Eliurus majori complex

21 p. : ill. (1 col.), 1 map ; 26 cm.Includes bibliographical references (p. 19-20).A new species of Eliurus, E. danieli (Nesomyidae: Nesomyinae), is described from the Parc National de l'Isalo in south-central Madagascar. Although geographically intermediate to eastern and western forms, diagnostic traits convincingly relate the new species to E. majori and E. penicillatus, forms distributed primarily in eastern humid forest; it is morphometrically most similar to E. penicillatus. In view of the increase in number of Eliurus species (11 now described), discussion is devoted to emerging species associations (5 are identified) and to taxonomic and distributional problems introduced by the accumulation of larger series and new localities over the past decade

New species of Oecomys.

32 p. : ill. (1 col.), 1 map ; 26 cm. "August 28, 2009." Abstract also in Spanish. Includes bibliographical references (p. 27-30).We describe a new species of Oecomys, O. sydandersoni (Cricetidae: Sigmodontinae), from the Parque Nacional Noel Kempff Mercado in eastern Bolivia. One of its diagnostic traits, a derived carotid circulatory plan, provides morphological evidence for its close relationship to O. concolor and O. mamorae among the 15 species of Oecomys currently recognized. Notwithstanding this shared trait, other morphological contrasts and morphometric analyses demonstrate the sharp differentiation of the eastern Bolivian form from both of those species. Oecomys sydandersoni, n. sp., is arboreal and was encountered above ground on limbs and woody vines only in densely wooded hummocks scattered through grassland, in contrast to adjacent closed tropical deciduous forest where three other species of Oecomys (O. bicolor, O. roberti, O. trinitatis) were obtained. The new species represents the fourth sigmodontine rodent to be named from this restricted region within eastern Bolivia since 1999. Its documentation served as a platform to summarize the nomenclatural history, morphological recognition, and geographic distribution of O. concolor (Wagner, 1845) and O. mamorae (Thomas, 1906) based on fresh examination of all type material and museum specimens

Oryzomyine rodents

376 p. : ill., maps (1 col.) ; 26 cm.Includes bibliographical references (p. 324-337)."We describe the morphological species boundaries and geographic distributions of 10 Neotropical Oryzomys based on analyses of museum specimens (skins and skulls, examples preserved in fluid, chromosomal spreads, and information about collection sites from skin tags, field catalogs, and other sources). These species have been regarded as members of an Oryzomys capito complex and for a long time were consolidated into a single entity identified as O. capito. Our study documents the following: 1. Defining the limits of species within the O. capito complex first requires a comprehensive review and rigorous definition of O. capito itself. We consider Fischer's (1814) Mus megacephalus to be valid and available, designate a neotype to bear the name, and reinstate it as a senior synonym of capito Olfers (1818). We then provide a working definition of O. megacephalus and its close relative, O. laticeps, derived from analyses of morphometric variation, estimates of geographic distributions, and evaluations of synonyms. In our view, O. megacephalus occurs in Amazonia but also extends into eastern Paraguay; its synonyms are capito Olfers (1818), cephalotes Desmarest (1819), velutinus Allen and Chapman (1893), goeldi Thomas (1897), modestus Allen (1899), and perenensis Allen (1901). Oryzomys laticeps Lund (1840) occurs in the Atlantic Forest region of eastern Brazil. We designate a lectotype for laticeps and allocate the names saltator Winge (1887) and oniscus Thomas (1904) as synonyms. 2. We provide the first comprehensive taxonomic revision of Oryzomys yunganus Thomas (1902). Its range covers tropical evergreen rainforest formations in the Guiana Region and the Amazon Basin where, as documented by voucher specimens, it has been collected at the same localities as O. megacephalus, O. nitidus, and O. macconnelli. Specimens of O. yunganus can be distinguished from those of the other three by a combination of body size, pelage texture and coloration, pattern of carotid arterial circulation, occlusal patterns of second upper and lower molars, cranial proportions, and chromosomal features. Appreciable intraspecific geographic variation occurs in diploid number of chromosomes and frequency of occurrence of the hypothenar plantar pad, but sampling inadequacies obscure the significance of this variation. Large body size is characteristic of populations in the western Amazon Basin and in the tepui region of eastern Venezuela; smaller size characterizes populations in the Guianas and along the eastern margin of the Amazon Basin. No other scientific name has been correctly associated with the species. Samples from Mirador, Palmera, and Mera in the western Andean foothills of central Ecuador possess a combination of pelage, cranial, and dental traits that distinguish them from all samples of O. yunganus. These specimens are the basis for a new species we describe here, one that is more closely related to O. yunganus than to any other member of the former O. 'capito' complex. 3. We redescribe Oryzomys bolivaris (reviewed by Pine, 1971, under the name O. bombycinus), amplify its geographic range, and contrast it with O. talamancae and O. alfaroi, two sympatric congeners with which it is often confused. A distinctive set of morphological traits allows unambiguous identification of specimens belonging to O. bolivaris. It is a trans-Andean species recorded from very wet tropical evergreen rain forests extending from eastern Honduras and Nicaragua through Costa Rica and Panamá to western Colombia and Ecuador. Allen's (1901) bolivaris is the oldest name for this species; castaneus Allen (1901), rivularis Allen (1901), bombycinus Goldman (1912), alleni Goldman (1915), and orinus Pearson (1939) are synonyms. 4. We revise the definition of Oryzomys talamancae Allen (1891) provided by Musser and Williams (1985), document additional specimens, describe karyotypes from Ecuadoran and Venezuelan samples, and contrast its morphology, chromosomes, and distribution with those of O. alfaroi and O. megacephalus. The geographic distribution of O. talamancae is also trans-Andean, but it inhabits a wider variety of habitats than does O. bolivaris. We also provide a new synonymy and identify the following scientific names as synonyms of O. talamancae: mollipilosus Allen (1899), magdalenae Allen (1899), villosus Allen (1899), sylvaticus Thomas (1900), panamensis Thomas (1901), medius Robinson and Lyon (1901), and carrikeri Allen (1908). 5. We present hypotheses of species boundaries of four morphologically similar species that we identify as members of the Oryzomys nitidus group: O. nitidus Thomas (1884), O. macconnelli Thomas (1910), O. russatus Wagner (1848), and a species described as new. We recognize the four species by morphological and chromosomal traits, and contrast characteristics of each species with one another. One synonym, boliviae Thomas (1901), is associated with O. nitidus, and two scientific names, incertus Allen (1913) and mureliae Allen (1915), are allocated to O. macconnelli. Synonyms of O. russatus are physodes Brants (1827), intermedia Leche (1886), coronatus Winge (1887), lamia Thomas (1901), legatus Thomas (1925), kelloggi Ávila-Pires (1959), and moojeni Ávila-Pires (1959). We designate lectotypes for russatus and intermedia and identify the holotype of coronatus. Based on voucher specimens, the geographic distribution of O. nitidus is mainly along the Andean foothills and adjacent lowlands in Perú, Bolivia, and nearby western Brazil, but scattered records document its eastward extension through south-central Brazil to Paraguay and northeastern Argentina. Oryzomys macconnelli inhabits the tropical evergreen rain forests of Amazonia. Its distribution partially overlaps that of O. nitidus in western Amazonia, where the two species have been collected together at one locality in Perú, and it is sympatric with the new species, which is recorded only from the lower regions of rios Xingu and Tocantins in northern Pará, Brazil. The distribution of O. russatus is documented by specimens from southeastern and south-central Brazil, southern Bolivia, and northern Argentina; its range is allopatric to those of O. macconnelli, the new species, and O. nitidus except in southern Bolivia, where the latter was collected at the same site with O. russatus. We also examined types and descriptions of taxa associated with Oryzomys subflavus and O. ratticeps to determine if any of those names actually reference members of the O. nitidus group. Although the original description of subflavus Wagner (1842) is vague, the holotype clearly represents an example of that very distinctive species; vulpinus Lund (1840), for which we designate a lectotype, and vulpinoides Schinz (1845) are synonyms of O. subflavus. The oldest name for the species currently known as Oryzomys ratticeps is Mus angouya Fischer (1814), a name not based on a specimen but on Azara's (1801) description of 'Rat troisième, ou Rat Angouya.' Azara's account is so general that it could also apply to individuals of O. subflavus, O. nitidus, or O. russatus. To stabilize the nomenclature of these species, we designate a neotype for Mus angouya Fischer (1814) and treat the following scientific names as synonyms: buccinatus Olfers (1818), leucogaster Wagner (1845), ratticeps Hensel (1872), rex Winge (1887), tropicius Thomas (1924), and paraganus Thomas (1924). We also designate lectotypes for leucogaster and ratticeps. We have not analyzed phylogenetic relationships among the species in the former O. 'capito' complex discussed here. Documenting morphological and distributional boundaries of other biological species now grouped in the genus Oryzomys (alfaroi and its close relatives, for example) must precede, in our view, attempts at phylogenetic reconstruction"--P. 5-6

Application of a correlation correction factor in a microarray cross-platform reproducibility study

Background Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations. Results In this paper, three technical replicate microarrays were hybridized to each of three platforms. The three platforms were then analyzed to assess both intra- and cross-platform reproducibility. We present various methods for examining intra-platform reproducibility. We also examine cross-platform reproducibility using Pearson\u27s correlation. Additionally, we previously developed a correction factor for Pearson\u27s correlation which is applicable when X and Y are measured with error. Herein we demonstrate that correcting for measurement error by estimating the disattenuated correlation substantially improves cross-platform correlations. Conclusion When estimating cross-platform correlation, it is essential to thoroughly evaluate intra-platform reproducibility as a first step. In addition, since measurement error is present in microarray gene expression data, methods to correct for attenuation are useful in decreasing the bias in cross-platform correlation estimates

QCD thermodynamics with two flavors of Wilson quarks at N_t=6

We report on a study of hadron thermodynamics with two flavors of Wilson quarks on 12^3x6 lattices. We have studied the crossover between the high and low temperature regimes for three values of the hopping parameter, kappa=0.16, 0.17, and 0.18. At each of these values of kappa we have carried out spectrum calculations on 12^3x24 lattices for two values of the gauge coupling in the vicinity of the crossover in order to set an energy scale for our thermodynamics calculations and to determine the critical value of the gauge coupling for which the pion and quark masses vanish. For kappa=0.17 and 0.18 we find coexistence between the high and low temperature regimes over 1,000 simulation time units indicating either that the equilibration time is extremely long or that there is a possibility of a first order phase transition. The pion mass is large at the crossover values of the gauge coupling, but the crossover curve has moved closer to the critical curve along which the pion and quark masses vanish, than it was on lattices with four time slices. In addition, values of the dimensionless quantity T_c/m_rho are in closer agreement with those for staggered quarks than was the case at N_t=4. (A POSTSCRIPT VERSION OF THIS PAPER IS AVAILABLE BY ANONYMOUS FTP FROM sarek.physics.ucsb.edu (128.111.8.250) IN THE FILE pub/wilson_thermo.ps)Comment: 24 page

Last technology and results from the IOTA interferometer

The infrared optical telescope array (IOTA), one of the most productive interferometers in term of science and new technologies was decommissioned in summer 2006. We discuss the testing of a low-resolution spectrograph coupled with the IOTA-3T integrated-optics beam combiner and some of the scientific results obtained from this instrument

Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae : Murinae : Otomyini) : revision of the Otomys typus complex

We combined evidence from biogeography, craniodental traits, linear and geometric morphometrics (233 skulls), cytogenetics (karyotypes of 18 individuals) and mitochondrial DNA sequences (44 cytochrome b and 21 12S rRNA sequences) to test species limits within Otomys typus s.l. (Muridae: Murinae: Otomyini), a complex that is patchily distributed across alpine zones of Ethiopia and East Africa. Our results confirm the specific validity of O. dartmouthi, O. jacksoni, O. orestes, and O. uzungwensis, forms recently removed from synonymy under typus s.l.; support elevation of four other alpine forms to species (O. fortior, O. helleri, O. thomasi, and O. zinki); identify three additional new species (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.); and enable redefinition of O. typus s.s. as a species restricted to certain mountains west of the Great Rift Valley in Ethiopia (Simien and Guna Mountains in the north, extending to the highlands of the western rim of the Rift Valley). Phylogenetic interpretation of the cytochrome b data clearly demonstrates that the alpine morphotype once united under O. typus s.l. has originated independently at high elevations on several mountain ranges in eastern and northeastern Africa; although generally adapted to high-elevation vegetation, such alpine species are ecologically segregated from one another. Patterns of morphometric, genetic, and ecological differentiation among populations once misassigned to nominal O. tropicalis and O. typus more parsimoniously reflect regional cladogenesis along elevational gradients, rather than multiple, successive colonization by different ancestral forms from southern Africa as earlier supposed. Although incomplete and preliminary, information gathered for O. tropicalis indicates that it too is a species composite; several lines of research are discussed to redress its polyphyletic content. Our results, together with other recent taxonomic studies of Otomys, appreciably elevate the level of endemism within eastern Africa and underscore the significance of Africa's eastern highlands to the continental diversification of Otomyini.Nous avons combiné un ensemble de données, biogéographiques craniodentaires, morphométriques (linéaires et géométriques; 233 crânes), cytogénétiques (caryotypes de 18 individus) et moléculaires (ADN mitochondrial: 44 séquences de cytochrome b et 21 séquences de 12 rRNA) afin d’évaluer les délimitations d'espèces au sein d’Otomys typus s.l. (Muridae: Murinae: Otomyini), un complexe d’espèces distribué à travers les zones alpestres de l'Éthiopie et d'Afrique de l'Est. Nos résultats 1) confirment le statut spécifique d'O. dartmouthi, O. jacksoni, O. orestes et O. uzungwensis, des formes dont la synonymie avec typus s.l. a récemment été infirmée, 2) soutiennent l'élévation au statut d’espèce de quatre autres formes alpestres (O. fortior, O. helleri, O. thomasi et O. zinki), 3) permettent d’identifier trois nouvelles espèces supplémentaires (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.), et 4) nous permettent de redéfinir O. typus s.s. comme une espèce restreinte à certaines montagnes à l'ouest de la Vallée du Rift en Éthiopie (les montagnes Simien et Guna au nord, s'étendant aux pays montagneux du bord occidental de la vallée du Rift). L'interprétation phylogénétique des séquences de cytochrome b démontre clairement que la forme alpestre autrefois incluse dans O. typus s.l. est apparue de façon indépendante à de hautes altitudes sur plusieurs massifs montagneux en Afrique de l'Est et du Nord-Est. Bien que généralement adaptées à la végétation de haute altitude, de telles espèces alpestres sont écologiquement distinctes les unes des autres. Les différentiations morphométrique, génétique et écologique au sein des populations regroupées de façon incorrecte sous les noms O. tropicalis et O. typus reflètent plus parcimonieusement une diversification régionale suivant des gradients altitudinaux, plutôt qu’unecolonisation multiple, successive par différentes formes ancestrales d'Afrique du Sud, comme supposé antérieurement. Bien qu'incomplètes et préliminaires, les données obtenues pour O. tropicalis indiquent qu’il constitue aussi un complexe d'espèces. Plusieurs lignes de recherche sont envisagées afin de réévaluer son statut polyphylétique. Nos résultats, ajoutés à d'autres études taxinomiques récentes d'Otomys, élèvent sensiblement le niveau d'endémisme en l'Afrique de l'Est et soulignent l’importancedes hautes terres de l'est de l'Afrique dans la diversification continentale des Otomyini.We gratefully acknowledge the financial assistance of the Smithsonian Institution Short Term Visitor Award (in 2006), and a South African National Research Foundation Grant (between 2005 and 2007), which allowed P.J.T. to visit and study important North American and European museum collections of Otomys.http://www.mapress.com/zootaxa/nf201

Zero temperature string breaking in lattice quantum chromodynamics

The separation of a heavy quark and antiquark pair leads to the formation of a tube of flux, or "string", which should break in the presence of light quark-antiquark pairs. This expected zero-temperature phenomenon has proven elusive in simulations of lattice QCD. We study mixing between the string state and the two-meson decay channel in QCD with two flavors of dynamical sea quarks. We confirm that mixing is weak and find that it decreases at level crossing. While our study does not show direct effects of internal quark loops, our results, combined with unitarity, give clear confirmation of string breaking.Comment: 20 pages, 7 figures. With small clarifications and two additions to references. Submitted to Phys. Rev.