Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)

After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.publishedVersio

Rediscovery of the Threatened River Sharks, Glyphis garricki and G. glyphis, in Papua New Guinea

Recent surveys of the shark and ray catches of artisanal fishers in the Western Province of Papua New Guinea (PNG) resulted in the rediscovery of the threatened river sharks, Glyphis garricki and Glyphis glyphis. These represent the first records of both species in PNG since the 1960s and 1970s and highlight the lack of studies of shark biodiversity in PNG. Two individuals of G. garricki and three individuals of G. glyphis were recorded from coastal marine waters of the Daru region of PNG in October and November 2014. The two G. garricki specimens were small individuals estimated to be 100–105 cm and ~113 cm total length (TL). The three G. glyphis specimens were all mature, one a pregnant female and two adult males. These are the first adults of G. glyphis recorded to date providing a more accurate maximum size for this species, i.e. ~260 cm TL. A single pup which was released from the pregnant female G. glyphis, was estimated to be ~65 cm TL. Anecdotal information from the fishers of pregnant females of G. glyphis containing 6 or 7 pups provides the first estimate of litter size for this species. The jaws of the pregnant female G. glyphis were retained and a detailed description of the dentition is provided, since adult dentition has not been previously documented for this species. Genetic analyses confirmed the two species cluster well within samples from these species collected in northern Australia

Quantum self-consistency of AdS×ΣAdS \times \Sigma brane models

Continuing on our previous work, we consider a class of higher dimensional brane models with the topology of $AdS_{D_1+1} \times \Sigma$, where $\Sigma$ is a one-parameter compact manifold and two branes of codimension 1 are located at the orbifold fixed points. We consider a set-up where such a solution arises from Einstein-Yang-Mills theory and evaluate the one-loop effective potential induced by gauge fields and by a generic bulk scalar field. We show that this type of brane models resolves the gauge hierarchy between the Planck and electroweak scales through redshift effects due to the warp factor $a=e^{-\pi kr}$. The value of $a$ is then fixed by minimizing the effective potential. We find that, as in the Randall Sundrum case, the gauge field contribution to the effective potential stabilises the hierarchy without fine-tuning as long as the laplacian $\Delta_\Sigma$ on $\Sigma$ has a zero eigenvalue. Scalar fields can stabilise the hierarchy depending on the mass and the non-minimal coupling. We also address the quantum self-consistency of the solution, showing that the classical brane solution is not spoiled by quantum effects.Comment: 10 page

Glycoprotein gene truncation in avian metapneumovirus subtype C isolates from the United States

The length of the published glycoprotein (G) gene sequences of avian metapneumovirus subtype-C (aMPV-C) isolated from domestic turkeys and wild birds in the United States (1996–2003) remains controversial. To explore the G gene size variation in aMPV-C by the year of isolation and cell culture passage levels, we examined 21 turkey isolates of aMPV-C at different cell culture passages. The early domestic turkey isolates of aMPV-C (aMPV/CO/1996, aMPV/MN/1a-b, and 2a-b/97) had a G gene of 1,798 nucleotides (nt) that coded for a predicted protein of 585 amino acids (aa) and showed >97% nt similarity with that of aMPV-C isolated from Canada geese. This large G gene got truncated upon serial passages in Vero cell cultures by deletion of 1,015 nt near the end of the open reading frame. The recent domestic turkey isolates of aMPV-C lacked the large G gene but instead had a small G gene of 783 nt, irrespective of cell culture passage levels. In some cultures, both large and small genes were detected, indicating the existence of a mixed population of the virus. Apparently, serial passage of aMPV-C in cell cultures and natural passage in turkeys in the field led to truncation of the G gene, which may be a mechanism of virus evolution for survival in a new host or environment

White shark comparison reveals a slender body for the extinct megatooth shark, Otodus megalodon (Lamniformes: Otodontidae)

The extinct megatooth shark, †Otodus megalodon, which likely reached at least 15 m in total length, is an iconic extinct shark represented primarily by its gigantic teeth in the Neogene fossil record. As one of the largest marine carnivores to ever exist, understanding the biology, evolution, and extinction of †O. megalodon is important because it had a significant impact on the ecology and evolution of marine ecosystems that shaped the present-day oceans. Some attempts inferring the body form of †O. megalodon have been carried out, but they are all speculative due to the lack of any complete skeleton. Here we highlight the fact that the previous total body length estimated from vertebral diameters of the extant white shark for an †O. megalodon individual represented by an incomplete vertebral column is much shorter than the sum of anteroposterior lengths of those fossil vertebrae. This factual evidence indicates that †O. megalodon had an elongated body relative to the body of the modern white shark (Carcharodon carcharias). Although its exact body form remains unknown, this proposition represents the most parsimonious empirical evidence, which is a significant step towards deciphering the much-debated body form of †O. megalodon

High-dimensional maximum marginal likelihood item factor analysis by adaptive quadrature

Although the Bock–Aitkin likelihood-based estimation method for factor analysis of dichotomous item response data has important advantages over classical analysis of item tetrachoric correlations, a serious limitation of the method is its reliance on fixed-point Gauss-Hermite (G-H) quadrature in the solution of the likelihood equations and likelihood-ratio tests. When the number of latent dimensions is large, computational considerations require that the number of quadrature points per dimension be few. But with large numbers of items, the dispersion of the likelihood, given the response pattern, becomes so small that the likelihood cannot be accurately evaluated with the sparse fixed points in the latent space. In this paper, we demonstrate that substantial improvement in accuracy can be obtained by adapting the quadrature points to the location and dispersion of the likelihood surfaces corresponding to each distinct pattern in the data. In particular, we show that adaptive G-H quadrature, combined with mean and covariance adjustments at each iteration of an EM algorithm, produces an accurate fast-converging solution with as few as two points per dimension. Evaluations of this method with simulated data are shown to yield accurate recovery of the generating factor loadings for models of upto eight dimensions. Unlike an earlier application of adaptive Gibbs sampling to this problem by Meng and Schilling, the simulations also confirm the validity of the present method in calculating likelihood-ratio chi-square statistics for determining the number of factors required in the model. Finally, we apply the method to a sample of real data from a test of teacher qualifications.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43596/1/11336_2003_Article_1141.pd

Analyzing and Modeling Real-World Phenomena with Complex Networks: A Survey of Applications

The success of new scientific areas can be assessed by their potential for contributing to new theoretical approaches and in applications to real-world problems. Complex networks have fared extremely well in both of these aspects, with their sound theoretical basis developed over the years and with a variety of applications. In this survey, we analyze the applications of complex networks to real-world problems and data, with emphasis in representation, analysis and modeling, after an introduction to the main concepts and models. A diversity of phenomena are surveyed, which may be classified into no less than 22 areas, providing a clear indication of the impact of the field of complex networks.Comment: 103 pages, 3 figures and 7 tables. A working manuscript, suggestions are welcome