Benthic macroalgae of Shark Bay, Western Australia

One hundred and sixty one taxa of benthic macro-algae are reported from Shark Bay, Western Australia, growing either on subtidal rock platforms, on the extensive sandflats that dominate the bay, or as epiphytes on seagrasses and other algae. In addition many species survive as drift algae amongst the seagrass beds. Tropical taxa predominate. The Rhodophyta are represented by the greatest number of taxa, but these tend to be inconspicuous epiphytes. Members of the Chlorophyta are the most conspicuous in most areas, with Penicillus nodulosus and Polyphysa peniculus the most common species. Polyphysa peniculus dominates the high salinity areas south of the Faure Sill. The brown algae Hormophysa cuneiformis and Dictyota furcellata were also common in high salinity areas. Benthic algal species richness was lower in areas of high salinity

Benthic algae and seagrasses of the Walpole and Nornalup Inlets Marine Park, Western Australia

A survey of the marine plants of the Walpole and Nornalup Inlets Marine Park has recorded 49 species of marine benthic algae and seagrasses, including 15 green algae, 11 brown algae, 18 red algae, 4 seagrasses, and one cyanobacterium, representing a substantial increase on the 14 previously recorded species. Most species are relatively common elements of the south-western Australian marine flora, but several are of taxonomic or biogeographic and ecological interest. Included in this group are: a new species of the green algal genus Codium, the first records of previously unknown reproductive phases in the red algae Mazoyerella australis and Spermothamnion cymosum, and a new distribution record for Ossiella pacifica, a species hitherto known only from warmer waters of the Pacific Ocean and not recorded for mainland Australia. The species diversity in the inlets decreases markedly with increasing distance from the ocean, reflecting a reducing marine and increasing estuarine influence

Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia

Populations at the edges of their geographical range tend to have lower genetic diversity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic diversity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal diversity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic diversity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic diversity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.Elizabeth A. Sinclair, Jane M. Edgeloe, Janet M. Anthony, John Statton, Martin F. Breed and Gary A. Kendric

Historic and contemporary biogeographic perspectives on range‐wide spatial genetic structure in a widespread seagrass

Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterize intraspecific genetic diversity and spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia. Predictive modeling was used to contrast the current Posidonia australis distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognized biogeographic provinces and largely consistent with the finer-scale IMCRA bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional IMCRA bioregions. Clonal diversity was highly variable but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance. Our approach suggests how shared seascape drivers have influenced the capacity of P. australis to effectively track sea level changes associated with natural climate cycles over millennia, and in particular, the recolonization of meadows across the Continental Shelf following the LGM. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure.Elizabeth A. Sinclair, Renae K. Hovey, Siegfried L. Krauss, Janet M. Anthony, Michelle Waycott, Gary A. Kendric

Optimal limits on f_{NL}^{local} from WMAP 5-year data

We have applied the optimal estimator for f_{NL}^{local} to the 5 year WMAP data. Marginalizing over the amplitude of foreground templates we get -4 < f_{NL}^{local} < 80 at 95% CL. Error bars of previous (sub-optimal) analyses are roughly 40% larger than these. The probability that a Gaussian simulation, analyzed using our estimator, gives a result larger in magnitude than the one we find is 7%. Our pipeline gives consistent results when applied to the three and five year WMAP data releases and agrees well with the results from our own sub-optimal pipeline. We find no evidence of any residual foreground contamination.Comment: [v1] 21 pages, 7 figures. [v2] minor changes matching published versio

Local stochastic non-Gaussianity and N-body simulations

Large-scale clustering of highly biased tracers of large-scale structure has emerged as one of the best observational probes of primordial non-Gaussianity of the local type (i.e. f_{NL}^{local}). This type of non-Gaussianity can be generated in multifield models of inflation such as the curvaton model. Recently, Tseliakhovich, Hirata, and Slosar showed that the clustering statistics depend qualitatively on the ratio of inflaton to curvaton power \xi after reheating, a free parameter of the model. If \xi is significantly different from zero, so that the inflaton makes a non-negligible contribution to the primordial adiabatic curvature, then the peak-background split ansatz predicts that the halo bias will be stochastic on large scales. In this paper, we test this prediction in N-body simulations. We find that large-scale stochasticity is generated, in qualitative agreement with the prediction, but that the level of stochasticity is overpredicted by ~30%. Other predictions, such as \xi independence of the halo bias, are confirmed by the simulations. Surprisingly, even in the Gaussian case we do not find that halo model predictions for stochasticity agree consistently with simulations, suggesting that semi-analytic modeling of stochasticity is generally more difficult than modeling halo bias.Comment: v3: minor changes matching published versio

Extreme differences in 87Sr/86Sr between Samoan lavas and the magmatic olivines they host: Evidence for highly heterogeneous 87Sr/86Sr in the magmatic plumbing system sourcing a single lava

.Investigations of mantle heterogeneity in ocean island basalts (OIB) frequently compare heavy radiogenic isotopes (i.e. 87Sr/86Sr), often measured in whole rock powders, with 3He/4He and δ18O, commonly measured in olivines. However, the 87Sr/86Sr in the olivines, which is dominated by Sr in melt inclusions, may not be in equilibrium with the 87Sr/86Sr in the whole rock. Here we present new 87Sr/86Sr measurements made on Samoan magmatic olivines, where multiple olivine crystals are aggregated for a single isotopic measurement. The olivines host abundant melt inclusions, and yielded relatively large quantities of Sr (13.0 to 100.6 ng) in 19 to 185 mg aliquots of fresh olivine, yielding high Srsample/Srblank ratios (≥ 427). These new data on olivines show that samples can exhibit significant 87Sr/86Sr disequilibrium: in one extreme sample, where the basaltic whole rock 87Sr/86Sr (0.708901) is higher than several different aliquots of aggregate magmatic olivines (0.707385 to 0.707773), the whole rock-olivine 87Sr/86Sr disequilibrium is > 1590 ppm. The 87Sr/86Sr disequilibrium observed between whole rocks and bulk olivines relates to the isotopic disequilibrium between whole rocks and the average 87Sr/86Sr of the population of melt inclusions hosted in the olivines. Therefore, a population of olivines in a Samoan lava must have crystallized from (and trapped melts of) a different 87Sr/86Sr composition than the final erupted lava hosting the olivines. A primary question is how melts with different 87Sr/86Sr can exist in the same magmatic plumbing system and contribute heterogeneous 87Sr/86Sr to a lava and the magmatic olivines it hosts. We explore potential mechanisms for generating heterogeneous melts in magma chambers. The reliance, in part, of chemical geodynamic models of the relationships between isotopic systems measured in whole rocks (87Sr/86Sr) and systems measured in olivines (3He/4He and δ18O) means that whole rock-olivine Sr-isotopic disequilibrium will be important for evaluating relationship among these key isotopic tracer systems. Moving forward, it will be important to evaluate whether whole rock-olivine Sr-isotopic disequilibrium is a pervasive issue in OIB globally

Non-Gaussianities in Single Field Inflation and their Optimal Limits from the WMAP 5-year Data

Using the recently developed effective field theory of inflation, we argue that the size and the shape of the non-Gaussianities generated by single-field inflation are generically well described by two parameters: f_NL^equil, which characterizes the size of the signal that is peaked on equilateral configurations, and f_NL^orthog, which instead characterizes the size of the signal which is peaked both on equilateral configurations and flat-triangle configurations (with opposite signs). The shape of non-Gaussianities associated with f_NL^orthog is orthogonal to the one associated to f_NL^equil, and former analysis have been mostly blind to it. We perform the optimal analysis of the WMAP 5-year data for both of these parameters. We find no evidence of non-Gaussianity, and we have the following constraints: -125 < f_NL^equil < 435, -369 < f_NL^orthog < 71 at 95% CL. We show that both of these constraints can be translated into limits on parameters of the Lagrangian of single-field inflation. For one of them, the speed of sound of the inflaton fluctuations, we find that it is either bounded to be c_s > 0.011 at 95% CL. or alternatively to be so small that the higher-derivative kinetic term dominate at horizon crossing. We are able to put similar constraints on the other operators of the inflaton Lagrangian.Comment: 46 pages, 12 figures. v2: JCAP published version. Added references and minor corrections. v3: Corrected minor typo in App.

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy