Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation

<p>Abstract</p> <p>Background</p> <p>Understanding the processes driving speciation in marine ecosystems remained a challenge until recently, due to the unclear nature of dispersal boundaries. However, recent evidence for marine adaptive radiations and ecological speciation, as well as previously undetected patterns of cryptic speciation is overturning this view. Here, we use multi-gene phylogenetics to infer the family-level evolutionary history of Fucaceae (intertidal brown algae of the northern Pacific and Atlantic) in order to investigate recent and unique patterns of radiative speciation in the genus <it>Fucus </it>in the Atlantic, in contrast with the mainly monospecific extant genera.</p> <p>Results</p> <p>We developed a set of markers from 13 protein coding genes based on polymorphic cDNA from EST libraries, which provided novel resolution allowing estimation of ancestral character states and a detailed reconstruction of the recent radiative history. Phylogenetic reconstructions yielded similar topologies and revealed four independent trans-Arctic colonization events by Fucaceae lineages, two of which also involved transitions from hermaphroditism to dioecy associated with Atlantic invasions. More recently, reversion of dioecious ancestral lineages towards hermaphroditism has occurred in the genus <it>Fucus</it>, particularly coinciding with colonization of more extreme habitats. Novel lineages in the genus <it>Fucus </it>were also revealed in association with southern habitats. These most recent speciation events occurred during the Pleistocene glaciations and coincided with a shift towards selfing mating systems, generally southward shifts in distribution, and invasion of novel habitats.</p> <p>Conclusions</p> <p>Diversification of the family occurred in the Late-Mid Miocene, with at least four independent trans-Artic lineage crossings coincident with two reproductive mode transitions. The genus <it>Fucus </it>arose in the Pliocene but radiated within a relatively short time frame about 2.5 million years ago. Current species distributions of <it>Fucus </it>suggest that climatic factors promoted differentiation between the two major clades, while the recent and rapid species radiation in the temperate clade during Pleistocene glacial cycles coincided with several potential speciation drivers.</p

Proceedings of the second "international Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST'14)

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference.Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist1

The Parallelized Large-Eddy Simulation Model (PALM) version 4.0 for atmospheric and oceanic flows: model formulation, recent developments, and future perspectives

In this paper we present the current version of the Parallelized Large-Eddy Simulation Model (PALM) whose core has been developed at the Institute of Meteorology and Climatology at Leibniz Universität Hannover (Germany). PALM is a Fortran 95-based 5 code with some Fortran 2003 extensions and has been applied for the simulation of a variety of atmospheric and oceanic boundary layers for more than 15 years. PALM is optimized for use on massively parallel computer architectures and was recently ported to general-purpose graphics processing units. In the present paper we give a detailed description of the current version of the model and its features, such as an embedded 10 Lagrangian cloud model and the possibility to use Cartesian topography. Moreover, we discuss recent model developments and future perspectives for LES applications.DFG/RA/617/3DFG/RA/617/6DFG/RA/617/16DFG/RA/617/27-

Low-latency, query-driven analytics over voluminous multidimensional, spatiotemporal datasets

2017 Summer.Includes bibliographical references.Ubiquitous data collection from sources such as remote sensing equipment, networked observational devices, location-based services, and sales tracking has led to the accumulation of voluminous datasets; IDC projects that by 2020 we will generate 40 zettabytes of data per year, while Gartner and ABI estimate 20-35 billion new devices will be connected to the Internet in the same time frame. The storage and processing requirements of these datasets far exceed the capabilities of modern computing hardware, which has led to the development of distributed storage frameworks that can scale out by assimilating more computing resources as necessary. While challenging in its own right, storing and managing voluminous datasets is only the precursor to a broader field of study: extracting knowledge, insights, and relationships from the underlying datasets. The basic building block of this knowledge discovery process is analytic queries, encompassing both query instrumentation and evaluation. This dissertation is centered around query-driven exploratory and predictive analytics over voluminous, multidimensional datasets. Both of these types of analysis represent a higher-level abstraction over classical query models; rather than indexing every discrete value for subsequent retrieval, our framework autonomously learns the relationships and interactions between dimensions in the dataset (including time series and geospatial aspects), and makes the information readily available to users. This functionality includes statistical synopses, correlation analysis, hypothesis testing, probabilistic structures, and predictive models that not only enable the discovery of nuanced relationships between dimensions, but also allow future events and trends to be predicted. This requires specialized data structures and partitioning algorithms, along with adaptive reductions in the search space and management of the inherent trade-off between timeliness and accuracy. The algorithms presented in this dissertation were evaluated empirically on real-world geospatial time-series datasets in a production environment, and are broadly applicable across other storage frameworks

Phylogenetic Analysis Informed by Geological History Supports Multiple, Sequential Invasions of the Mediterranean Basin by the Angiosperm Family Araceae

Despite the remarkable species richness of the Mediterranean flora and its well-known geological history, few studies have investigated its temporal and spatial origins. Most importantly, the relative contribution of geological processes and long-distance dispersal to the composition of contemporary Mediterranean biotas remains largely unknown. We used phylogenetic analyses of sequences from six chloroplast DNA markers, Bayesian dating methods, and ancestral area reconstructions, in combination with paleogeographic, paleoclimatic, and ecological evidence, to elucidate the time frame and biogeographic events associated with the diversification of Araceae in the Mediterranean Basin. We focused on the origin of four species, Ambrosina bassii, Biarum dispar, Helicodiceros muscivorus, Arum pictum, subendemic or endemic to Corsica, Sardinia, and the Balearic Archipelago. The results support two main invasions of the Mediterranean Basin by the Araceae, one from an area connecting North America and Eurasia in the Late Cretaceous and one from the Anatolian microplate in western Asia during the Late Eocene, thus confirming the proposed heterogeneous origins of the Mediterranean flora. The subendemic Ambrosina bassii and Biarum dispar likely diverged sympatrically from their widespread Mediterranean sister clades in the Early-Middle Eocene and Early-Middle Miocene, respectively. Combined evidence corroborates a relictual origin for the endemic Helicodiceros muscivorus and Arum pictum, the former apparently representing the first documented case of vicariance driven by the initial splitting of the Hercynian belt in the Early Oligocene. A recurrent theme emerging from our analyses is that land connections and interruptions, caused by repeated cycles of marine transgressions-regressions between the Tethys and Paratethys, favored geodispersalist expansion of biotic ranges from western Asia into the western Mediterranean Basin and subsequent allopatric speciation at different points in time from the Late Eocene to the Late Oligocen

Proceedings of the Scientific Data Compression Workshop

Continuing advances in space and Earth science requires increasing amounts of data to be gathered from spaceborne sensors. NASA expects to launch sensors during the next two decades which will be capable of producing an aggregate of 1500 Megabits per second if operated simultaneously. Such high data rates cause stresses in all aspects of end-to-end data systems. Technologies and techniques are needed to relieve such stresses. Potential solutions to the massive data rate problems are: data editing, greater transmission bandwidths, higher density and faster media, and data compression. Through four subpanels on Science Payload Operations, Multispectral Imaging, Microwave Remote Sensing and Science Data Management, recommendations were made for research in data compression and scientific data applications to space platforms

Comparative genomics of Bistorta vivipara

High Northern latitudes are predicted to change considerably in forthcoming climate scenarios, and empirical evidence detailing a species\u27 capacity to cope with extreme variability is needed. Tundra plants make for an excellent study because their genetic histories were impacted by the dramatic transitions of historic glacial and interglacial ages. Here, thousands of restriction site-associated DNA (RAD) markers from geographically isolated Alaskan (Arctic) and Coloradan (Alpine) Bistorta vivipara (Polygonaceae) populations are compared in an investigation of evolutionary response to rapid climate change. Non-coding nuclear markers were analyzed in a coalescent framework to estimate an effective ancestral population size (Na) and divergence date (t) of the two populations of ~23 000 individuals and ~140 000 years before present. Nucleotide substitutions per synonymous site (dS) and nonsynonymous site (dN) were calculated for putative orthologous protein-coding sequences to determine the form of selection acting on the subsampled genome in the context of t. Most sequences were either 100% conserved or exhibited dS \u3e dN, suggesting purifying selection. The few sequences suggesting positive selection (dS \u3c dN) were identified as retroelements, which are expected to escape purifying selection. There were two exceptions: a putative protein phosphatase and a kinase involved with steroid signaling. The results suggest genetic adaptation is not a readily apparent option for B. vivipara’s response to climate change. This, and other organisms whose habitats will shift quickly or disappear, may depend on demographic and plastic responses as alternatives to extinction

Further studies with Melianthus L. : a molecular phylogeny, evolutionary patterns of diversification in the genus and pollinator syndromes

Bibliography: leaves 84-100.A phylogeny was produced for the eight taxa comprising the largely South African genus Melianthus L. based on two plastid markers (trnL-F and psbA-trnH) and one nuclear marker (ITS). Topological comparisons with a tree based on an existing morphological data set revealed significant incongruence leading to a loss of resolution upon combination. Ultimately, the combined three-gene data tree was selected as the strongest phylogenetic estimate for Melianthus based on its better resolution and greater support levels. This tree confirms the monophyly of Melianthus with M. major being resolved as sister to the remainder of the genus. Within the remaining clade, M. villosus is resolved sister to a clade comprising two morphologically distinct subclades, one of these being noted for a western distribution (comprising M. elongatus and the M. pectinatus complex), the other being centred farther east (comprising M. cocomosus and the M dregeanus complex). A molecular clock analysis was employed to date the emergence of specific taxa and clades, while ancestral range and habitat reconstructions were performed to determine historical conditions under which these groups and their morphological novelties arose. A scenario depicting the evolution and diversification of Melianthus is developed against a backdrop of the paleo-history of southern Africa. The genus appears to have originated in the eastern part of South Africa during a mild, mesic Oligocene with subsequent westward expansion into drier habitats of Miocene and Pliocene origins. Observations of bird visitors to a range of Melianthus species indicate that the genus employs a generalist pollination syndrome, thus refuting suggestions of a co-exclusive relationship with sunbirds (Nectariniidae). Nevertheless, the genus is undeniably ornithophilous. Nectar studies reveal interspecific variation in both the volume and concentration of nectar produced as well as in nectar colourition

Zooplankton visualization system: design and real-time lossless image compression

In this thesis, I present a design of a small, self-contained, underwater plankton imaging system. I base the imaging system’s design on an embedded PC architecture based on PC/104-Plus standards to meet the compact size and low power requirements. I developed a simple graphical user interface to run on a real-time operating system to control the imaging system. I also address how a real-time image compression scheme implemented on an FPGA chip speeds up image transfer speeds of the imaging system. Since lossless compression of the image is required in order to retain all image details, I began with an established compression scheme like SPIHT, and latter proposed a new compression scheme that suits the imaging system’s requirements. I provide an estimate of the total amount of resources required and propose suitable FPGA chips to implement the compression scheme. Finally, I present various parallel designs by which the FPGA chip can be integrated into the imaging system