Model choice problems using approximate Bayesian computation with applications to pathogen transmission data sets

Analytically or computationally intractable likelihood functions can arise in complex statistical inferential problems making them inaccessible to standard Bayesian inferential methods. Approximate Bayesian computation (ABC) methods address such inferential problems by replacing direct likelihood evaluations with repeated sampling from the model. ABC methods have been predominantly applied to parameter estimation problems and less to model choice problems due to the added difficulty of handling multiple model spaces. The ABC algorithm proposed here addresses model choice problems by extending Fearnhead and Prangle (2012, Journal of the Royal Statistical Society, Series B 74, 1–28) where the posterior mean of the model parameters estimated through regression formed the summary statistics used in the discrepancy measure. An additional stepwise multinomial logistic regression is performed on the model indicator variable in the regression step and the estimated model probabilities are incorporated into the set of summary statistics for model choice purposes. A reversible jump Markov chain Monte Carlo step is also included in the algorithm to increase model diversity for thorough exploration of the model space. This algorithm was applied to a validating example to demonstrate the robustness of the algorithm across a wide range of true model probabilities. Its subsequent use in three pathogen transmission examples of varying complexity illustrates the utility of the algorithm in inferring preference of particular transmission models for the pathogens.

Fungal Planet description sheets: 128-153

Novel species of microfungi described in the present study include the following from Australia: Catenulostroma corymbiae from Corymbia, Devriesia stirlingiae from Stirlingia, Penidiella carpentariae from Carpentaria, Phaeococcomyces eucalypti from Eucalyptus, Phialophora livistonae from Livistona, Phyllosticta aristolochiicola from Aristolochia, Clitopilus austroprunulus on sclerophyll forest litter of Eucalyptus regnans and Toxicocladosporium posoqueriae from Posoqueria. Several species are also described from South Africa, namely: Ceramothyrium podocarpi from Podocarpus, Cercospora chrysanthemoides from Chrysanthemoides, Devriesia shakazului from Aloe, Penidiella drakensbergensis from Protea, Strelitziana cliviae from Clivia and Zasmidium syzygii from Syzygium. Other species include Bipolaris microstegii from Microstegium and Synchaetomella acerina from Acer (USA), Brunneiapiospora austropalmicola from Rhopalostylis (New Zealand), Calonectria pentaseptata from Eucalyptus and Macadamia (Vietnam), Ceramothyrium melastoma from Melastoma (Indonesia), Collembolispora aristata from stream foam (Czech Republic), Devriesia imbrexigena from glazed decorative tiles (Portugal), Microcyclospora rhoicola from Rhus (Canada), Seiridium phylicae from Phylica (Tristan de Cunha, Inaccessible Island), Passalora lobeliaefistulosis from Lobelia (Brazil) and Zymoseptoria verkleyi from Poa (The Netherlands). Valsalnicola represents a new ascomycete genus from Alnus (Austria) and Parapenidiella a new hyphomycete genus from Eucalyptus (Australia). Morphological and culture characteristics along with ITS DNA barcodes are also provided. © 2012 Nationaal Herbarium Nederland & Centraalbureau voor Schimmelcultures.

Upper-mantle seismic structure beneath SE and Central Brazil from P- and S-wave regional traveltime tomography

We present models for the upper-mantle velocity structure beneath SE and Central Brazil using independent tomographic inversions of P- and S-wave relative arrival-time residuals (including core phases) from teleseismic earthquakes. The events were recorded by a total of 92 stations deployed through different projects, institutions and time periods during the years 1992-2004. Our results show correlations with the main tectonic structures and reveal new anomalies not yet observed in previous works. All interpretations are based on robust anomalies, which appear in the different inversions for P-and S-waves. The resolution is variable through our study volume and has been analyzed through different theoretical test inversions. High-velocity anomalies are observed in the western portion of the Sao Francisco Craton, supporting the hypothesis that this Craton was part of a major Neoproterozoic plate (San Franciscan Plate). Low-velocity anomalies beneath the Tocantins Province (mainly fold belts between the Amazon and Sao Francisco Cratons) are interpreted as due to lithospheric thinning, which is consistent with the good correlation between intraplate seismicity and low-velocity anomalies in this region. Our results show that the basement of the Parana Basin is formed by several blocks, separated by suture zones, according to model of Milani & Ramos. The slab of the Nazca Plate can be observed as a high-velocity anomaly beneath the Parana Basin, between the depths of 700 and 1200 km. Further, we confirm the low-velocity anomaly in the NE area of the Parana Basin which has been interpreted by VanDecar et al. as a fossil conduct of the Tristan da Cunha Plume related to the Parana flood basalt eruptions during the opening of the South Atlantic.

Re-Os isotope and highly siderophile element systematics of the Parana continental flood basalts (Brazil)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Sr-Nd-Pb isotopic constraints on the nature of the mantle sources involved in the genesis of the high-Ti tholeiites from northern Paraná Continental Flood Basalts (Brazil)

There has been little research on geochemistry and isotopic compositions in tholeiites of the Northern region from the Paraná Continental Flood Basalts (PCFB), one of the largest continental provinces of the world. In order to examine the mantle sources involved in the high-Ti (Pitanga and Paranapanema) basalt genesis, we studied Sr, Nd, and Pb isotopic systematics, and major, minor and incompatible trace element abundances. The REE patterns of the investigated samples (Pitanga and Paranapanema magma type) are similar (parallel to) to those of Island Arc Basalts' REE patterns. The high-Ti basalts investigated in this study have initial (133Ma) 87Sr/86Sr ratios of 0.70538-0.70642, 143Nd/144Nd of 0.51233-0.51218, 206Pb/204Pb of 17.74-18.25, 207Pb/204Pb of 15.51-15.57, and 208Pb/204Pb of 38.18-38.45. These isotopic compositions do not display any correlation with Nb/Th, Nb/La or P2O5/K2O ratios, which also reflect that these rocks were not significantly affected by low-pressure crustal contamination. The incompatible trace element ratios and Sr-Nd-Pb isotopic compositions of the PCFB tholeiites are different to those found in Tristan da Cunha ocean island rocks, showing that this plume did not play a substantial role in the PCFB genesis. This interpretation is corroborated by previously published osmium isotopic data (initial γOs values range from+1.0 to+2.0 for high-Ti basalts), which also preclude basalt generation by melting of ancient subcontinental lithospheric mantle. The geochemical composition of the northern PCFB may be explained through the involvement of fluids and/or small volume melts related to metasomatic processes. In this context, we propose that the source of these magmas is a mixture of sublithospheric peridotite veined and/or interlayered with mafic components (e.g., pyroxenites or eclogites). The sublithospheric mantle (dominating the osmium isotopic compositions) was very probably enriched by fluids and/or magmas related to the Neoproterozoic subduction processes. This sublithospheric mantle region may have been frozen and coupled to the base of the Parana basin lithospheric plate above which the Paleozoic subsidence and subsequent Early Cretaceous magmatism occurred. © 2013 Elsevier Ltd.

Re-Os isotope and highly siderophile element systematics of the Parana continental flood basalts (Brazil)

Basalts of the Parana continental flood basalt (PCFB) province erupted through dominantly Proterozoic continental crust during the Cretaceous. In order to examine the mantle source(s) of this major flood basalt province, we studied Os, Sr, Nd, and Pb isotope systematics, and highly siderophile element (HSE) abundances in tholeiitic basalts that were carefully chosen to show the minimal effects of crustal contamination. These basalts define a precise Re-Os isochron with an age of 131.6 +/- 2.3 Ma and an initial Os-187/Os-188 of 0.1295 +/- 0.0018 (gamma Os-187 = +2.7 +/- 1.4). This initial Os isotopic composition is considerably more radiogenic than estimates of the contemporary Depleted Mantle (DM). The fact that the Re-Os data define a well constrained isochron with an age similar to Ar-40/Ar-39 age determinations, despite generally low Os concentrations, is consistent with closed-system behavior for the HSE. Neodymium, Sr, and Pb isotopic data suggest that the mantle source of the basalts had been variably hybridized by melts derived from enriched mantle components. To account for the combined Os, Nd, Sr, and Pb isotopic characteristics of these rocks, we propose that the primary melts formed from metasomatized asthenospheric mantle (represented by arc-mantle peridotite) that underwent mixing with two enriched components, EM-I and EM-II. The different enriched components are reflected in minor isotopic differences between basalts from southern and northern portions of the province. The Tristan da Cunha hotspot has been previously suggested to be the cause of the Parana continental flood basalt magmatism. However, present-day Tristan da Cunha lavas have much higher Os-187/Os-188 isotopic compositions than the source of the PCFB. These data, together with other isotopic and elemental data, preclude making a definitive linkage between the Tristan plume and the PCFB. (C) 2012 Elsevier B.V. All rights reserved.

A variationist approach to the examination of insertion and deletion of /h/ in Kosraean English

I report on language variation in the unresearched variety of English emerging on Kosrae, Federated States of Micronesia. English is spoken as the inter-island lingua franca throughout Micronesia and has been the official language of FSM since gaining its independence in 1986, though still retaining close ties with the US through and economic “compact” agreement. I present here an analysis of a corpus of over 90 Kosraean English speakers, compiled during a three month fieldwork trip to the island in the Western Pacific. The 45 minute sociolinguistically sensitive recordings are drawn from a corpus of old and young, with varying levels of education and occupations, and off-island experiences. In the paper I analyse two variables. The first variable is the realisation of /h/, often subject to deletion in both L1 and L2 varieties of English. Such occurrences are commonly associated with Cockney English, but also found in Caribbean English and the postcolonial English of Australia. For example:  Male, 31: yeah I build their house their local huts and they pay me /h/ deletion is frequent in Kosraean English, but, perhaps expectedly, occurs slightly less among people with higher contact with American English, through having spent longer periods off island. The second feature under scrutiny is the variable epenthesis of [h] to provide a consonantal onset to vowel-initial syllables.  Male, 31: that guy is really hold now This practice is also found beyond Kosraean English. Previous studies find h-epenthesis arising in L1 varieties including Newfoundland and Tristan de Cunha English, while similar manifestations are identified in Francophone L2 learners of English. My variationist statistical analysis has shown [h] insertion:  to disproportionately occur intervocalically;  to be constrained by both speaker gender and age: older males are much more likely to epenthesis [h] in their speech;  to be more likely in the onset of stressed as opposed to unstressed syllables. In light of the findings of my analysis, I consider the relationship between h-deletion and h-epenthesis, the plausibility of hypercorrection as a motivation for the variation, and the potential influence of the substrate language, alongside sociolinguistic factors such as attitudes towards the US based on mobility. The analysis sheds light on the extent to which different varieties share this characteristic and the comparability of them in terms of linguistic constraints and attributes. Clarke, S. (2010). Newfoundland and Labrador English. Edinburgh: Edinburgh University Press Hackert, S. (2004). Urban Bahamian Creole: System and Variation. Varieties of English Around the World G32. Amsterdam: Benjamins Milroy, J. (1983). On the Sociolinguistic History of H-dropping in English in Current topics in English historical linguistics: Odense UP

Rb, Sr, Sm and Nd concentrations and isotopic composition of basalts from DSDP Leg 74 (Table 1)

Basement intersected in DSDP holes 525A, 528 and 527 on the Walvis Ridge consists of submarine basalt flows and pillows with minor intercalated sediments. These holes are situated on the crest and mid and lower northwest flank of a NNW-SSE-trending ridge block which would have closely paralleled the paleo mid-ocean ridge (Rabinowitz and LaBrecque, 1979 doi:10.1029/JB084iB11p05973, Moore et al. (1983 doi:10.1130/0016-7606(1983)94<907:TWRTDS>2.0.CO;2). The basalts were erupted approximately 70 m.y. ago, an age equivalent to that of immediately adjacent oceanic crust in the Angola Basin and coraistent with formation at the paleo mid-ocean ridge (Moore et al., 1983). The basalt types vary from aphyric quartz tholeiites on the ridge crest to highly plagioclase phyric olivine tholeiites on the ridge flank. These show systematic differences in incompatible trace element and isotopic composition. Many element and isotope ratio pairs form systematic trends with the ridge crest basalts at one end and the highly phyric ridge flank basalts at the other. The low 143Nd/144Nd (0.51238), 206Pb/204Pb (17.54), 207Pb/204Pb (15.47), 208Pb/204Pb (38.14) and high 87Sr/86Sr (0.70512) ratios of the ridge crest basalts suggest derivation from an old Nd/Sm-, Rb/Sr- and Pb/U-enriched mantle source. This isotopic signature is similar to that of alkaline basalts on Tristan da Cunha but offset to significantly lower Nd and Pb isotopic ratios. The isotopic ratio trends may be extrapolated beyond the ridge flank basalts with higher 143Nd/144Nd (0.51270), 206Pb/204Pb (18.32), 207Pb/204Pb (15.52), 208Pb/204Pb (38.77) and lower 87Sr/86Sr (0.70417) ratios in the direction of increasingly Nd/Sm-, Rb/Sr- and Pb/U-depleted source compositions. These isotopic correlations are equally consistent with mixing of depleted and enriched end member melts or partial melting of an inhomogeneous, variably enriched mantle source. However, observed Zr-Ba-Nb-Y interelement relationships are inconsistent with any simple two-component model of magma mixing, as might result from the rise of a lower mantle plume through the upper mantle. Incompatible element and Pb isotopic systematics also preclude extensive involvement of depleted (N-type) MORB material or its mantle sources. In our preferred petrogenetic model the Walvis Ridge basalts were derived by partial melting of mantle similar to an enriched (E-type) MORB source which had become heterogeneous on a small scale due to the introduction of small-volume melts and metasomatic fluids.

Chemical and isotopic compositions of lavas from the Broken Ridge and Southern Kerguelen Plateau

Lavas from several major bathymetric highs in the eastern Indian Ocean that are likely to have formed as Early to Middle Cretaceous manifestations of the Kerguelen hotspot are predominantly tholeiitic; so too are glass shards from Eocene to Paleocene volcanic ash layers on Broken Ridge, which are believed to have come from eruptions on the Ninetyeast Ridge. The early dominance of tholeiitic compositions contrasts with the more recent intraplate, alkalic volcanism of the Kerguelen Archipelago. Isotopic and incompatible-element ratios of the plateau lavas are distinct from those of Indian mid-ocean ridge basalts; their Nd, Sr, 207Pb/204Pb and 2078b/204Pb isotopic ratios overlap with but cover a much wider range than measured for more recent oceanic products of the Kerguelen hotspot (including the Ninetyeast Ridge) or, indeed, oceanic lavas from any other hotspot in the world. Samples from the Naturaliste Plateau and ODP Site 738 on the southern tip of the Kerguelen Plateau are particularly noteworthy, with e-Nd(T) = -13 to -7, (87Sr/86Sr)T=0.7090 to 0.7130 and high 207Pb/204Pb relative to 206Pb/204Pb. In addition, the low-e-Nd(T) Naturaliste Plateau samples are elevated in SiO2 (>54 wt%). In contrast to "DUPAL" oceanic islands such as the Kerguelen Archipelago, Pitcairn and Tristan da Cunha, the plateau lavas with extreme isotopic characteristics also have relative depletions in Nb and Ta (e.g., Th/Ta, La Nb > primitive mantle values); the lowest e-Nd(T) and highest Th/Ta and La Nb values occur at sites located closest to rifted continental margins. Accepting a Kerguelen plume origin for the plateau lavas, these characteristics probably reflect the shallow-level incorporation of continental lithosphere in either the head of the early Kerguelen plume or in plume-derived magmas, and suggest that the influence of such material diminished after the period of plateau construction. Contamination of asthenosphere with the type of material affecting Naturaliste Plateau and Site 738 magmatism appears unlikely to be the cause of low-206Pb/204Pb Indian mid-ocean ridge basalts. Finally, because isotopic data for the plateaus do not cluster or form converging arrays in isotope-ratio plots, they provide no evidence for either a quickly evolving, positive ?Nd, relatively high-206Pb/204Pb plume composition, or a plume source dominated by mantle with e-Nd of -3 to ~0.

Major and trace elements at DSDP Leg 74 Holes

Deep Sea Drilling Project Leg 74 drilled basement on the Walvis Ridge at Sites 525, 527, and 528. These sites are located on the crest and flanks of the segment of the Ridge about 68 to 70 m.y. old in the central province of the Ridge. Each site has a number of distinct subaqueous flows separated by sediment layers. Although variation in geochemistry among units and sites is related in part to alteration or crystal fractionation, some is caused by small-scale compositional variation in the mantle source of the basalts. Leg 74 basalts are similar to other basalts recovered from the Walvis Ridge and the Rio Grande Rise. They show distinct compositional differences to mid-ocean ridge basalts in general, to those recovered from the South Atlantic at this latitude, and to basalts presently erupting in Tristan da Cunha. The composition of the Walvis Ridge basalts does not suggest simple mixtures of present-day MORB and Tristan da Cunha melts. If the Walvis Ridge represents the trace of the Tristan da Cunha hot spot as the plates separated, then the composition of the mantle source has differed at different times in the past, which suggests mantle heterogeneity.

(Table 1) K-Ar age determinations on biotite from coarse sand within DSDP Sample 72-516F-76-4,107-115

Qualitative petrographic study of selected clastic horizons within the Eocene section of Hole 516F has revealed the presence of abundant fine-grained lithic fragments, probably volcanic, along with coarser fragments of quartz and feldspar apparently derived from a nearby plutonic terrain. In detail, poor sorting, presence of graded bedding, and an abundance of clay suggest these are turbidite horizons locally derived from a mixed volcanic/plutonic terrain, possibly with some direct contribution from contemporary volcanic ash falls. A progressive increase in plutonic versus volcanic components with time is, however, more consistent with an erosional origin for most of this material. Unusual euhedral dark biotite is abundant in several of the lower clastic horizons; it is most easily interpreted as microphenocrysts weathered in situ out of alkalic volcanic ash. Biotite separated from Sample 516F-76-4,107-115 cm, has been dated by the K-Ar method at about 46 Ma. Alkaline volcanoes active on the Rio Grande Rise in the middle Eocene would be the most probable source of this ash and would be consistent with other evidence for potassic, alkaline volcanism along the Rio Grande Rise and at the Tristan da Cunha hot spot.

(Table 1) Basalt geochemsitry at DSDP Hole 72-516F

Basalts from Hole 516F, DSDP Leg 72 on the Rio Grande Rise are tholeiitic in character but differ from normal mid-ocean ridge basalts in the South Atlantic in higher concentrations of incompatible elements such as Ti, K, V, Sr, Ba, Zr, Nb, and light rare-earth elements and in lower concentrations of Mg, Cr, and Ni. They contrast with previously reported basalts from the Rio Grande Rise, which were highly alkalic in character. The Rio Grande Rise basalts from Hole 516F (age 84.5 Ma) are generally similar to basalts from the eastern end of the Walvis Ridge (80-100 Ma). It is suggested that they either originated, like the Walvis Ridge, from a mantle hot spot that is different from the present-day hot spot (Tristan da Cunha) and that has changed composition with time, or from a spreading center that was shallow and chemically influenced by the adjacent hot spot, similar to the present-day Mid-Atlantic Ridge near the Azores and Tristan da Cunha.

Geochemistry of basalts at DSDP Leg 73 Holes

During Deep Sea Drilling Project Leg 73 (South Atlantic), basaltic pillow lava, flows, and sills were encountered in Holes 519A, 520, 522B, and 524. Paleomagnetic data indicate that the basalts from Holes 519A (magnetic Anomaly 51) and 522B (Anomaly 16) have ages of about 12 m.y. and about 38 m.y., respectively. The major- and trace- (including rare-earth-) element characteristics of the Hole 519A basalts (a total of 27 m) demonstrate that these basalts are typical normal-type mid-ocean-ridge basalts (N-type MORB). In composition the basalts overlap olivine tholeiites from other normal Mid-Atlantic Ridge segments. Both the spectra of incompatible, or less-hygromagmatophile elements (such as Ti, V, Y, and Zr) and REE abundances indicate that these basalts are the result of a low-pressure fractionation of olivine, spinel, and Plagioclase prior to eruption. In Hole 520 only 1.7 m of basalt were recovered from a total drilling depth of 10.5 m. These pillow basalts crystallized from fairly evolved (N-type MORB) tholeiitic melts. In total, 19 m of basaltic pillow lavas and flows were penetrated in Hole 522B. Thirteen cooling units were distinguished on the basis of glassy margins and fine quench textures. In contrast to Holes 519A and 520, the basalts of the Hole 522B ridge section can be divided into two major groups of tholeiites: (1) Cooling Units 1 through 12 and (2) Cooling Unit 13. The basalts in this ridge section are also N-type MORBs but are generally more differentiated than those of Holes 519A and 520. The lowermost basalts (Cooling Unit 13) have the most primitive composition and make up a compositional group distinct from the more evolved basalts in the twelve units above it. Hole 524 was drilled on the south flank of the Walvis Ridge and thus provided samples from a more complex part of the South Atlantic seafloor. Three different basaltic rock suites, interlayered with volcanic detrital sediments, were encountered. The rock suites are, from top to bottom, an alkali basaltic pillow lava; a 16-m-thick alkaline diabase sill with an age of about 65 m.y. (according to K-Ar dating and planktonic foraminifers); and a second sill that is approximately 9 m thick, about 74 m.y. in age, and tholeiitic in composition, thus contrasting strongly with the overlying alkaline rocks. The alkali basalts of Hole 524 show chemical characteristics that are very similar to the basaltic lavas of the Tristan da Cunha group volcanoes, which are located approximately 400 km east of the Mid-Atlantic Ridge crest. Thus, the Walvis Ridge may plausibly be interpreted as a line of hot-spot alkaline volcanoes.