Conserved patterns of axogenesis in the panarthropod brain

Neuropils in the cerebral midline of Panarthropoda exhibit a wide spectrum of neuroarchitectures – from rudimentary to highly elaborated – and which at first sight defy a unifying neuroarchitectural principle. Developmental approaches have shown that in model arthropods such as insects, conserved cellular and molecular mechanisms first establish a simple axon scaffold in the brain. However, to be adapted for adult life, this immature ground plan is transformed by a developmental process – known in the grasshopper as “fascicle switching” – in which subsets of neurons systematically redirect their growth cones at stereotypic locations across the brain midline. A topographic system of choice points along the transverse brain axis where axons decussate features in all panarthropods studied even though different modes of neurogenesis and varying degrees of neuropilar elaboration are involved. This suggests that the molecular mechanisms regulating choice point selection may be conserved. In combination with recent cladistic interpretations of arthropod phylogeny based on nuclear protein-coding sequences the data argue for this topographic decussation as having evolved early and being a conserved feature of the Panarthropoda. Differences in elaboration likely reflect both the extent to which neuropilar reorganization has progressed during development and the lifestyle of the individual organism.     

Tardigrades — Are They Really Miniaturized Dwarfs?

Tardigrades are animals of small body size which is often regarded to be a secondary phenomenon. This interpretation makes sense in the traditional concept that tardigrades are closely related to Onychophora, Euarthropoda and Annelida. A large body size in the ancestor of this common taxon (Articulata) is probable. Small size and the absence of organs such as a dorsal heart, segmental coelomic cavities and metanephridia must then be interpreted as derived in tardigrades. However, when Cycloneuralia are taken as an outgroup instead of Annelida (taxon Ecdysozoa), an interpretation of small body size as a primary feature is plausible. This also accounts for the absence of heart, coelom and nephridia.The choice of outgroup influences hypotheses about sister-group relationships within Panarthropoda, with either Onychophora (Articulata-concept) or Tardigrada (Ecdysozoa-concept) being basal.     

Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda

Onychophora or velvet worms are of considerable importance in current reconstructions of animal phylogeny. Despite their otherwise conservative morphology, the detailed anatomy of the onychophoran ovary displays significant variation. However, the evolutionary significance of this variation is not well understood. We recognize three major ovarian types in the Onychophora: (1) the exogenous ovary; (2) the pseudoendogenous ovary; and (3) the endogenous ovary. The germ cells in all three ovarian types are intraepithelial in that they occur between the basal lamina and the epithelial cells that line the cavity of the gonad. This is the condition found in the endogenous ovary. Even in the exogenous ovary, with stalked oocytes projecting into the haemocoel, the maturating oocytes are still covered by a basal lamina. Stalked oocytes that are similar to those found in the exogenous ovary, but retain their intra‐ovarian position, characterize the pseudoendogenous ovary. This and additional observations support the assumption that the pseudoendogenous ovary is derived from an exogenous type and the similarities with the endogenous ovary are superficial. Embryological data and an outgroup comparison with arthropods suggest that the exogenous ovary is the ancestral condition in velvet worms and a synapomorphy of Onychophora and Arthropoda. The embryonic origin, growth, and position of oocytes outside the ovarian lumen in Onychophora and various groups of Arthropoda do not support the Articulata hypothesis, which proposes a sister‐group relationship of Panarthropoda and Annelida.     

The relationships of mammals

A cladistic analysis generates alternative hypotheses regarding both the origin and the interrelationships of mammals to those most widely accepted at the present time. It is proposed that the tritylodontids are more closely related to mammals than is Probainognathus ; that the non-therian mammals do not constitute a monophyletic group; and that the monotremes are related to the modern therians, the ear ossicles among other characters having evolved only once. The multituberculates may be related to the monotremes.
It is argued that the current views are variously based on an overemphasis of superficial dental similarities, misinterpretation of the structure of the mammalianbraincaseand too readyacceptance of parallel evolution amongstthe groups concerned. The hypotheses proposed here are apparently much more parsimonious.     

The Mouth Cone and Mouth Ring of Echiniscus viridissimus Peterfi, 1956 (Heterotardigrada) with Comparisons to Corresponding Structures in Other Tardigrades

The mouth cone and mouth ring of the tardigrade Echiniscus viridissimus are described and their primary homology is assessed by comparing them to structures considered to be homologous in other heterotardigrades, eutardigrades, and ecdysozoans. In E. viridissimus the mouth cone is divided into anterior and posterior regions that differ in the ultrastructure of their cuticle. The mouth ring of the buccopharyngeal apparatus lies just anterior to the buccal tube. It is connected to it by a narrow flange or ridge of cuticle that allows the rostral end of the mouth tube to telescope part way into the mouth ring. Sensilla innervating the mouth cone and mouth ring in E. viridissimus correspond to sensilla of the circumoral and suboral sensory regions described for eutardigrades. The sensory fields, of both the mouth cone and mouth ring, exhibit two planes of mirror image or biradial symmetry. Although the relative dimensions of mouth ring differ markedly between E. viridissimus and eutardigrades, homologous areas can be identified easily. For example, the supporting rods of the mouth ring in E. viridissimus appear to be homologous to the supporting plates in the lamellae of eutardigrades. The widespread occurrence of the mouth cone and mouth ring in hetero- and eutardigrades suggests that these structures were present in the last common ancestor of all tardigrades. Expression of these characters in other ecdysozoans is more problematic. Tentatively the mouth cone and mouth ring are considered to be homologous to the circumoral plates of onychophorans and the ring of radiating plates found in the ‘Peytoia’ apparatus of Cambrian arthropods. These structures are not thought to be homologous to the introverts of scalidophorans or the circumoral structures of nematodes or nematomorphs, and are considered to be absent in these taxa. Thus, the mouth cone and mouth ring are potentially key synapomorphies for Panarthropoda.     

The relationships of the Tritylodontidae (Synapsida)

From a detailed anatomical survey of the Tritylodontidae, it is possible to examine the phylogenetic status of this taxon of advanced synapsids. The Tritylodontidae are considered to be the sister-group of the Traversodontidae, specifically the Exaerelodon-Massetognathus assemblage, rather than that of the Mammalia plus Tritheledontidae as recently postulated. Numerous character contradictions reveal considerable parallel evolution among advanced synapsids.     

The systematic relationships of the snake genus Anomochilus

Phylogenetic analysis of 38 skeletal characters, 12 muscular characters and 15 visceral characters in 17 major snake clades plus Anomochilus suggests that Anomochilus is the sister taxon of all other living alethinophidian snakes. However, skeletal, muscular and visceral character sets analysed separately or in pairs give four groups of nonconcordant tree topologies. Based on the cladogram derived from the total evidence, two families are erected to prevent the existing family Uropeltidae from becoming paraphyletic: Anomochilidae, for the Malaysian and Indonesian genus Anomochilus , and Cylindrophiidae, for the Sri Lankan, Southeast Asian and Indonesian genus Cylindrophis and the Upper Eocene fossil Eoanilius.     

The influence of phylogenetic uncertainty on the detection of positive Darwinian selection

The power of maximum likelihood tests of positive selection on protein-coding genes depends heavily on detecting and accounting for potential biases in the studied data set. Although the influence of transition:transversion and codon biases have been investigated in detail, little is known about how inaccuracy in the phylogeny used during the calculations affects the performance of these tests. In this study, 3 empirical data sets are analyzed using sets of simulated topologies corresponding to low, intermediate, and high levels of phylogenetic uncertainty. The detection of positive selection was largely unaffected by errors in the underlying phylogeny. However, the number of sites identified as being under positive selection tended to be overestimated.     

The phylogenetic relationships of the pentastomida: The case for their inclusion within the crustacea

Pentastomids are a distinct systematic assemblage of worm-like animals which, as adults, are parasitic in the respiratory tracts of vertebrates. Recent evidence regarding the phylogenetic affinities of the group is assessed. Evidence favouring a descent from annelids, or from an annelid-like ancestor of the arthropods, is dismissed because it is based on gross comparative anatomy and fails to take into account the many adaptive features of these highly specialised endoparasites. Theories according pentastomids the status of an independent phylum, sharing a similar rank with tardigrades and onychophorans are dismissed similarly.Three crucial items of evidence, embryogenesis, the structure of the integument, and gametogenesis are considered to confirm previous hypotheses of genuine arthropod homologies. Spermatogenesis particularly, clearly establishes pentastomids as a crustacean sub-class, closely allied to the Branchiura. We postulate that the pentastomid progenitor was originally a parasite of fish which subsequently became adapted to an endoparasitic existence in aquatic reptiles through predation.     

The phylogenetic relationships of argyrolagid marsupials

New material of the oldest known argyrolagid marsupial Proargyrolagus bolivianus from the late Oligocene of Bolivia is described. The new specimen preserves previously unknown aspects of the anterior dentition that solve the long-standing homology problem concerning the identity (i2) of the procumbent lower incisors in argyrolagids. This new anatomical information is incorporated into a morphology-based phylogenetic analysis of all extant marsupial families and Argyrolagidae, with the aim of testing the monophyly of Paucituberculata and evaluating the relationships among extant marsupial families. Eleven features support the monophyly of Paucituberculata, the following three unique among Marsupialia: small size of the paraconid, procumbent second lower incisor, and supraoccipital without distinct lambdoid crest resulting in globular form of braincase. Paucituberculata is the sister group of an Australian clade of marsupials that includes Dromiciops, but these results are not robust, as shown by sensitivity analyses. The foramen ovale surrounded completely by the alisphenoid supports the association of Dromiciops with diprotodontians.     

The braincases of mosasaurs and Varanus, and the relationships of snakes

The braincase structure of the mosasaur Platecarpus is described in detail and compared to that of Varanus and snakes. The braincase of mosasaurs and Varanus is found to be closely similar in most respects other than the consequences of obliteration of the metakinetic axis in mosasaurs. Neither Varanus, nor mosasaurs, approach snakes in braincase structure. The hypothesis of a sister-group relationship of snakes and mosasauroids is discussed in the light of how hypotheses of homology, or synapomorphy, can be established on an empirical, i.e. testable and potentially falsifiable basis. The establishment of homology qua synapomorphy is recognized as a procedure involving at least two levels of generalization. The most basic level is the conjecture of similarity of constituent elements of two or more organisms. Such conjectures of similarity maintain their testability, and falsifiability, only if established by reference to topographical equivalence, or equivalence of connectivity.     

The Rutland Cetiosaurus: the anatomy and relationships of a Middle Jurassic British sauropod dinosaur

A relatively well–preserved specimen of Cetiosaurus oxoniensis, from the Middle Jurassic (Bajocian) of Rutland, United Kingdom, is described in detail. The material includes a nearly complete cervical series, representative dorsal vertebrae, a fragment of sacrum, anterior caudals, the right femur, and numerous rib and limb fragments. Contrary to previous suggestions that this specimen possesses 14 cervical and ten dorsal vertebrae, it seems more probable that there were at most 13 cervicals and at least 12 dorsals. The vertebral column displays several autapomorphic features which supplement the generic diagnosis of Cetiosaurus, including: (1) a stout, anteriorly directed process located at the top of the neural spine of the twelfth (?) cervical vertebra; and (2) the presence of lateral pits, separated by a thin midline septum, below the transverse processes of middle dorsal vertebrae. Cladistic analysis indicates that Cetiosaurus is probably the sister–taxon to the advanced neosauropod clade. This relationship affects the distribution of particular character states that have played an important role in determining sauropod phylogeny.     

Phylogenetic relationships of galeaspids (Agnatha)

We present the first parsimony analysis of the agnathan subclass Galeaspida based on the analysis of 53 morphological characters.Three most parsimonious cladograms (126 steps in length;CI=0.508;RI=0.801)were discovered.An amended classification of the Galeaspida is proposed corresponding to the present analysis.Our results suggest that hanyangaspids,xiushuiaspids and dayongaspids from the Llandovery-Wenlock of Silurian are basal galeaspids.Within the remaining galeaspids,three major monophyletic groups (the Eugaleaspidiformes,the Polybranchiaspidiformes and the Huananaspidiformes)are well supported.It is shown that the dorsal fenestrae of the headshield evolved twice within the Galeaspida,one in the polybranchiaspidiform lineage,and the other in the huananaspidiform lineage (nested within the Huananaspidae).The chronological distribution of galeaspids highlights two radiations of the group,one for basal galeaspids and eugaleaspids in the Telychian (Llandovery)of Silurian,and the other for polybranchiaspidiforms and huananaspidiforms in the Lochkovian of Early Devonian.     

Phylogenetic relationships of galeaspids (Agnatha)

We present the first parsimony analysis of the agnathan subclass Galeaspida based on the analysis of 53 morphological characters. Three most parsimonious cladograms (126 steps in length; CI = 0.508; RI = 0.801) were discovered. An amended classification of the Galeaspida is proposed corresponding to the present analysis. Our results suggest that hanyangaspids, xiushuiaspids and day on-gaspids from the Llandovery-Wenlock of Silurian are basal galeaspids. Within the remaining galeaspids, three major monophyletic groups (the Eugaleaspidiformes, the Polybranchiaspidiformes and the Huananaspidiformes) are well supported. It is shown that the dorsal fenestrae of the headshield evolved twice within the Galeaspida, one in the polybranchiaspidiform lineage, and the other in the huananaspidiform lineage (nested within the Huananaspidae). The chronological distribution of galeaspids highlights two radiations of the group, one for basal galeaspids and eugaleaspids in the Telychian (Llandovery) of Silurian, and the other for polybranchiaspidiforms and huananaspidiforms in the Lochkovian of Early Devonian. Selected from Vertebrata PalAsiatica, 2006, 44 (1): 1–27     

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.     

The morphology and relationships of the Carboniferous amphibian Eoherpeton watsoni Panchen

The oldest recorded anthracosaur amphibian Eoherpeton watsoni Panchen, from localities in the Visean and Namurian of the Scottish Carboniferous, is described. It lacks a distinct otic notch, and reconstruction of the position of cranial ligaments and muscles suggest that a tympanum was never developed. On the basis of these observations it is concluded that arguments used to refute a relationship between anthracosaurs and amniotes, based on apparent differences in the morphology of their otic regions, are invalid. The order Anthracosauria is considered to be a monophyletic group characterized by the development of a sutural connection between the tabular and parietal bones on a skull table which includes both the intertemporal and supratemporal as well as the tabular. It is divided into two suborders: Seymouriamorpha characterized by a sutural connection between the squamosal and intertemporal and the presence of a lateral otic tube, and Anthracosauroideae characterized by the absence of post-temporal fossae. The Discosauriscidae, Kotlassiidae and Seymouriidae are included in the Seymouriamorpha, and the Eoherpetontidae, Gephyrostegidae and Embolomeri comprise the Anthracosauroideae. The Proterogyrinidae are considered the most primitive family of embolomeres. A new phylogeny of Amphibia is presented. The old groupings of Labyrinthodontia, Lepospondyli and Lissamphibia are rejected and Amphibia is divided, on the basis of differences in morphology of the neurocranium and its relationship with the surrounding bones of the skull, into two major groups, the first including the Ichthyostcgalia, Temnospondyli, Microsauria and the extant Anura, Apoda and Urodela, while the Aistopoda, Nectridea, Palaeostegalia, Loxommatoidea, Anthracosauria and Diadectomorpha, together with the Amniota, form the second. Similarities in the dentition of the palaeostegalian Crassigyrinus and loxommatoids suggest the two taxa are sister-groups, but the immediate relationships of anthracosaurs remain indeterminate and they here form an unresolved trichotomy with diadectomorphs and amniotes.     

The cranial morphology and relationships of the aberrant Carboniferous amphibian Spathicephalus mirus Watson

The skull of Spathicephalus mirus Watson, an amphibian from the Namurian, basal Upper Carboniferous, of Scotland is described. It shares with the Loxommatoidea a closed palate, palatal ornament and antorbital vacuities, and the family Spathicephalidae is recognized as the sister group of the Loxommatidae. A new diagnosis of the Loxommatoidea is presented together with one of the Spathicephalidae. An analysis of the functional morphology of the Spathicephalus skull suggests that it was incapable of rapid jaw closure required for catching fish. Instead it is proposed that Spathicephalus was a sluggish bottom-dwelling filter-feeder of small, soft invertebrates.