Development and evolution of dentition pattern and tooth order in the Skates and Rays (Batoidea; Chondrichthyes)

Shark and ray (elasmobranch) dentitions are well known for their multiple generations of teeth, with isolated teeth being common in the fossil record. However, how the diverse dentitions characteristic of elasmobranchs form is still poorly understood. Data on the development and maintenance of the dental patterning in this major vertebrate group will allow comparisons to other morphologically diverse taxa, including the bony fishes, in order to identify shared pattern characters for the vertebrate dentition as a whole. Data is especially lacking from the Batoidea (skates and rays), hence our objective is to compile data on embryonic and adult batoid tooth development contributing to ordering of the dentition, from cleared and stained specimens and micro-CT scans, with 3D rendered models. We selected species (adult and embryonic) spanning phylogenetically significant batoid clades, such that our observations may raise questions about relationships within the batoids, particularly with respect to current molecular-based analyses. We include developmental data from embryos of recent model organisms Leucoraja erinacea and Raja clavata to evaluate the earliest establishment of the dentition. Characters of the batoid dentition investigated include alternate addition of teeth as offset successional tooth rows (versus single separate files), presence of a symphyseal initiator region (symphyseal tooth present, or absent, but with two parasymphyseal teeth) and a restriction to tooth addition along each jaw reducing the number of tooth families, relative to addition of successor teeth within each family. Our ultimate aim is to understand the shared characters of the batoids, and whether or not these dental characters are shared more broadly within elasmobranchs, by comparing these to dentitions in shark outgroups. These developmental morphological analyses will provide a solid basis to better understand dental evolution in these important vertebrate groups as well as the general plesiomorphic vertebrate dental condition

MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families

Background: Phylogenetic study of protein sequences provides unique and valuable insights into the molecular and genetic basis of important medical and epidemiological problems as well as insights about the origins and development of physiological features in present day organisms. Consensus phylogenies based on the bootstrap and other resampling methods play a crucial part in analyzing the robustness of the trees produced for these analyses. Methodology: Our focus was to increase the number of bootstrap replications that can be performed on large protein datasets using the maximum parsimony, distance matrix, and maximum likelihood methods. We have modified the PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time. This paper discusses the methodology used to parallelize the PHYLIP programs and reports the performance of the parallel PHYLIP programs that are relevant to the study of protein evolution on several protein datasets. Conclusions: Calculations that currently take a few days on a state of the art desktop workstation are reduced to calculations that can be performed over lunchtime on a modern parallel computer. Of the three protein methods tested, the maximum likelihood method scales the best, followed by the distance method, and then the maximum parsimony method. However, the maximum likelihood method requires significant memory resources, which limits its application to mor

An Estimation of Erinaceidae Phylogeny: A Combined Analysis Approach

BACKGROUND: Erinaceidae is a family of small mammals that include the spiny hedgehogs (Erinaceinae) and the silky-furred moonrats and gymnures (Galericinae). These animals are widely distributed across Eurasia and Africa, from the tundra to the tropics and the deserts to damp forests. The importance of these animals lies in the fact that they are the oldest known living placental mammals, which are well represented in the fossil record, a rarity fact given their size and vulnerability to destruction during fossilization. Although the Family has been well studied, their phylogenetic relationships remain controversial. To test previous phylogenetic hypotheses, we combined molecular and morphological data sets, including representatives of all the genera. METHODOLOGY AND PRINCIPAL FINDINGS: We included in the analyses 3,218 bp mitochondrial genes, one hundred and thirty-five morphological characters, twenty-two extant erinaceid taxa, and five outgroup taxa. Phylogenetic relationships were reconstructed using both partitioned and combined data sets. As in previous analyses, our results strongly support the monophyly of both subfamilies (Galericinae and Erinaceinae), the Hylomys group (to include Neotetracus and Neohylomys), and a sister-relationship of Atelerix and Erinaceus. As well, we verified that the extremely long branch lengths within the Galericinae are consistent with their fossil records. Not surprisingly, we found significant incongruence between the phylogenetic signals of the genes and the morphological characters, specifically in the case of Hylomys parvus, Mesechinus, and relationships between Hemiechinus and Paraechinus. CONCLUSIONS: Although we discovered new clues to understanding the evolutionary relationships within the Erinaceidae, our results nonetheless, strongly suggest that more robust analyses employing more complete taxon sampling (to include fossils) and multiple unlinked genes would greatly enhance our understanding of the Erinaceidae. Until then, we have left the nomenclature of the taxa unchanged; hence it does not yet precisely reflect their phylogenetic relationships or the depth of their genetic diversity

Digital Cranial Endocast of Hyopsodus (Mammalia, “Condylarthra”): A Case of Paleogene Terrestrial Echolocation?

We here describe the endocranial cast of the Eocene archaic ungulate Hyopsodus lepidus AMNH 143783 (Bridgerian, North America) reconstructed from X-ray computed microtomography data. This represents the first complete cranial endocast known for Hyopsodontinae. The Hyopsodus endocast is compared to other known “condylarthran” endocasts, i. e. those of Pleuraspidotherium (Pleuraspidotheriidae), Arctocyon (Arctocyonidae), Meniscotherium (Meniscotheriidae), Phenacodus (Phenacodontidae), as well as to basal perissodactyls (Hyracotherium) and artiodactyls (Cebochoerus, Homacodon). Hyopsodus presents one of the highest encephalization quotients of archaic ungulates and shows an “advanced version” of the basal ungulate brain pattern, with a mosaic of archaic characters such as large olfactory bulbs, weak ventral expansion of the neopallium, and absence of neopallium fissuration, as well as more specialized ones such as the relative reduction of the cerebellum compared to cerebrum or the enlargement of the inferior colliculus. As in other archaic ungulates, Hyopsodus midbrain exposure is important, but it exhibits a dorsally protruding largely developed inferior colliculus, a feature unique among “Condylarthra”. A potential correlation between the development of the inferior colliculus in Hyopsodus and the use of terrestrial echolocation as observed in extant tenrecs and shrews is discussed. The detailed analysis of the overall morphology of the postcranial skeleton of Hyopsodus indicates a nimble, fast moving animal that likely lived in burrows. This would be compatible with terrestrial echolocation used by the animal to investigate subterranean habitat and/or to minimize predation during nocturnal exploration of the environment

Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins

Despite the rising interest in homeotic genes, little has been known about the course and pattern of evolution of homeotic traits across the mammalian radiation. An array of emerging and diversifying homeotic gradients revealed by this study appear to generate new body plans and drive evolution at a large scale.This study identifies and evaluates a set of homeotic gradients across 250 extant and fossil mammalian species and their antecedents over a period of 220 million years. These traits are generally expressed as co-linear gradients along the body axis rather than as distinct segmental identities. Relative position or occurrence sequence vary independently and are subject to polarity reversal and mirroring. Five major gradient modification sets are identified: (1)--quantitative changes of primary segmental identity pattern that appeared at the origin of the tetrapods ; (2)--frame shift relation of costal and vertebral identity which diversifies from the time of amniote origins; (3)--duplication, mirroring, splitting and diversification of the neomorphic laminar process first commencing at the dawn of mammals; (4)--emergence of homologically variable lumbar lateral processes upon commencement of the radiation of therian mammals and ; (5)--inflexions and transpositions of the relative position of the horizontal septum of the body and the neuraxis at the emergence of various orders of therian mammals. Convergent functional changes under homeotic control include laminar articular engagement with septo-neural transposition and ventrally arrayed lumbar transverse process support systems.Clusters of homeotic transformations mark the emergence point of mammals in the Triassic and the radiation of therians in the Cretaceous. A cluster of homeotic changes in the Miocene hominoid Morotopithecus that are still seen in humans supports establishment of a new "hominiform" clade and suggests a homeotic origin for the human upright body plan

Fatou’s Associates

Suppose that f is a transcendental entire function, V⊊C is a simply connected domain, and U is a connected component of f-1(V). Using Riemann maps, we associate the map f : U→V to an inner function g : D→D. It is straightforward to see that g is either a finite Blaschke product, or, with an appropriate normalisation, can be taken to be an infinite Blaschke product. We show that when the singular values of f in V lie away from the boundary, there is a strong relationship between singularities of g and accesses to infinity in U. In the case where U is a forward-invariant Fatou component of f, this leads to a very significant generalisation of earlier results on the number of singularities of the map g. If U is a forward-invariant Fatou component of f there are currently very few examples where the relationship between the pair (f, U) and the function g has been calculated. We study this relationship for several well-known families of transcendental entire functions. It is also natural to ask which finite Blaschke products can arise in this manner, and we show the following: for every finite Blaschke product g whose Julia set coincides with the unit circle, there exists a transcendental entire function f with an invariant Fatou component such that g is associated with f in the above sense. Furthermore, there exists a single transcendental entire function f with the property that any finite Blaschke product can be arbitrarily closely approximated by an inner function associated with the restriction of f to a wandering domain