numerous historical figures that are not included whose works we greatly admire and have contributed to our own development as morphologists (e.g., Edward Phelps Allis, 1851Allis, -1947)). It is our contention that no such historical review can be comprehensive, so we have rather picked and chosen among what we consider to be the highlights. Further, there are useful and important reviews that focus on various aspects of this history of morphological research on fishes from historical (e.g., [START_REF] Cuvier | Histoire naturelle des poissons[END_REF]see Pietsch, 1995) and contemporary times (e.g., many papers in [START_REF] Pietsch | Collection Building in Ichthyology and Herpetology[END_REF], as well as aspects of the science of morphology generally (e.g., [START_REF] Nyhart | Biology Takes Form[END_REF]. However, we feel that this history provides an important backdrop for where comparative morphological study of fishes currently lies and where it can go in the future. We use our own experiences with actinopterygian fishes as the basis for this discussion, but also note that modern morphology is relevant for the systematic study of other groups of fishes as well, including chondrichthyans (e.g., [START_REF] Carvalho | Comparative neurocranial morphology of angelsharks from the south-western Atlantic Ocean (Chondrichthyes, Elasmobranchii, Squatinidae): implications for taxonomy and phylogeny[END_REF][START_REF] Maisey | What is an 'elasmobranch'? The impact of palaeontology in understanding elasmobranch phylogeny and evolution[END_REF]Soares andCarvalho, 2013a, 2013b;[START_REF] Silva | Morphology and phylogenetic significance of the pectoral articular region in elasmobranchs (Chondrichthyes)[END_REF] and sarcopterygians (e.g., [START_REF] Northcutt | Cranial nerves of the Coelacanth Latimeria chalumnae (Osteichthyes: Sarcopterygii: Actinistia) and comparisons with other Craniata[END_REF][START_REF] Forey | History of the Coelacanth Fishes[END_REF][START_REF] Arratia | Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology[END_REF]. Our second goal for this paper is to discuss what is possible at this point in history in the anatomical study of fishes, and to speculate on the future of systematic morphology of actinopterygian fishes, which, to extend from the quotation from Darwin presented as the epigraph, forms the very soul of ichthyology.

THE MORPHOLOGICAL TRADITION

Historically, the basic framework of the classification and evolution of fishes has come from analysis of their morphology. Today, molecular data provides additional information, resolution, or in the very least additional testable hypotheses for various problematic taxa (e.g., Stylephorus; [START_REF] Miya | Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae)[END_REF], or helps to understand patterns within large groups of fishes (e.g., Alepocephaliformes; [START_REF] Lavoue | Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences[END_REF]. Recent broad scale phylogenetic analyses of actinopterygian fishes (e.g., [START_REF] Smith | Casting the percomorph net widely: the importance of broad taxonomic sampling in the search for the placement of serranid and percid fishes[END_REF][START_REF] Near | Resolution of ray-finned fish phylogeny and timing of diversification[END_REF][START_REF] Betancur-R | The Tree of Life and a New Classification of Bony Fishes[END_REF] have added to the understanding of the relationships of fishes, improving the resolution for unwieldy and seemingly intractable groups such as Percomorpha. However, it remains that many of the primary groups of actinopterygian fishes have been established through an iterative process of anatomical study and comparison of fishes that has spanned a time period approaching 500 years.

Through the effort of early workers, such as Pierre Belon (1517Belon ( -1564)), some of the basic groups of fishes (and animals generally) that are still accepted and considered valid today, were first described (e.g., in Belon's 1553 De aquatilibus, libre duo he identified Pleuronectiformes-his "Spiny oviparous fishes of a flat form"; [START_REF] Pietsch | Georges Cuvier's Historical Portrait of the Progress of Ichthyology, from Its Origins to Our Own Time[END_REF]. This was accomplished by personal observation of specimens. Also from the studies of Belon, we have the development of a formalized and systematic method for the homology of elements within the skeleton [START_REF] Belon | L'Histoire de la nature des oyseaux, avec leurs descriptions; & naı ¨fs portraicts retirez du naturel[END_REF]Fig. 1A). Hypotheses of homology, as the basic conceptual unit of morphology, provide the core point of discussion for comparative statements linking taxa through hypotheses of common ancestry. These hypotheses of homology are fundamental to all comparative works. Belon's image comparing the skeleton of a bird and that of a human can be seen as the basis for all that follows in comparative anatomy. Similar comparative figures to this adorn most published comparative studies since, and show, through visual connections, the hypotheses of homology that are being advanced. Simply, the images of specimens are at once both the raw data being presented for documentation and consideration, as well as the interpretation of "meaning" of the data. In a similar way, Geoffroy Saint-Hilaire (1772-1844) presented his views of the homology of the axial skeleton of vertebrates in a figure published in his Anatomical Philosophy (1818; Fig. 1B). By removing the appendicular skeletons from the specimens and arranging the skeletons in similar positions-unnatural in some cases (e.g., the tetrapods)-the similarities between the different taxa are immediately conveyed. Sir Richard Owen (1804Owen ( -1892) ) formalized the "similarity" that struck Belon and Geoffroy Saint-Hilaire, and introduced to biology the word "homology": "The same organ in different animals under every variety of form and function" (Owen, 1843:379). These similarities are the data that support homology statements. Without a doubt, the concept of homology is not that simple as evidenced by the volume of literature debating its meaning and nuance (see papers [START_REF] Hall | Homology. The Hierarchical Basis of Comparative Biology[END_REF]; also [START_REF] Remane | Die Grundlagen des natu ¨rlichen Systems, der vergleichenden Anatomie und der Phylogenetik[END_REF][START_REF] Remane | Morphologie als Homologienforschung[END_REF][START_REF] Rieppel | Similarity[END_REF]. However, homology is the basis for all comparative works, historical and modern.

Owen also advanced the concept of the archetype [START_REF] Owen | On the Archetype and Homologies of the Vertebrate Skeleton[END_REF]see Panchen, 1994), which provides a conceptual organization of the vertebrate bauplan (Fig. 1C). Although this form of idealistic morphology can mask and overly atomize particular structures, we do see some use in it as an organizing construct for approaching the morphology of fishes, particularly in studies of development. Further, the archetype provides a simplification of the body plan that allows for effective conceptualization of vertebrate anatomy, and a modern equivalent to Owen's depiction of the archetype is still used for its didactic value (e.g., Liem et al., 2001:fig. 7-3;Fig. 1D). The concept of an archetype was, in part, built upon generalities seen in nature and derived from embryology. Before Owen's introduction of the term homology and the concept of the archetype, Karl Ernst von Baer (1792Baer ( -1876) ) emphasized the importance of embryology (i.e., ontogeny). Through his broad zoological knowledge, he became aware of the importance of character transformation during ontogeny and described his "Four Laws of Embryology" [START_REF] Baer | U ¨ber Entwicklungsgeschichte der Thiere[END_REF] stating that 1) general characters develop before the more specific, 2) general relationships between elements develop before more specific relationships, 3) the anatomy of an embryo of a given taxon is not the same as that of other forms but rather separates itself from them, and 4) the embryo of a derived taxon never resembles the adult of an ancestral taxon, but rather its embryo. Although neither Owen nor Baer were approaching the anatomy of fishes (and vertebrates generally) from an evolutionary perspective, they provided these great insights in comparative morphology. From these laws, Ernst H. P. A. Haeckel (1834Haeckel ( -1919)), who was strongly influenced by Darwinian evolution, derived his Biogenetic Law [START_REF] Haeckel | von Charles Darwin reformirte descendenztheorie[END_REF]. This has famously and succinctly been restated as "ontogeny recapitulates phylogeny." Haeckel artistically illustrated his works to show the repeating patterns he saw in ontogeny, combining the beauty and scientific content of comparative anatomy (Fig. 2). These guiding principles inspired the works of those that followed, including such as Gegenbaur (1872, 1888), Fu ¨rbringer (1897), [START_REF] Goodrich | Studies on the Structure and Development of the Vertebrates[END_REF], de Beer (1937), and others. Notably, for instance, Charles Tate Regan (1878Regan ( -1943)), whose inroads into systematic ichthyology and the classification of fishes were based primarily in comparative osteology, understood and incorporated larval characters into his studies (e.g., [START_REF] Regan | Larval and post-larval fishes. British antarctic ("Terra Nova") expedition[END_REF]. However, until the proceedings of the ASIH Ahlstrom symposium were published [START_REF] Moser | Ontogeny and Systematics of Fishes[END_REF], the inclusion of larval fishes in morphological systematic studies to test homology and common ancestry remained scarce.

This interplay between ontogeny and phylogeny offers compelling support for evolution. It is therefore ironic that this support was greatly extended by a steadfast special creationist, Jean Louis Rodolphe Agassiz (1801-1878). Agassiz (1857; Fig. 3) conceptualized his so-called "threefold parallelism," in which he saw a reciprocal relationship between morphology, paleontology, and ontogeny. As pointed out by Grande and Bemis (1998), Agassiz's threefold parallelism (5"three-fold congruence" in modern terminology) actually included a fourth distinct line of evidence, biogeography: "Even now, some curious coincidences may be pointed out which go far to show that the geographical distribution of animals [5biogeography] stands in direct relation to their standing in their respective classes [5phylogeny], and to the order of their succession in past geological ages [5paleontology, or stratigraphy], and more indirectly, also to their embryonic growth [5ontogeny]" (Agassiz, 1857:120-121). Collectively, these four avenues of study offer explanation for the order observed in nature, and although Agassiz would deny it, evolution is the uniting principle among them [START_REF] Grande | A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history[END_REF]. Moreover, there is now a fifth source of information available-molecular data-that must be considered [START_REF] Grande | A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history[END_REF]), yet comparative anatomy remains a linking discipline for all these areas of evolutionary biology.

We would be remiss if we did not include discussion of the role that morphology plays in understanding the geological history of fishes, namely through the fossil record. More so than any other group of vertebrates, the preservation bias that fishes have because of their habitat (i.e., aquatic habitats are more likely to be fossiliferous than terrestrial habitats) has produced a long and important fossil record of fishes. Their study, however, and especially for actinopterygians, is disproportionately low relative to their abundance [START_REF] Grande | A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history[END_REF]. The so-called Stockholm School of paleoichthyology, centered around Erik Stensio ¨(1891Stensio ¨( -1984)), epitomizes the importance of the morphology of fishes not only for understanding the morphology of fossil forms in and of themselves but also for putting the fossil taxa into a broader context (e.g., see [START_REF] Stensio | Antaomical Studies on the Arthrodiran head. Part 1. Preface, geological and geographical distribution, the organization of the arthrodires, the anatomy of the head in the Dolichothoraci, Coccosteomorphi and the Pachyosteomorphi. Taxonomic appendix[END_REF]Fig. 4). Stensio ¨, and his students and fellow researchers such as Erik Jarvik and others approached the study of fossil fishes from the perspective of an anatomist, using the works of Allis (e.g., 1897Allis (e.g., , 1920Allis (e.g., , 1921) ) and others on extant fishes such as Polypterus, Polyodon, and Amia as guidance [START_REF] Schultze | The international influence of the Stockholm School[END_REF]. It is from this anatomical perspective, including a strong embryological and developmental perspective (e.g., [START_REF] Stensio | The sensory lines and dermal bones of the cheek in fishes and amphibians[END_REF], combined with painstaking preparation methods that Stensio ¨could extract such a high level of information from his fossils (Fig. 4). This Stockholm School had broad international influence during its heyday, and its influence persists through to the present day [START_REF] Schultze | The international influence of the Stockholm School[END_REF].

Ultimately, morphology of fishes has served as the basis of much of what is known about the evolutionary relationships among fishes, and these hypotheses of relationships are then translated into classifications. From the earliest stages of fish classifications, beginning with C. Linnaeus and P. Artedi moving through the reigns of G. Cuvier, L. Agassiz, J. Mu ¨ller, E. D. Cope, C. T. Regan, and others in late 19 th Century and early 20 th Century, when, of course, there was no alternative. Greenwood et al. (1966) in their synthesis of teleostean classification summarized some of this history. Some of the groups identified by Greenwood et al. (1966) have withstood the test of time, such as the Osteoglossomorpha and the Ostariophysi, specifically from a cladistic approach to analysis, while others have changed (e.g., the Myctophoidei). More importantly these authors offered discrete morphological characters as evidence for the groups they were proposing that served as a morphological fundament for future generations to come. This process is inherent in the progress of science. [START_REF] Wiley | A teleost classification based on monophyletic groups[END_REF] continue this process, now with an expanded literature including molecular analyses. Even with modern hypotheses from "modern" data sets, these authors never lose sight of the morphology of fishes and offer morphological characters supporting their classification.

CONTINUING THE TRADITION

Broadly based integrated studies have as their basis descriptive and comparative morphological data. Few, if any, descriptive studies, however, are pure descriptions (i.e., "morphology for morphology's sake") and are often related to a comparative (i.e., systematic or evolutionary) study. A basic tenet of systematic morphology is that there are more data to be gathered from every specimen. With each new specimen collected, prepared, examined, and analyzed, new data become available for inclusion in the total sum of knowledge of fishes. Further, different methods and different perspectives may lead to different interpretations of morphology. These different interpretations are, in turn, at the heart of the morphology of fishes.

The caudal skeleton of actinopterygian fishes, and in particular Teleostei, is the source of many phylogenetically informative characters (e.g., [START_REF] Patterson | Review of ichthyodectiform and other mesozoic teleost fishes nad the theory and practice of classifying fossils[END_REF][START_REF] Arratia | The caudal skeleton of Jurassic teleosts: a phylogenetic analysis[END_REF][START_REF] Schultze | The caudal skeleton of basal teleosts, its conventions, and some of its major evolutionary novelties in a temporal dimension[END_REF]Arratia, 2015, in this volume) because it offers such broad diversity across fishes [START_REF] Fujita | The Caudal Skeleton of Teleostean Fishes[END_REF] and is open to so many different interpretations (Fig. 5). As such, it provides a good example of how the systematic morphology of fishes can reach different conclusions regarding the "same" elements. By labeling in a figure or referencing an element in text as a hypural, for instance, there is a fundamental, implied hypothesis that a specific element is, in an evolutionary sense, the "same" hypural of another taxon. In basal teleosts there are typically two hypurals ventral to the diastema (h1 and h2) and a variable number of hypurals dorsal to the diastema (Fig. 5B), if one exists (e.g., see Fig. 5C). Frequently, and particularly in more derived taxa, there is only a single hypural ventral to the diastema (e.g., Fig. 5D-F), and this element loses its relationship to supporting centra or centrum, as these are often reduced or consolidated. This raises the question of what that single element represents when compared to the two ventral hypural condition found in more basal taxa. Is it an enlarged h1? Is it a fusion between h1 and h2? Does the fact that there is one element ventral to the diastema in one taxon and two in the other imply homology between the two conditions (i.e., the separate elements h1 and h2 in one taxon are equivalent to a combined h1+2)? Similarly, the parhypural may be also incorporated in this compound element; inclusion of the parhypural can be identified by the presence of a canal for the caudal vessels (Fig. 5F). Comparative ontogeny offers one potential determining factor, although often there is only a single cartilage found in this ventral position at all points in ontogeny (e.g., [START_REF] Hilton | Skeletal anatomy of the Shortnose Sturgeon, Acipenser brevirostrum Lesueur, 1818, and the systematics of Sturgeons (Acipenseriformes, Acipenseridae)[END_REF][START_REF] Konstantinidis | A comparative ontogenetic study of the tetraodontiform caudal complex[END_REF]Wiley et al., 2015, in this volume), resulting in a so-called "phylogenetic fusion" (see discussion of this phenomenon by Hilton, 2002:129-132). Topological relationships of the elements relative to other structures is another potential source of homology statements.

Highlighting the different possibilities in identification of hypurals serves as an example of the continued need for careful morphological analyses to explore such issues and the origin of different interpretations of anatomical structure. Recent studies of euteleostean fishes (e.g., [START_REF] Doosey | Epural bones in teleost fishes: a problem of phylogenetic homology[END_REF]Wiley et al., 2015, in this volume) further document the development of various skeletal elements (e.g., epurals) and discuss alternate ways of naming skeletal elements across phylogenetically disparate taxa. The presence of so-called "condensation fields" as precursors for cartilaginous structures in early development known from studies of the model organism Danio also offers new avenues for homology statements for the evolutionary anatomy of fishes [START_REF] Crotwell | Gene expression patterns underlying proximal-distal skeletal segmentation in late-stage zebrafish, Danio rerio[END_REF]Wiley et al., 2015, in this volume). The use of gene expression patterns to trace the homology of structures during development potentially offers a very powerful tool to add to the robustness of these hypotheses, although it is not yet commonly employed. Part of the problem derives from a general lack of communication between researchers working in broadly different fields, although there are a number of labs that are bridging historical divides between comparative and systematic morphology and developmental genetics. Online community resources, such as Phenoscape [START_REF] Mabee | 500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology[END_REF], the Teleost Anatomy Ontology [START_REF] Dahdul | The teleost anatomy ontology: anatomical representation for the genomics age[END_REF][START_REF] Dahdul | A unified anatomy ontology of the vertebrate skeletal system[END_REF], and the Zebrafish Information Network [START_REF] Bradford | ZFIN: enhancements and updates to the zebrafish model organism database[END_REF], offer potential mechanisms to bridge systematic morphology with research on the genetic underpinnings of morphology. [START_REF] Cass | Expression of a lung developmental cassette in the adult and developing zebrafish swimbladder[END_REF] provide a good example of the power of this approach in a study showing that the zebrafish swimbladder and the tetrapod lung share the same unique gene expression during development (although the onset time of some late genes is slightly altered). These authors conclude that the similarity of gene expression pattern is due to common ancestry. This only reiterates our thesis-there is still much to discover about the fundamental morphological structure of actinopterygian fishes generally.

PERSPECTIVES ON THE FUTURE OF MORPHOLOGICAL DATA COLLECTION FOR THE SYSTEMATICS OF FISHES

. . . get the anatomy wrong and the rest is meaningless. Stiassny et al., 1996:xii) From our perspective, the advancement of the field of morphology of fishes, and morphology generally, lies along three fronts: 1) development of new approaches and technology to understand anatomical structure more fully; 2) new hypotheses that can be critically examined with morphology, as well as revisiting hypotheses proposed in the literature; and 3) there are new reasons for studying the anatomy of fishes in descriptive, systematic, and comparative frameworks. Advancements in the field of morphology have been tied to advancements in the preparation of specimens. Alizarin staining for visualization of bone has been used since the early 1900s, and although by today's standards these early attempts at clearing and staining were rather primitive, their results added substantially to the understanding, for instance, of the development and structure of the caudal skeleton of teleostean fishes [START_REF] Hollister | Caudal skeleton of Bermuda shallow water fishes. I. Order Isospondyli: Elopidae, Megalopidae, Albulidae, Clupeidae, Dussumieriidae, Engraulidae[END_REF]. With the addition of trypsin clearing [START_REF] Taylor | An enzyme method of clearing and staining small vertebrates[END_REF] and alcian staining for cartilage (e.g., [START_REF] Dingerkus | Enzyme clearing of alcian blue stained whole small vertebrates for demonstration of cartilage[END_REF][START_REF] Potthoff | Clearing and staining[END_REF][START_REF] Taylor | Revised procedures for staining and clearing small fishes and other vertebrates for bone and cartilage[END_REF], new avenues, including observations on even earlier developmental stages (e.g., [START_REF] Walker | A two-color acidfree cartilage and bone stain for zebrafish larvae[END_REF], could be included in descriptive and comparative studies (Fig. 6D). Although precise data documenting the effect that clearing and staining as a method had on the field of morphology of fishes (e.g., number of papers employing these techniques following the publication of the protocols) would be difficult if not impossible to generate (because of such a scattered literature), it is generally held that these methodological improvements in the morphology of fishes have been the basis of an increase in the number of specimen-based studies and the ways researchers have used specimens (G. D. Johnson, pers. comm.). Indeed, there are many research programs that produce exquisite morphology through the use of clearing and staining, combined with modern microscopes with different optical capabilities, innovative cameras, new imaging software capabilities (e.g., Z-stacking, which produce microscopic images with increased depth of field) and new illustration techniques (e.g., recent examples include [START_REF] Arratia | Early ossification and development of the cranium and paired girdles of Chanos chanos (Teleostei, Gonorynchiformes)[END_REF][START_REF] Hilton | Skeletal anatomy of the Shortnose Sturgeon, Acipenser brevirostrum Lesueur, 1818, and the systematics of Sturgeons (Acipenseriformes, Acipenseridae)[END_REF][START_REF] Britz | Ontogeny and homology of the skeletal elements that form the sucking disc of remoras (Teleostei, Echeneoidei, Echeneidae)[END_REF][START_REF] Mattox | Skeletal development and ossification sequence of the characiform Salminus brasiliensis (Ostariophysi: Characidae). Ichthyological Exploration of[END_REF][START_REF] Carvalho | Development of the splanchnocranium in Prochilodus argenteus (Teleostei: Characiformes) with a discussion of the basal developmental patterns in the Otophysi[END_REF][START_REF] Kubicek | Developmental osteology of Sciaenops ocellatus and Cynoscion nebulosus (Teleostei: Sciaenidae), economically important sciaenids from the western Atlantic[END_REF]Johnson and Schnell, 2015, in this volume;Wiley et al., 2015, in this volume). Numerous modifications of the clearing-and-double-staining protocols exist adapted to the specific needs, e.g., the use of ethanol solutions of alizarin red instead of a KOH-alizarin solution dye for staining bone in fishes in order to preserve skeletal muscles [START_REF] Springer | Use and advantages of ethanol solution of alizarin red S dye for staining bone in fishes[END_REF][START_REF] Datovo | Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis[END_REF][START_REF] Datovo | The infrabranchial musculature and its bearing on the phylogeny of percomorph fishes (Osteichthyes: Teleostei)[END_REF]. Complementary methodological developments including the whole-mount staining of nerves [START_REF] Freihofer | The sihler technique of staining nerves for systematic study especially of fishes[END_REF][START_REF] Filipski | Sudan black-B as a nerve stain for whole cleared fishes[END_REF][START_REF] Song | Clearing and staining whole fish specimens for simultaneous demonstration of bone, cartilage, and nerves[END_REF] offer extensions to clearing and staining, and insight into homology and the systematic morphology of fishes [START_REF] Parenti | Phylogenetic significance of the pectoral-pelvic fin association in acanthomorph fishes: a reassessment using comparative neuroanatomy[END_REF]Nakae and Sasaki, 2004;[START_REF] Kenaley | Comparative innervation of cephalic photophores of the loosejaw dragonfishes (Teleostei: Stomiiformes: Stomiidae): evidence for parallel evolution of long-wave bioluminescence[END_REF][START_REF] Schnell | New insights into the complex structure and ontogeny of the occipito-vertebral gap in Barbeled Dragonfishes (Stomiidae, Teleostei)[END_REF]. Similar "revolutions" are seen also in paleoichthyology, with the development of acid preparations of [START_REF] Toombs | The use of acids in the preparation of vertebrate fossils[END_REF], as perfected by [START_REF] Grande | A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history[END_REF] and [START_REF] Grande | An empirical synthetic pattern study of gars (Lepisosteiformes) and closely related species, based mostly on skeletal anatomy: the resurrection of Holostei[END_REF]; unfortunately, this method of preparation is applicable for relatively few fossil taxa, as clearing and staining is practical for fishes up to a certain size. Although large specimens can be cleared and stained and important morphological data can be derived uniquely from such specimens, this process can be time intensive (e.g., two or more years for 25 cm specimens of Elops sp. and 50 cm specimens of Chanos sp.; G. Arratia, pers. comm., 2015). Therefore, for the study of numerous large specimens, radiography is much more convenient.

Colin Patterson (attributed to him by

X-ray computed tomography (i.e., CT scanning) was first used in the morphology of fishes on a specimen of Latimeria chalumnae (Schultze and Cloutier, 1991). Ten years later, the use of CT scanning for studying the morphology of fishes was further refined and used in the study of a fossil chondrichthyan (Maisey, 2001a) and the inner ear morphology of elasmobranchs (Maisey, 2001b). Since that time, advances in technology and computing power let CT scanning and the resulting three-dimensional digital renderings of hard structures (i.e., bones; Fig. 7) to become a widely used tool in the systematic morphology of fishes (and vertebrates generally). It since has been successfully applied to a number of fossil and living fishes representing a broad taxonomic breadth, including stem gnathostomes [START_REF] Giles | Osteichthyan-like cranial conditions in an Early Devonian stem gnathostome[END_REF], elasmobranchs (Maisey, 2001a(Maisey, , 2001b[START_REF] Maisey | Morphology of the braincase in the Broadnose Sevengill Shark Notorynchus (Elasmobranchii, Hexanchiformes), based on CT Scanning[END_REF][START_REF] Pradel | Skull and brain of a 300 million-year-old fish revealed by synchrotron holotomography[END_REF][START_REF] Mollen | Comparative morphology of rostral cartilages in extant mackerel sharks (Chondrichthyes, Lamniformes, Lamnidae) using CT scanning[END_REF][START_REF] Moyer | Development and microstructure of tooth histotypes in the Blue Shark, Prionace glauca (Carcharhiniformes: Carcharhinidae) and the Great White Shark, Carcharodon carcharias (Lamniformes: Lamnidae)[END_REF], basal sarcopterygians [START_REF] Snitting | A redescription of the anatomy of the Late Devonian Spodichthys buetleri Jarvik, 1985 (Sarcopterygii, Tetrapodomorpha) from East Greenland[END_REF][START_REF] Boisvert | The humerus of Panderichthys in three dimensions and its significance in the context of the fishtetrapod transition[END_REF], polypterids [START_REF] Claeson | New interpretations of the skull of a primitive bony fish Erpetoichthys calabaricus (Actinopterygii: Cladistia)[END_REF]Claeson and Hagedorn, 2008), catostomids [START_REF] Fink | Morphological description of the extinct North American Sucker Moxostoma lacerum (Ostariophysi, Catostomidae), based on high-resolution x-ray computed tomography[END_REF], gymnotiforms [START_REF] Carvalho | Redescription and phylogenetic position of the enigmatic Neotropical electric fish Iracema caiana Triques (Gymnotiformes: Rhamphichthyidae) using x-ray computed tomography[END_REF][START_REF] Maxime | Redescription of the Tuvirao, Gymnotus inaequilabiatus Valenciennes, 1839, using high-resolution x-ray computed tomography[END_REF], siluriforms [START_REF] Rodiles-Herna ´ndez | Lacantunia enigmatica (Teleostei: Siluriformes) a new and phylogenetically puzzling freshwater fish from Mesoamerica[END_REF]Claeson et al., 2008;[START_REF] Lundberg | Phylogenetic position and notes on the natural history of Pimelabditus moli Parisi & Lundberg, 2009 (Teleostei: Siluriformes), a recently discovered pimelodid catfish from the Maroni River basin[END_REF][START_REF] Lundberg | A tomographic osteology of the taxonomically puzzling catfish Kryptoglanis shajii (Siluriformes, Siluroidei, incertae sedis): description and a first phylogenetic interpretation[END_REF]Lundberg and Luckenbill, 2015, in this volume), lophiiforms [START_REF] Pietsch | A new genus and species of the shallow-water anglerfish family Tetrabrachiidae (Teleostei: Lophiiformes: Antennarioidei) from Australia and Indonesia[END_REF][START_REF] Chanet | Visceral anatomy of ocean sunfish (Mola mola (L., 1758), Molidae, Tetraodontiformes) and angler (Lophius piscatorius (L., 1758), Lophiidae, Lophiiformes) investigated by noninvasive imaging techniques[END_REF], fundulids [START_REF] Parenti | Osteology identifies Fundulus capensis Garman, 1895 as a killifish in the family Fundulidae (Atherinomorpha: Cyprinodontiformes)[END_REF], kurtids [START_REF] Carpenter | Swim bladder and posterior lateral line nerve of the nurseryfish, Kurtus gulliveri (Perciformes: Kurtidae)[END_REF], anarhichadids (Bemis and Bemis, 2015, in this volume), and molids [START_REF] Chanet | Visceral anatomy of ocean sunfish (Mola mola (L., 1758), Molidae, Tetraodontiformes) and angler (Lophius piscatorius (L., 1758), Lophiidae, Lophiiformes) investigated by noninvasive imaging techniques[END_REF]. CT scanning also has been applied successfully to questions of functional morphology and other aspects of the morphology of fishes. For instance, this technique has been the basis of biomechanical studies of jaws of durophagous elasmobranchs [START_REF] Summers | Structure and function of the horn shark (Heterodontus francisci) cranium through ontogeny: development of a hard prey specialist[END_REF], the functional properties of cranial sutures in Polypterus [START_REF] Markey | In vivo cranial suture function and suture morphology in the extant fish Polypterus: implications for inferring skull function in living and fossil fish[END_REF], and the feeding mechanics of seahorses [START_REF] Van Wassenbergh | Mechanics of snout expansion in suctionfeeding seahorses: musculoskeletal force transmission[END_REF]. CT scanning has in some ways replaced the more time consuming histology, although the latter is unparalleled regarding its resolution. As technology has improved, CT scanning has extended to smaller and smaller individuals, such that high-resolution x-ray CT scanning (HRXCT) is becoming the state of the art. For example, [START_REF] Lundberg | A tomographic osteology of the taxonomically puzzling catfish Kryptoglanis shajii (Siluriformes, Siluroidei, incertae sedis): description and a first phylogenetic interpretation[END_REF] used HRXCT to examine the enigmatic miniature catfish Kryptoglanis shajii. This study produced remarkable images of a 65 mm SL individual. These fishes are rare, and this methodology allows for nondestructive sampling of morphological data. A study published nearly simultaneously [START_REF] Britz | Osteology of Kryptoglanis shajii, a stygobitic catfish (Teleostei: Siluriformes) from Peninsular India with a diagnosis of the new family Kryptoglanidae[END_REF] that was based on a single 60 mm SL cleared-and-stained individual of the same species produced anatomical similar results and conclusions-the morphology of this species was highly peculiar and in many ways unlike other catfishes. This example provides a testament to the power of morphology-independent studies coming to similar conclusions using different methodology and technology.

We see parallels to the so-called "clearing and staining revolution" (G. D. Johnson, pers. comm.) in recent developments of new approaches to the morphology of fishes, such as whole mount immunohistochemistry for tracing the early development of muscles (Fig. 6C). This technique allows the incorporation of broader taxonomic sampling for comparative and ontogenetic myology than was possible until recently. Immunohistochemistry, such as antibody staining of developmental series, has the potential to resolve long standing questions of homology, as shown in [START_REF] Konstantinidis | Same but different: ontogeny and evolution of the musculus adductor mandibulae in the Tetraodontiformes[END_REF] on the homology of the different portions of the adductor mandibulae in Tetraodontiformes. Tetraodontiformes are known for their complex jaw musculature particularly in the case of the adductor mandibulae (Fig. 8). Some monacanthids have up to eight and some pufferfishes up to six partitions. In comparison, generalized percomorphs have only four partitions of the adductor mandibulae. If ontogenetic material and/or a sufficient technique are not available, other criteria provide the only evidence of homology. However, [START_REF] Konstantinidis | Same but different: ontogeny and evolution of the musculus adductor mandibulae in the Tetraodontiformes[END_REF] were able to demonstrate that the traditional indicators for homology, such as the origin and insertion of muscle partitions as well as function, do not reflect their developmental origin and therefore their homology.

No preparation method should be used exclusively and in isolation, and between this method and other recent advances in visualization of soft tissues, such as confocal microscopy of labeled muscles [START_REF] Konstantinidis | Same but different: ontogeny and evolution of the musculus adductor mandibulae in the Tetraodontiformes[END_REF]Fig. 8), micro-CT scanning (Fig. 6A, B; Metscher, 2009aMetscher, , 2009b;;Konstantinidis et al., 2015, in this volume), magnetic resonance imaging or MRI (e.g., [START_REF] Perry | Quantification of red myotomal muscle volume and geometry in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis) using T 1 -weighted magnetic resonance imaging[END_REF][START_REF] Runcie | Evidence for cranial endothermy in the opah (Lampris guttatus)[END_REF][START_REF] Chakrabarty | Evolution of the light organ system in ponyfishes (Teleostei: Leiognathidae)[END_REF]see Berquist et al., 2012 andThe Digital Fish Library, 2015), and others, we predict a similar advance in the myology of fishes as that which took place in the late 1970s and early 1980s when clearing and staining became more commonly applied. In 30 to 40 years, it may be as common and "easy" to acquire myological data as it is now to acquire osteological data. This stands in contrast to the difficult and time consuming, yet elegant, dissection-based collection of myological data (e.g., [START_REF] Springer | Study of the dorsal gill-arch musculature of the teleostome fishes, with special reference to the Actinopterygii[END_REF][START_REF] Datovo | The infrabranchial musculature and its bearing on the phylogeny of percomorph fishes (Osteichthyes: Teleostei)[END_REF]. We predict, therefore, that in the future there will be an increase in new muscular (and other soft-tissue) characters in phylogenetic data sets. Advances in preparation of specimens are being matched by advances in imaging techniques [START_REF] Lauridsen | Inside out: modern imaging techniques to reveal animal anatomy[END_REF]. Given the large size of the data files generated from all of these modern imaging methods, accessible repositories such as MorphoBank (O'Leary and Kaufmann, 2011; MorphoBank, http://www.morphobank. org/index.php/Home/Index, Accessed: 1 June 2015) and Digimorph (http://digimorph.org/, Accessed: 1 June 2015) are becoming increasingly important.

Given such advancements in data acquisition, it should not be surprising that there has been a similar advancement of novel hypotheses and reexamination of previously proposed hypotheses regarding the systematic relationships of fishes using morphological data. Some of these novel hypotheses regarding the comparative anatomy of fishes (e.g., hypotheses of homology, i.e., synapomorphy) have come from morphological investigation of relationships initially proposed by molecular analysis (e.g., a paracanthopterygian relationship of Stylephorus; [START_REF] Miya | Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae)[END_REF][START_REF] Grande | Limits and relationships of Paracanthopterygii: a molecular framework for evaluating past morphological hypotheses[END_REF]. Our intent is not to critically examine any individual example here, but rather to point out that this process (called "pseudomorphology" by some; Mooi and Gill, 2010) is, in principle, no different than examining and comparing the morphology of fishes in light of hypotheses of relationships based on different morphological studies, historical or current. Data are data, and interpretations of these data can be-and should be-evaluated in the context of all data available [START_REF] Dillman | The cause and effect of polarization: thoughts on the "morphological vs. molecular debate" in systematics, with examples from the study of sturgeons (Actinopterygii: Acipenseridae)[END_REF].

Past morphological analyses provide rich sources of hypotheses to test with new morphological data. The phylogenetic placement of the Stomiiformes for example has changed significantly over the past 50 years. Greenwood et al. (1966) placed them as a suborder within the Salmoniformes. [START_REF] Rosen | Interrelationships of higher euteleostean fishes[END_REF] and [START_REF] Fink | Relationships of the stomiiform fishes (Teleostei), with a description of Diplophos[END_REF] reanalyzed stomiiform interrelationships and considered this group sister to the Eurypterygii and placed them as a separate order of the Neoteleostei. This placement is still the currently accepted hypothesis, although recent molecular studies recover the Stomiiformes as sister to Osmeriformes [START_REF] Lo ´pez | Esociform phylogeny[END_REF][START_REF] Li | Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci[END_REF][START_REF] Li | Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleostean fishes[END_REF][START_REF] Betancur-R | The Tree of Life and a New Classification of Bony Fishes[END_REF]. Synapomorphies such as the retractor dorsalis muscle shared by the Stomiiformes and all other neoteleosts are striking, but nonetheless there is morphological evidence found in early life history stages of stomiids (e.g., the development of the gill arches and the caudal skeleton) that suggest that the ontogeny of Stomiiformes needs to be further scrutinized [START_REF] Doosey | Early development of the caudal fin skeleton of Capelin, Mallotus villosus (Osmeridae)[END_REF]Schnell and Johnson, unpubl. data). Simply, hypotheses from the literature-whether based on morphological or molecular data-must be reconsidered (supported or refuted) in light of new anatomical data generated by new generations of morphologists.

Finally, the use of morphological data is not limited to understanding phylogeny and evolution of fishes. Personally this is what we find most attractive and compelling for our own research in morphology. However, morphology is the first line of understanding alpha-taxonomic diversity. Further, morphology contributes to understanding the interaction fishes have with their environment, as an organism's anatomy can be the basis for understanding many aspects of its behavior and ecology (i.e., the interrelated approaches of ecomorphology, functional anatomy, and biomechanics). Such subfields of morphology can have meaningful implications for elements of conservation biology (i.e., understanding how an organism uses its environment can be predicted based on morphological analysis). The dimensions of these aspects to which morphology can contribute will only become more diverse as new questions arise, such as how the ontogeny and osteology of teleostean larvae are impacted by environmental changes like ocean acidification (Schnell and Clemmesen, unpubl. data). Recognition of deviation from the normal ontogeny for a taxon can be recognized and greatly informed by an appreciation and understanding of the systematic anatomy of early life history stages.

CONCLUSIONS

But the progress of science needs not only the rare genius who in one leap covers a large step in the ascent to the summit but also the slow, continuous walkers, pushing up in small steps.

Richard Goldschmidt (1956:181) Morphology, in its strictest sense, is inherently an observational science: the analysis of form is, in its essence, a discussion of facts related to the structure of an organism. Once comparisons are made, however, there are elements of hypothesis-driven science. Ultimately, the strengths and relevance of morphology in the modern comparative biology of fishes lie in the fundamental fact that a thread can be found tying everything in comparative biology of fishes to morphology. Said another way, all facets of comparative biology-no matter what level of organization-can find their roots in morphology. This is because morphology is a broad discipline, each sub-disciple having different goals and different purposes but that all can relate to any level of the phenotype, from cellular to behavioral. In particular, morphology has a unique place in both the history and future of systematic ichthyology, and continues to grow with each new technological advance. With each new generation it returns to become a new and vibrant science.

Fig. 1 .

 1 Fig. 1. Illustrations from the early history of the morphology of fishes, showing concepts of homology and archetypes. (A) Illustration from Belon (1555; modified from Grande, 2010:fig. 557) showing homology of the vertebrate skeleton. (B) Illustration from Geoffroy Saint-Hilaire (1818) showing homology among the axial skeletons of vertebrates. Image courtesy of T. W. Pietsch. (C) The archetype of the vertebrate (Owen, 1849; also used by Owen, 1848). (D) Conceptualized/simplified schematic of the vertebrate head; modified from Liem et al. (2001:fig. 7.3) by William E. Bemis.

Fig. 2 .

 2 Fig. 2. Illustration from Haeckel's Antropogenie oder Entwicklungsgeschichte des Menschen (1877). The image shows early ontogenetic stages of four mammals (human, bat, cat, and sheep). Although not directly associated with the biogenetic law, the illustration clearly yet artistically shows Haeckel's hypothesis of repeating ontogenetic stages across phylogeny.

Fig. 3 .

 3 Fig. 3. Title page of Agassiz (1857) in which he outlined his views on the congruence between comparative anatomy, embryology, stratigraphy, and biogeography.

Fig. 4 .

 4 Fig. 4. Illustrations showing a specimen (A, B) and reconstructions (C-G) of the head of the coccosteomorph arthrodire {Tapinosteus heintziStensio ¨, 1959. From Stensio ¨(1963:pl. 7 figs. 2, 3, and figs. 70, 76, 47, 71A, 62A, respectively).

Fig. 5 .

 5 Fig. 5. Caudal skeletons of actinopterygian fishes, showing different numbering schemes and inferences of homology. (A) Amia calva, VIMS 19093. (B) Hiodon alosoides, UMA F10592. (C) Channa argus, VIMS 19091. (D) Astroscopus guttatus, VIMS 19094. (E) Caranx crysos, UMA F11596. (F) Zaprora silenus, VIMS 19093. Scale bars equal 10 mm. Anatomical abbreviations: h, hypural; phy, parhypural. Institutional abbreviations: UMA, University of Massachusetts Amherst; VIMS, Nunnally Ichthyology Collection, Virginia Institute of Marine Science.

Fig. 6 .

 6 Fig. 6. Different morphological techniques used in early ontogenetic stages of the paddlefish, Polyodon spatula. (A, B) Reconstructions of a micro-CT scan. (A) Reconstruction of musculature (red) and skeletal structures (blue and gray) with an overlay of the actual CT scan. (B) Reconstruction as a standalone model. (C) Image of the cranial musculature stained with an antibody specific for muscle tissue. (D) Classical clearing-and-staining method for skeletal structures (bone stained red, cartilage stained blue). Scale bars equal 0.5 mm.

Fig. 7 .

 7 Fig. 7. Computed tomography images of sturgeons. (A) Dorsal and (B) ventral views of the skull of Huso huso (MCZ 54269). (C) Dorsal and (D) ventral views of the skull of Scaphirhynchus platorynchus (FMNH 45024). (E) Dorsal and (F) ventral views of the skull of Pseudoscaphirhynchus kaufmanni (UAIC 13265.01). Institutional abbreviations: FMNH, Field Museum of Natural History; MCZ, Museum of Comparative Zoology, Harvard University; UAIC, University of Alabama Ichthyology Collection. Scale bars equal 1 cm.

Fig. 8 .

 8 Fig. 8. Confocal microscopy of antibody stained specimens of tetraodontiform fishes showing early stages of development of cranial musculature. (A-C) Ontogenetic series of Balistapus undulatus. (D) An unidentified monacanthid larva. (E, F) Two different stages of the freshwater pufferfish Monotrete suvattii. Abbreviations represent different muscle portions of the musculus adductor mandibulae.

Copeia 103, No. 4, 2015

ACKNOWLEDGMENTS

We take this opportunity to thank those friends, mentors, and colleagues who (among others) have encouraged our own appreciation of the morphology of fishes, and especially Gloria Arratia, William E. Bemis, Ralf Britz, Bruce B. Collette, Peter L. Forey, Lance Grande, Matthew Harris, G. David Johnson, John G. Lundberg, and John E. Olney. We thank Ted W. Pietsch for supplying an image of the plate from Geoffroy Saint-Hilaire (1818), and William E. Bemis for giving us access to his copy of Owen (1848) for photographing. We thank Matthew Colbert, Jennifer Olori, and Stephen Roberson (Digimorph) for providing scans and image processing of specimens used in Figure 7. We thank Gloria Arratia and G. David Johnson for inviting us to contribute to this symposium and this volume and for their continued patience during the writing of stage of the manuscript. This is contribution number 3496 of the Virginia Institute of Marine Science, College of William & Mary.


Juliette Marais

Syed Ali Kazim

Zaynab El Mawas

Maan El

Badaoui El Najjar

Jeremy Skelton

Contributions to the development of safe and accurate localisation solutions: The LOCSP project

Keywords: Localisation, Cooperative localisation, GNSS, Multi-sensor data fusion, autonomous vehicles 1

GNSS are now in everybody's pocket, embedded in our smartphones and is widely used for informative uses (navigation, leisure…). In future transportation modes, and in particular autonomous vehicles or for safety related railways applications, localisation needs to be accurate and/or safe and trustful. In many of the environments crossed by users, satellite signal propagation is disturbed by buildings, trees or other obstacles that degrade performance. To contribute to the development of safe and accurate localisation solutions in these environments, the LOCSP project intends to evaluate and compare past algorithms on a new shared database but also focuses on the development of two research proposals: through cooperative vehicle localisation using artificial intelligence and with interference mitigation. This paper aims to introduce the project and the first results on these two axes.

Introduction

Revolution of the transportation systems, evolving toward autonomous cars or trains in a world where digitalizatio n will be everywhere, implies the development of a panel of embedded technologies among which localisation and communication are key elements. In this framework, the LOCSP project focuses on the localisation function and in particular for accurate and safe positions. Indeed, the new positioning solutions shall provide on one hand the minimu m accuracy required by the application (road level, track identification, position of the vehicle on a track…) and, on the other hand, ensure the user that the position can be trusted through the development of integrity monitoring solutions.

However, if satellite-based localisation solutions (GNSS -Global Navigation Satellite Systems) are largely deployed in every day's life, it is well-known and investigated that their performance suffer from propagation disturbances in most of the land transport environments and in particular in urban areas, where buildings mask or reflect signals before their reception. The detection and mitigation of multipath and Non -Line of Sight signals (signals received only after reflection) are largely studied solutions as done by [START_REF] Groves | A portfolio approach to NLOS and multipath mitigation in dense urban areas[END_REF] or [START_REF] Hsu | Analysis and modeling GPS NLOS effect in highly urbanized area[END_REF]. Based on observables, thanks to external sensors (cameras or Lidar), or more recently with Machine Learning algorithms, the panel of solutions tested is quite large. In order to enhance accuracy but also availability in land transport environments, some numerous solutions, as reviewed by [START_REF] Yeong | Sensor and sensor fusion technology in autonomous vehicles: A review[END_REF], also focus on multi-sensor hybridization in order to benefit from the advantages of heterogeneous sensors and mitigate their drawbacks for a better accuracy and reliability. Hybridization can also benefit from cooperation of several vehicles of a fleet. Indeed, in multi-vehicle system, collaborative localization (CL) can be applied by fusing between the proprioceptive (odometer, inertial centre, Gyroscope…) and exteroceptive (GNSS, vision, LASER range finder…) sensors and others information sources (2D/3D cartographical information system) in order to optimize the position estimation. One of the existing techniques consists in the fact that each vehicle detects the others and calculates relative observations leading to an improvement in the localization integrity of the overall system and in autonomous navigation safety in different situation like intersection and overtaking specially in urban and peri-urban areas. Last, let's mention the increase of interference phenomena, named jamming, that need to be considered if the system developed has to be robust in any environment.

The LOCSP is funded in order to contribute to these developments of safe and accurate localisation solutions in these harsh land transport environments. This paper will present the main results of the LOCSP project that is at its middle term. Two main topics are addressed in particular in this paper: fault tolerant data fusion and cooperative solutions, and interference detection and mitigation. After a brief presenta tion of the project and the methodology followed, main highlights of these two scientific topics will be presented before conclusion.

2.

Methodol ogy

The LOCSP project, started in 2020 and funded by the French National Research Agency (ANR) intends to contribute to the development of positioning algorithms capable of computing a position in nominal conditions of reception as well as in the presence of faults. The faults targeted will be system failures, multipath and interferences. The capacity of the system to detect and mitigate these faults is investigated through different research directions and evaluated based on a realistic database under construction extracted from measurements and simulations. The project is a 4 years project, started in 2020. The project aims to answer the two following high-level challenges: 1/ propose new research solutions for a fail-safe positioning and 2/ allow everyone to benefit from a complete and detailed database for evaluation of the different solutions.

Therefore, different tasks are progressing in parallel. The project will contribute on three main directions. The two scientific directions are introduced in the paper:

• First, on fault tolerant data fusion and cooperative solutions. It consists in developing a framework for Fault Detection and Exclusion (FDE) as done by Makkawi (2021) for a Collaborative Localisation (CL) of a mult ivehicle fleet, equipped with multi-sensors solutions. First results will show the distributed architecture selected, and introduce a hybrid diagnostic methodology based on both models and data by Harbaoui (2021). An overview of the progress on a digital twin development for dataset generation will be proposed.

• Second, LOCSP investigates the different techniques for interference detection and mitigation, evaluates and compares their respective performance. In particular, we will investigate the capacity of these different techniques to face RFI and in particular, the one from RAIM algorithms (Receiver Autonomous Integrity Monitoring) as well as the behaviour of fusion algorithms in a PhD work. An illustration of advantages and drawbacks of first precorrelation signal processing techniques (Notch Filters and Continuous Wavelet Transform) to detect and remove interference signals will be proposed.

The third work axis aims to provide a reference database, composed as a representative set of crossed environments (rural, urban, forests) and feared events (multipath, reflected paths, interferences…). It intends to answer the need to evaluate and compare our algorithms but also allow the community to do so, on a shared database. Most of the data will be collected along experimental campaigns, but will also be complemented with simulated data thanks to the STELLA NGC tool suite. First datasets will be presented during the TRA presentation. This database will be the basis for evaluation of the scientific contributions proposed but also shall allow everyone (scientific and industrial communities) to compare performance of positioning solutions on a common frame.

3.

Cooperati ve vehicles localisation using artificial intelligence

Fault detection in a collaborative scheme

The developed approach for fault detection, originally based on information theory as done by Al Hage, ( 2017) is stochastic and non-deterministic. Its main interest is the diagnosis of the vehicle localisation solution via the fault detection and exclusion (FDE) method but for a decentralised cooperative localisation. It is based on the fact that all sensors are prone to errors. They can be represented as gaussian distributions of sensor data whose means are the output of the sensor at the acquisition time and whose variance is obtained by the specification of the technology used in the sensor. Each observation data is fused with all the different non-faulty observations of the environment in order to produce a much more accurate and safe solution. In this work, the novelty of the approach is the use of AI algorithms to enhance the detection of errors by information theory.

This hybrid approach tends to compare the measure of dissimilarity between the distribution of observations, in order to identify the divergent solution and exclude it from the fusion step and declare its sensor as faulty for the ongoing iteration. It uses the diagnosis model generated by learning the different patterns of fault from scenarios provided by the DT and the model-based approach applied through the data acquisition and filtering for the on -going trajectory. In doing so, the safety and the tolerance to faults are increased in the system. That makes the system more available even in faulty cases, giving the most accurate solution it can provide regardless of the case that the vehicle is in. The proposed approach for each vehicle of the system is presented in Fig. 1. It starts by the data reception at each iteration, followed by the filtering and fusion of data, and ends by the diagnosis of the obtained solution in order to exclude faulty sensors and provide the final accurate and safe localisation solution.

A Digital Twin for supporting datasets

The development of a multi-autonomous cooperative connected (MACC) vehicle's localisation solution requires the adequate dataset composed of data for several vehicles and sensors simultaneously. Moreover, in order to be exhaustive, many trajectory and fault scenarios should be considered. This is done by the deployment of a Digital Twin (DT) system, which constitutes the main data provider and testing environment for the Artificial Intelligence (AI) method. The DT is composed of two parts: a hardware in the loop component with a GNSS signal simulato r coupled with a simulated environment. The DT provides the data entry of the GNSS signal simulator. They consist in GNSS data (KML, Rinex files, pseudoranges …).

The main benefits of using a DT are the capacity to inject real localisation dat a provided by a real GNSS receiver in a virtual simulated environment, that also contains additional sensors such as wheel encoders, Lidar, IMU. As a result, the AI generated models from simulated scenarios become more accurate as they are processed back to the virtual environment. Moreover, by comparing the result of the two solutions , simulated and real environment, the difference between the real world and the virtual environment data is minimised, leading to a more realistic result. This tool also allows the generation of multiple scenarios having sensor failures with fault injection on real and simulated sensor measurements without creating dangerous test situations and without damaging the real prototype vehicles. These scenario trajectories can be created in a continuous way in a very short time for the generation of measurements databases for a significant number of kilometres that is hard to do in a real environment. The DT developed in the CRIStAL Lab is presented in Fig. 2, where the GNSS simulator Stella NGC of M3Systems is coupled with the environment simulator CARLA, and the data acquisition is done via ROS (Robot Operating System) platform.

First results

The results of this method for a team of three MACC is presented in Fig. 4. In this example, the three vehicles are tb3 robots equipped with indoor localisation sensor Marvelmind providing (x,y) coordinates, IMU providing orientation, encoders for evolution model and Lidar for inter-measurement providing interdistance and bearing angle. The results show that the localisation solution is improved by excluding the detected faulty sensors using the presented me thod, whereas for robot1, the localisation error decreased in x-axis by 97,6116% and y-axis by 99,0558% after isolation. More numeric comparison is provided in Table I. with the Root Mean Square Deviation (RMSD) before and after isolation. There are a significant number of interference incidents reported in the past decade around the world. The main contributor behind these incidents includes spill over signals from the radio systems operating close or within the GNSS band and illegal transmissions to deliberately disturb or detract the receiver. These large numbers of reported incidence confirm RFI as an existing threat to GNSS services. Therefore, it still demands robust solutions to counter interference to meet performance requirements.

The LOCSP contribution on this topic will be a step towards the development of an interference managemen t suite with improved strategies to ensure the resilience of the overall system. It will require robust countermeasures that will incorporate strategies for the detection, characterization, mitigation, and in some cases localization of RFI signals.

Context

In literature, there exist several methodologies to detect and mitigate various types of interference signals (pulsed, continuous wave and chirp signal). Figure 2 shows interference suppression applied at different stages of the receiver chain. They are mainly grouped as the front-end, pre-correlation, post-correlation, and navigation level techniques. This study deals with the interference mitigation at the pre-correlation level prior to satellite signal dispreading process. This early stage mitigation could be beneficial especially dealing with strong interferences since techniques in the later stages require normal acquisition and (or) tracking which cannot be guaranteed under such conditions. The interference suppression techniques at the pre-correlation level have been well investigated in the literature. Pulse blanking (PB) is among the simplest time domain technique. [START_REF] Musumeci | A comparative analysis of adaptive notch filtering and wavelet mitigation against jammers interference[END_REF] applied pulse blanking method to suppress interference coming from DME/TACAN system. [START_REF] Borio | Swept GNSS jamming mitigation through pulse blanking[END_REF] used PB method to mitigate wideband interference signal. [START_REF] Qin | An Assessment of Impact of Adaptive Notch Filters for Interference Removal on the Signal Processing Stages of a GNSS Receiver[END_REF], [START_REF] Gamba | Performance comparison of FLL adaptive notch filters to counter GNSS jamming[END_REF] and [START_REF] Borio | A multi-state notch filter for GNSS jamming mitigation[END_REF] studied different Adaptive Notch Filter (ANF) designs, filter parameters affecting mitigation performance while dealing with time -varying frequency of the interference signal also known as chirp interference. Borio (2008) investigated Wigner-Ville Distribution (WVD) to estimate the instantaneous frequency of the interference then the interference content is suppressed with the help of the notch filter. [START_REF] Musumeci | Use of the wavelet transform for interference detection and mitigation in global navigation satellite systems[END_REF][START_REF] Borio | Swept GNSS jamming mitigation through pulse blanking[END_REF], [START_REF] Huang | A GNSS Receiver Interference Suppression Technique based on Wavelet Packet Transform[END_REF], [START_REF] Seo | Performance of Interference Mitigation with Different Wavelets in Global Position ing Systems[END_REF] presented wavelet decomposition method to counter chirp and DME/TACAN interference.

These studies suggest the importance of robust countermeasures to eliminate the effects of interference. It also highlights the fact that the performance of any mitigation technique is very much dependent on the characteristics of interference signal such as power, modulation, bandwidth and others as concluded by [START_REF] Musumeci | Use of the wavelet transform for interference detection and mitigation in global navigation satellite systems[END_REF]. All these factors make it very much difficult to have a signal mitigation technique to deal with any kind of interference.

First results

First investigations done in the context of the project concern the suppression of the unwanted signal before the acquisition of the satellites, i.e., at pre-correlation stage.

Two methods have been implemented and tested: the adaptive Notch Filter and the Wavelet decomposition. Adaptive Notch filter (ANF) comprises of an adaptive block that is responsible to track the frequency of the interference signal and derives the notch position of a notch filter (NF) to remove the unnecessary frequency content. Wavelet Packed Decomposition (WPD) is a transformation domain technique that maps a time signal into timefrequency domain. It performs transformation by doing correlation with seve ral candidate functions derived from the mother wavelet by applying shift and scaling operations. Despite most of the papers published evaluate the mitigation performance at the signal level, we consider that it is of particular interest to evaluate how the mitigation applied will affect the user KPIs, and in particular accuracy and integrity, that is a measure of trust the user can have in the position provided.

Kazim (2022) has presented KPI results of three scenarios; 1) without interference, 2) with interference but no mitigation applied and 3) interference with active mitigation technique and the performance indicators such as accuracy, availability and integrity are analysed. The results show, as expected, that interferences when they are not mitigated, can have a bad impact on the availability of the system. Additionally, they c ause hazardous misleadin g information (HMI) which questions the integrity of the provided solution. But they also show that a good mitigatio n scheme allows from one side to is capable of increasing accuracy but also remove all the HMI which is of main importance for safety related applications.

Fig 3 . show some of the initial results from the implemented adaptive notch filter. We can see interference has a noticeable impact on the carrier to noise ratio (CN0) of the satellites. Generally, a minimum of 18 dB is required to ensure successful tracking of the satellites. The impact on the position due to very low CN0 is also visible that diverges for a static scenario while inducing a maximu m positioning error of 80 meter. After applying the mitigation technique, the signal quality improves (successfully acquired satellites with higher CN0) so as the position accuracy (points are more concentrated around the true position).

Conclusion and future works

The TRA event will be the opportunity to show the intention and first results of the LOCSP project, being at that time in the middle of its length. A first open dataset will be presented composed of GNSS data, but also images, inertial sensors and a reference trajectory. A first set of results will be available on the two scientific topics (cooperative localisation and interference mitigation). Next steps of the project will consist of completing the dataset, and last year of the project will be used for the definition of KPIs for performance comparison between different types of solution, from the simplest and cheapest (GNSS only without any help) to more complex solutions such as hybrid and/or cooperative solutions.

Fig. 1 .

 1 Fig. 1. T he Fault detection and exclusion (FDE) applied for one vehicle.

Fig. 2 .

 2 Fig. 2.. Digital T win for sensors measurements replaying and database generation for learning The generated scenarios constitute training and test cases for the development of a deep learning algorithm specifically deployed for the detection of simultaneous errors given the pattern of fault in the system. The model generated by the DT is then validated on the real vehicle platform (Renault ZOE robotized car), whose sensor data and configuration is compatible with its DT in the simulated environment. It is also compatible with the GNSS simulato r data entry in order to inject faults and compare the so lution obtained by the simulator and the behaviour of the developed algorithm in real case scenarios. The equipped sensors and the hardware implementation over the CRIStAL Lab experimental vehicle are presented in Fig. 3.

Fig. 3 .

 3 Fig. 3. T he Renault ZOE robotised car with the onboard sensors.

Fig. 4 .

 4 Fig. 4. T rajectory before and after exclusion of faulty sensors.

Fig. 2 .

 2 Fig. 2. Block diagram of a typical SatNav receiver inspired by Morales-Ferre (2020). The different stages of the GNSS receiver are shown where interference effects could be suppressed.

Fig. 3 .

 3 Fig. 3. Interference detection and mitigation. a/Spectrogram of the input signal (GNSS+IT F), b/Signal to noise ratio of satellites acquired c/Estimated position, no mitigation (upper panel) and after suppressing interference by Adaptive notch filter (bottom panel).

Acknowledgements

The present work has been performed in the framework of the ANR French Research Age ncy within the project LOCSP No 2019-CE22-0011


N Alharbi

M Alharbi

X Martinez

M Krone

A Rose

M Baaden

R S Laramee

M Chavent

Molecular Visualization of Computational Biology Data: A Survey of Surveys

Keywords:

Figure 1: List of surveys presented in this article indicating their time span, number of cited references per year, total number of references, and the ratio of papers coming from the Computational Biology (CB) and Computer Visualization (CV) fields respectively. If a paper refers to both types (CB and CV) of references for a same year, the cell is divided in two rows of different color. The collage to the right illustrates the scales covered by the visualizations in these surveys, ranging from small molecules over protein complexes to whole cells (screenshots made with UnityMol [DCP * 14], MegaMol [GKM * 15, KBE09], NGL Viewer [RH15, RBV * 16] (norovirus example), and CellVis [FKE13]).

Introduction and Motivation

In computational biology-comprising bioinformatics, molecular modeling, and structural biology-visualization is an important means to gain insight into molecular structures and their dynamics. Due to its demanding nature, visualizing molecular data has always been tightly linked to computer hardware development Levinthal [Lev66]. Originally, papers describing advances in molecular visu-alization were welcomed by the whole scientific community and published in journals with a broad audience such as Science Langridge et al [START_REF] Langridge R | Real-time color graphics in studies of molecular interactions[END_REF]. More recently, scientific fields have become more specialized, resulting in focused scientific communities publishing in dedicated journals. This fragmentation can lead to paradoxical situations where visualization challenges may be published in one type of journal while the solutions may appear in another.

With this first survey of surveys (SoS), we reunite the communities by describing both questions posed by the computational biology community and answers provided by (or new challenges for) the visualization community. This work provides, for newcomers and experienced researchers, a unique and concise perspective presenting state-of-the-art literature in molecular visualization.

Survey Scope: Our team of authors consists of experts in both scientific visualization and computational biology. We have selected 11 survey papers spanning both fields. We focused on literature reviews addressing the rapidly expanding fields of structural biology and molecular modelling with a focus on spatio-temporal simulation data. For readers interested in a broader view of visualizing biological data, we refer to O'Donoghue et al ). As a useful introduction to the links between molecular simulation and visualization, we discuss the review by Hirst et al. [HGB14]. As our literature selection covers a large time span, we focus on the last fifty years from the mid-sixties to 2016 (see Figure 1).

Survey of Surveys

In this section we describe each review and group them by main common themes such that closely related surveys are together. Details about references cited and literature time span are depicted in Figure 1.

Introduction to Molecular Visualization and Simulation

Hirst et al. [HGB14]

propose an overview of the recent literature on molecular simulation and visualization. They highlight the increasing importance of Human-Computer Interaction (HCI) and virtual reality in the molecular visualization context. This survey introduces a series of articles dedicated to molecular visualization. This review contains 107 citations covering 20 years of research with about two thirds of the citations referring to computational biology work and one third to computer science papers.

Visualization of Molecular Structures

O'Donoghue et al. [OGF * 10] review visualization methods and tools that enable the community of structural biologists to gain insight into macromolecular structures. This report covers an extensive list of web-based and stand-alone tools and discusses the advantages and disadvantages of the most common molecular structure acquisition techniques. The review covers 28 years of scientific literature containing 125 references, almost exclusively related to works published in the biological and experimental communities.

Goddard et al.

[GF07] discuss developments and challenges in visualization of molecular structure to better understand molecular systems such as Depth Perception, Level of Detail (LoD), 2D and abstract representations. This review focuses on 14 years, citing 36 papers, of which 5 are from computer science.

The recent state-of-the-art report by Kozlíková et al. [KKF * 16] proposes an extensive review of visualizing biological data covering a wide range of spatial scale from atoms to cells. The authors pay particular attention to molecular surface rendering with an interesting chronological perspective on visualization of the solvent excluded surface. Numerous challenges evoked by Goddard et al. [GF07] are addressed in this review such as LoD or the effective representation of dynamical data. This review covers more than fifty years of scientific research referring to 203 articles. These references are well balanced between computational biology and computer science literature.

Detection and Visualization of Cavities

While the previous selection of surveys discusses how it is possible to render a structure, here we present two reviews highlighting detection, visualization, and analysis of molecular cavities. These cavities are often important for the proper function of a molecule. This task is especially difficult as it needs to visualize voids which have to be well defined and detected. * 13] review programs that identify, visualize, and analyse protein voids. As the shape of the void may have an impact on the technique used to detect it, the authors compare different tools to assess which one is the best for a dedicated type of space. The review spans 39 years of literature, presenting a majority of articles published in computational biology journals. * 16] detail the technical background of the algorithms. Their report also covers visualization methods for cavities. The authors present the definition and the classification of cavities. They classify the methods according to the underlying algorithms or the type of cavity definition. This study constitutes a very comprehensive review, spanning 30 years and citing 112 papers. The ratio of computer science to computational biology related papers is about one third.

Brezovsky et al. [BCG

Complementary to Brezovsky et al., Krone et al. [KKL

GPU Computing

With the developments of programmable graphics cards in the early 2000's, development of new algorithms that harness this relatively new computing power are evolving rapidly.

Chavent et al. [CLK * 11] focus on studies that redesign traditional algorithms to exploit GPUs. This survey covers techniques that display small molecules up to macromolecular assemblies, and discusses visual effects to enhance molecular structure perception. It covers 34 years of research and cites 47 papers almost equally balanced between computer science and computational biology.

Even though it is not completely focused on visualization, we mention a closely related review from Stone et al. [START_REF] Stone | Gpu-accelerated molecular modeling coming of age[END_REF] discussing the development of GPU-computing to accelerate molecular simulations. This work covers 24 years of research and refers to 54 papers predominantly from computer science. Note that some of the previously cited reviews also discuss GPU computing (e.g. The review by Secrier et al. [START_REF] Secrier | Visualizing time-related data in biology, a review[END_REF] discusses the visualization of biological processes at different time scales. This survey reviews time-dependent biology visualization tools by categorizing them into seven groups based on their time scale: molecular level (nanoto micro-seconds), gene level (micro-seconds/hours), network level (micro-seconds/days), cellular level (hours/days), level of an organism (days/weeks), population level (billions of years) and evolutionary scales (multiple levels). This review covers 21 years and cites 115 references with 9 computer science papers.

Challenges in Computational Biology

Computational biology is evolving very quickly, thus, new challenges appear regularly. Here, we highlight two recent reviews that outline challenges in computational biology. For computer scientists, these reports can inspire future research directions. For computational biologists, these reports cover the latest state-of-the-art.

Chavent et al.

[CDS16] discuss the advances in molecular simulations of membrane proteins with a focus on protein-lipid interactions and modelling complex membranes at different scales. At the nanoscale resolution, simulations are used to predict and investigate fine lipid-protein interactions. Beyond the nanoscale, it is necessary to model very large and crowded systems requiring significant computing power. Reaching time-scales probed in experiments will require the development of new types of models. This review covers very recent work (the last 11 years), almost exclusively from the computational biology field. * 16] explore the modelling of biological systems at different scales. They discuss how to move from one scale to another while simultaneously maintaining a high resolution to develop meaningful models. The next big challenge is to reach the cell scale and combine models with experimental data. This survey covers a long time span (up to 53 years) and is constituted by 223 references, mostly from the computational biology field.

Im et al. [ILO

From Text to Information: Meta-analysis of the Reviews

We perform a meta-analysis of all eleven surveys based on reference origins (CB or CV), shared references, and extracted keywords. These analyses yield new comparisons and insights not available from simply reading each paper separately.

Methods: To construct Figures 1 and2, we extract the references from the Scopus database [Sco] and analyze them using in-house Python scripts. For Figure 1, the references are curated by us to define which category a reference belongs to. Briefly, if the reference was published in an ACM, IEEE or related conference and journal it is categorized as a computer visualization paper, otherwise it was tagged as a 'computational biology' paper. This category is kept very simple due to the paper format. We also investigated the concordance of important words across the surveys using the Natural Language Toolkit [START_REF] Bird | Nltk: The natural language toolkit[END_REF] and Python scripts (see supplementary material for more details). Figure 3 shows a parallel coordinates plot that highlights the most represented words for each survey and a word cloud generated using the script by Müller [Mue].

References as a Function of Time

Figure 1 shows that the selected reviews focus mainly on the last 25 years, even though some highlighted works were published before 1980. There is an imbalance between references from the CV and CB fields. The latter is clearly more represented. There is of course an intrinsic bias, as selected reviews are more from computational biology (9: [GF07, OGF * 10, SHUS10, CLK * 11, BCG * 13,SS13,HGB14,CDS16,ILO * 16]) than pure data visualization (2: [KKF * 16, KKL * 16]). Nevertheless, at least three of them ( [SHUS10, CLK * 11, HGB14]) are focusing on molecular graphics or algorithms development, which counter-balances the ratio to 6:5. Furthermore, even the reviews published in the scientific visualization field cite numerous computational biology papers. To explain this imbalance, we hypothesize that the technical orientation of CV papers and the dissemination through very dedicated conferences may prevent some researchers of being aware of these studies. Recent initiatives such as the VizBi [Viz] and BioVis [Bio] conference series may help to highlight work from computer visualization researchers. Another reason may be that, even if some CV papers are published in journals, some papers are only published as conference proceedings and may not be referenced in scientific article databases such as PubMed [Pub] commonly used by CB researchers. This situation may cause large parts of CV research to be almost invisible to the CB community. Some CB journals also publish methods dedicated to molecular visualization and analysis such as Journal of Molecular Graphics and Modeling, Journal of Computational Chemistry, PloS Computational Biology etc. This topical intersection may create some competition with journals dedicated to computer science.

Shared References

These surveys share several references (see radial representation in supplementary material). Figure 2 presented an Ambient Occlusion method applied to molecular visualization. This paper also describes a software application, the molecular viewer QuteMol. Thus, making computer graphics research available, even just as prototype, is a key step to highlight CV researchers' work. Another good example is the fast QuickSurf molecular surface visualization by Krone et al. [START_REF] Krone | Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories[END_REF], which was published at a major visualization conference but was also made available in the popular molecular visualization tool VMD. This makes the method widely known in both fields, as can be seen in the number of citations as well as the usage and feedback by CB researchers. Three references shared by the selected reviews are survey papers: [OGF * 10, SHUS10, Goo05] with two of them discussed in section 2. The last paper mentioned discusses the combination of molecular visualization and 3D printing [GSSO05]. The number of shared references in the selected survey is in very good agreement with the overall number of citations for each paper. We observe one clear outlier: the NAMD program for Molecular Dynamics simulations [PBW * 05] which is important for creating dynamic models but is out of the scope of these surveys.

Text Analysis

We performed a text analysis using the parallel coordinates plot depicted in Figure 3. An interactive version of the plot is available as supplementary material to allow interested readers to further investigate the data we collected for our survey. The interactive parallel coordinates plot is a useful way of exploring themes throughout the surveys. The user can exploit mouse motion to observe trends in the collecton of text over time. For example, if we hover the mouse over 'cavity' we can see that it is a popular topic in the surveys, i.e. [BCG * 13] and [KKL * 16]. Another example is with the term 'lipid' which reoccurs often in [CDS16, ILO * 16] but is never mentioned previously, with the exception of Brezovsky et al. [BCG * 13] , but only twice in the references. This may indicate an emerging important visualization topic. In contrast to the interactive plot that can show correlations or concordances between the individual surveys, the word cloud presented in Figure 3 gives a static overview of the most important keywords. This figure highlights biological topics (such as protein, cell, ligand, membrane, molecule, lipid) or a part of it (channel, cavities, atom, structure, tunnel) that can be interpreted as important application fields for CV reserachers. Some words are related to 3D objects (points, grid, surface, sphere) describing the essential graphical primitives used to render molecular objects. Some are potentially related to biological processes (binding, interact) which are important to analyse and visualize.

Solved Problems and Future Challenges

Visualizing molecular structures and models is one of the first analysis steps every computational biologist takes to assess their results. A broad spectrum of tools are available to visualize objects ranging from protein structure to cavities both as static items or dynamical data sets. Recent advances in GPU computing improve the efficiency and the quality of the rendering. Nevertheless, molecular visualization remains challenging due to the increasing amount of simulation data [KKF * 16]. First, dealing with models that can expand on different scales both in terms of structure [GF07, OGF * 10, CLK * 11, ILO * 16] and time [SS13, KKF * 16, OGF * 10] is not yet solved. This type of visualization needs to be coupled with other methods to grasp the full complexity of molecular systems. Thus, there is a need for real time 3D annotation [CLK * 11] and filtering [KKL * 16]. These visualization advances may be combined with HCI and VR [HGB14, OGF * 10] to help the user immerse in the system. Automating rendering and analysis [BCG * 13] and storing the result for further analyses [CDS16] will be equally important. Finally, a huge gap still exists between CV and CB posing the challenge to turn innovations developed by computer visualization researchers into useful tools for computational biologists [GF07] and making the respective CV publications visible to the CB field. As elucidated by the QuickSurf example in section 3, making novel visualization methods available in existing open-source tools is a solution and a rewarding way to foster exchange between the two communities, even if it may require additional implementation effort. We think that this target will require further collaboration between the communities. Our survey of surveys is an important step in this direction.

  Goddard and Ferrin [GF07], Hirst et al. [HGB14], Krone et al. [KKL * 16] and Kozlíková et al [KKF * 16]). Visualizing Time-dependent Biological Data Improved rendering efficiency now enables visualization of dynamical systems. Several reviews discuss this topic. O'Donoghue et al. [OGF * 10] present different tools to render molecular motions. Kozlíková et al. [KKF * 16] dedicate a full section to the visualization of molecular dynamics data.

Figure 2 :

 2 Figure 2: The most common references shared by our 11 selected surveys.The two papers cited in bold print are included in our selection. We only displayed papers shared by at least 3 surveys. On top of each bar is the number of citations for each paper. Blue: computational biology papers; Red: scientific visualization paper.

  shows that the most shared references are associated with software (VMD [HDS96], Chimera [PGH * 04], NAMD [PBW * 05], and CAVER [POB * 06]). Only one reference comes from the CV field: Tarini et al. [TCM06]

Figure 3 :

 3 Figure 3: Result of the text analysis. Left: Parallel coordinate plot displaying the collective concordance of the most frequent words in each survey. Right: Word cloud based on the collective concordance ranking. We categorized the keywords based on our expertise in both fields (category shown by color; blue: computational biology keywords; red: scientific visualization keywords; grey: neutral keywords).

  [OGG * 10]. The literature reviews cover selected, related topics: visualization of molecular structures (Goddard and Ferrin [GF07], Kozlíková et al. [KKF * 16]) and software dedicated to this task (O'Donoghue et al. [OGF * 10]), advances based on Graphics Processing Units (GPUs) (Chavent et al. [CLK * 11], Stone et al. [SHUS10]), detection and analysis of cavities in proteins (Brezovsky et al. [BCG * 13], Krone et al. [KKL * 16]), time-dependent biological data (Secrier and Schneider [SS13]), and new challenges in molecular modelling leading to new visualization questions (Chavent et al. [CDS16], Im et al [ILO * 16]

Acknowledgments

We would like to thank the Ministry of Education of Saudi Arabia and the Saudi Cultural Bureau in London for financial support. We would also like to thank the Department of Computer Science at Swansea University for their support. MK was partially funded by German Research Foundation as part of SFB 716. Finally, we would like to thank Liam McNabb, Dylan Rees and Dave Greten for proof-reading the paper.