@article{3770, abstract = {The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon and Orinoco basins, covering an area of approximately 7 million km2. Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present-day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male-mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male-mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's Fs tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene.}, author = {Hollatz, Claudia and Vilaça, Sibelle and Fernandes Redondo, Rodrigo A and Marmontel, Míriam and Baker, Cyndi and Santos, Fabrício}, journal = {Biological Journal of the Linnean Society}, number = {4}, pages = {812 -- 827}, publisher = {Wiley}, title = {{The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)}}, doi = {10.1111/j.1095-8312.2011.01616.x}, volume = {102}, year = {2011}, } @article{3771, abstract = {The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages.}, author = {Pavan, Ana and Martins, Felipe and Santos, Fabrício and Ditchfield, Albert and Fernandes Redondo, Rodrigo A}, journal = {Biological Journal of the Linnean Society}, number = {3}, pages = {527 -- 539}, publisher = {Wiley-Blackwell}, title = {{Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.}}, doi = {10.1111/j.1095-8312.2010.01601.x}, volume = {102}, year = {2011}, } @article{3778, author = {Barton, Nicholas H}, journal = {Heredity}, number = {2}, pages = {205 -- 206}, publisher = {Nature Publishing Group}, title = {{Estimating linkage disequilibria}}, doi = {10.1038/hdy.2010.67}, volume = {106}, year = {2011}, } @article{3781, abstract = {We bound the difference in length of two curves in terms of their total curvatures and the Fréchet distance. The bound is independent of the dimension of the ambient Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and it generalizes a result by Fáry and Chakerian.}, author = {Fasy, Brittany Terese}, journal = {Acta Sci. Math. (Szeged)}, number = {1-2}, pages = {359 -- 367}, publisher = {Szegedi Tudományegyetem}, title = {{The difference in length of curves in R^n}}, volume = {77}, year = {2011}, } @article{3784, abstract = {Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus.}, author = {Palero, Ferran and Guerao, Guillermo and Clark, Paul and Abello, Pere}, journal = {Journal of the Marine Biological Association of the United Kingdom}, number = {2}, pages = {485 -- 492}, publisher = {Cambridge University Press}, title = {{Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description}}, doi = {10.1017/S0025315410000287}, volume = {91}, year = {2011}, } @inbook{3791, abstract = {During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes.}, author = {Krens, Gabriel and Heisenberg, Carl-Philipp J}, booktitle = {Forces and Tension in Development}, editor = {Labouesse, Michel}, pages = {189 -- 213}, publisher = {Elsevier}, title = {{Cell sorting in development}}, doi = {10.1016/B978-0-12-385065-2.00006-2}, volume = {95}, year = {2011}, } @inbook{3796, abstract = {We address the problem of covering ℝ n with congruent balls, while minimizing the number of balls that contain an average point. Considering the 1-parameter family of lattices defined by stretching or compressing the integer grid in diagonal direction, we give a closed formula for the covering density that depends on the distortion parameter. We observe that our family contains the thinnest lattice coverings in dimensions 2 to 5. We also consider the problem of packing congruent balls in ℝ n , for which we give a closed formula for the packing density as well. Again we observe that our family contains optimal configurations, this time densest packings in dimensions 2 and 3.}, author = {Edelsbrunner, Herbert and Kerber, Michael}, booktitle = {Rainbow of Computer Science}, editor = {Calude, Cristian and Rozenberg, Grzegorz and Salomaa, Arto}, pages = {20 -- 35}, publisher = {Springer}, title = {{Covering and packing with spheres by diagonal distortion in R^n}}, doi = {10.1007/978-3-642-19391-0_2}, volume = {6570}, year = {2011}, } @article{386, abstract = {We present a detailed study of the local density of states (LDOS) associated with the surface-state band near a step edge of the strong topological insulator Bi2Te3 and reveal a one-dimensional bound state that runs parallel to the step edge and is bound to it at some characteristic distance. This bound state is clearly observed in the bulk gap region, while it becomes entangled with the oscillations of the warped surface band at high energy, and with the valence-band states near the Dirac point. We obtain excellent fits to theoretical predictions [Alpichshev, 2011] that properly incorporate the three-dimensional nature of the problem to the surface state. Fitting the data at different energies, we can recalculate the LDOS originating from the Dirac band without the contribution of the bulk bands or incoherent tunneling effects. }, author = {Alpichshev, Zhanybek and Analytis, J G and Chu, J H and Fisher, I R and Kapitulnik, A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {4}, publisher = {American Physical Society}, title = {{STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3}}, doi = {10.1103/PhysRevB.84.041104}, volume = {84}, year = {2011}, } @article{3965, abstract = {The elevation function on a smoothly embedded 2-manifold in R-3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in identifying coarse docking configurations for protein pairs. Transporting the concept from the smooth to the piecewise linear category, this paper describes an algorithm for finding all local maxima. While its worst-case running time is the same as of the algorithm used in prior work, its performance in practice is orders of magnitudes superior. We cast light on this improvement by relating the running time to the total absolute Gaussian curvature of the 2-manifold.}, author = {Wang, Bei and Edelsbrunner, Herbert and Morozov, Dmitriy}, journal = {Journal of Experimental Algorithmics}, number = {2.2}, pages = {1 -- 13}, publisher = {ACM}, title = {{Computing elevation maxima by searching the Gauss sphere}}, doi = {10.1145/1963190.1970375}, volume = {16}, year = {2011}, }