The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages

Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNPs. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNPs is not obtained. Here, we empirically test the robustness of phylogenetic inference based on SNP data for closely related lineages. We conducted a genomewide analysis of 75 712 SNPs, generated via GBS, of southern bull-kelp (Durvillaea). Durvillaea chathamensis co-occurs with D. antarctica on Chatham Island, but the two species have previously been found to be so genetically similar that the status of the former has been questioned. Our results show that D. chathamensis, which differs from D. antarctica ecologically as well as morphologically, is indeed a reproductively isolated species. Furthermore, our replicated analyses show that D. chathamensis cannot be reliably distinguished phylogenetically from closely related D. antarctica using subsets (ranging in size from 400 to 10 000 sites) of the 40 912 parsimony-informative SNPs in our data set and that bootstrap values alone can give misleading impressions of the strength of phylogenetic inferences. These results highlight the importance of independently replicating SNP analyses to verify that phylogenetic inferences based on nontargeted SNP data are robust. Our study also demonstrates that modern genomic approaches can be used to identify cases of recent or incipient speciation that traditional approaches (e.g. Sanger sequencing of a few loci) may be unable to detect or resolve.This research was supported by an Australian Research Council Discovery Early Career Research Award (DE140101715 to CIF) and University of Otago Performance Based Research Funding (to JMW)

Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp

<p>Abstract</p> <p>Background</p> <p>South America's western coastline, extending in a near-straight line across some 35 latitudinal degrees, presents an elegant setting for assessing both contemporary and historic influences on cladogenesis in the marine environment. Southern bull-kelp (<it>Durvillaea antarctica</it>) has a broad distribution along much of the Chilean coast. This species represents an ideal model taxon for studies of coastal marine connectivity and of palaeoclimatic effects, as it grows only on exposed rocky coasts and is absent from beaches and ice-affected shores. We expected that, along the central Chilean coast, <it>D. antarctica </it>would show considerable phylogeographic structure as a consequence of the isolating effects of distance and habitat discontinuities. In contrast, we hypothesised that further south - throughout the region affected by the Patagonian Ice Sheet at the Last Glacial Maximum (LGM) - <it>D. antarctica </it>would show relatively little genetic structure, reflecting postglacial recolonisation.</p> <p>Results</p> <p>Mitochondrial (COI) and chloroplast (<it>rbc</it>L) DNA analyses of <it>D. antarctica </it>from 24 Chilean localities (164 individuals) revealed two deeply divergent (4.5 - 6.1% for COI, 1.4% for <it>rbc</it>L) clades from the centre and south of the country, with contrasting levels and patterns of genetic structure. Among populations from central Chile (32° - 44°S), substantial phylogeographic structure was evident across small spatial scales, and a significant isolation-by-distance effect was observed. Genetic disjunctions in this region appear to correspond to the presence of long beaches. In contrast to the genetic structure found among central Chilean populations, samples from the southern Chilean Patagonian region (49° - 56°S) were genetically homogeneous and identical to a haplotype recently found throughout the subantarctic region.</p> <p>Conclusions</p> <p>Southern (Patagonian) Chile has been recolonised by <it>D. antarctica </it>relatively recently, probably since the LGM. The inferred trans-oceanic ancestry of these Patagonian populations supports the notion that <it>D. antarctica </it>is capable of long-distance dispersal via rafting. In contrast, further north in central Chile, the correspondence of genetic disjunctions in <it>D. antarctica </it>with long beaches indicates that habitat discontinuity drives genetic isolation among established kelp populations. We conclude that rafting facilitates colonisation of unoccupied shores, but has limited potential to enhance gene-flow among established populations. Broadly, this study demonstrates that some taxa may be considered to have either high or low dispersal potential across different temporal and geographic scales.</p

PENCIL: Towards a Platform-Neutral Compute Intermediate Language for DSLs

We motivate the design and implementation of a platform-neutral compute intermediate language (PENCIL) for productive and performance-portable accelerator programming

Genetic affinities between trans-oceanic populations of non-buoyant macroalgae in the high latitudes of the Southern Hemisphere

Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships - even shared haplotypes - were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.This work was funded by New Zealand Marsden contract 07-UOO-099, Department of Zoology and University of Otago Research grants to JMW and CIF; a Shackleton Scholarship to CIF; an Allan Wilson Centre for Molecular Ecology and Evolution postdoctoral grant to CIF; Australian Antarctic Division AAS project #2914

Eccentric Ellipsoidal Red Giant Binaries in the LMC: Complete Orbital Solutions and Comments on Interaction at Periastron

Modelling ellipsoidal variables with known distances can lead to exact determination of the masses of both components, even in the absence of eclipses. We present such modelling using light and radial velocity curves of ellipsoidal red giant binaries in the LMC, where they are also known as sequence E stars. Stars were selected as likely eccentric systems on the basis of light curve shape alone. We have confirmed their eccentric nature and obtained system parameters using the Wilson-Devinney code. Most stars in our sample exhibit unequal light maxima as well as minima, a phenomenon not observed in sequence E variables with circular orbits. We find evidence that the shape of the red giant changes throughout the orbit due to the high eccentricity and the varying influence of the companion. Brief intervals of pulsation are apparent in two of the red giants. We determine pulsation modes and comment on their placement in the period-luminosity plane. Defining the parameters of these systems paves the way for modelling to determine by what mechanism eccentricity is maintained in evolved binaries.Comment: 14 pages, 11 figures. Accepted to MNRAS 2012 January

Discovery of A New Retrograde Trans-Neptunian Object: Hint of A Common Orbital Plane for Low Semi-Major Axis, High Inclination TNOs and Centaurs

Although the majority of Centaurs are thought to have originated in the scattered disk, with the high-inclination members coming from the Oort cloud, the origin of the high inclination component of trans-Neptunian objects (TNOs) remains uncertain. We report the discovery of a retrograde TNO, which we nickname "Niku", detected by the Pan-STARRS 1 Outer Solar System Survey. Our numerical integrations show that the orbital dynamics of Niku are very similar to that of 2008 KV$_{42}$ (Drac), with a half-life of $\sim 500$ Myr. Comparing similar high inclination TNOs and Centaurs ($q > 10$ AU, $a 60^\circ$), we find that these objects exhibit a surprising clustering of ascending node, and occupy a common orbital plane. This orbital configuration has high statistical significance: 3.8-$\sigma$. An unknown mechanism is required to explain the observed clustering. This discovery may provide a pathway to investigate a possible reservoir of high-inclination objects.Comment: 18 pages, 4 figures, 1 table, accepted for publication in ApJ Letter

The genomic footprint of coastal earthquake uplift

Theory suggests that catastrophic earth-history events can drive rapid biological evolution, but empirical evidence for such processes is scarce. Destructive geological events such as earthquakes can represent large-scale natural experiments for inferring such evolutionary processes. We capitalized on a major prehistoric (800 yr BP) geological uplift event affecting a southern New Zealand coastline to test for the lasting genomic impacts of disturbance. Genome-wide analyses of three co-distributed keystone kelp taxa revealed that post-earthquake recolonization drove the evolution of novel, large-scale intertidal spatial genetic ‘sectors’ which are tightly linked to geological fault boundaries. Demographic simulations confirmed that, following widespread extirpation, parallel expansions into newly vacant habitats rapidly restructured genome-wide diversity. Interspecific differences in recolonization mode and tempo reflect differing ecological constraints relating to habitat choice and dispersal capacity among taxa. This study highlights the rapid and enduring evolutionary effects of catastrophic ecosystem disturbance and reveals the key role of range expansion in reshaping spatial genetic patterns

Multiphoton excitation spectra in biological samples

Multiphoton microscopy is becoming a popular mode of live and fixed cell imaging. This mode of imaging offers several advantages due to the fact that fluorochrome excitation is a nonlinear event resulting in excitation only at the plane of focus. Multiphoton excitation is enhanced by the use of ultrafast lasers emitting in the near IR, offering better depth penetration coupled with efficient excitation. Because these lasers, such as titanium:sapphire lasers, offer tunable output it is possible to use them to collect multiphoton excitation spectra. We use the software-tunable Coherent Chameleon laser coupled to the Zeiss LSM 510 META NLO to acquire x−y images of biological samples at multiple excitation wavelengths, creating excitation lambda stacks. The mean intensity of pixels within the image plotted versus excitation wavelength reveals the excitation spectra. Excitation lambda stacks can be separated into individual images corresponding to the signal from different dyes using linear unmixing algorithms in much the same way that emission fingerprinting can be used to generate crosstalk free channels from emission lambda stacks using the META detector. We show how this technique can be used to eliminate autofluorescence and to produce crosstalk-free images of dyes with very close overlap in their emission spectra that cannot be separated using emission fingerprinting. Moreover, excitation finger- printing can be performed using nondescanned detectors (NDDs), offering more flexibility for eliminating autofluorescence or crosstalk between fluorochromes when imaging deep within the sample. Thus, excitation fingerprinting complements and extends the functions offered by the META detector and emission fingerprinting. We correct biases in the laser and microscope transmission to acquire realistic multiphoton excitation spectra for fluorochromes within cells using the microscope, which enables the optimization of the excitation wavelength for single and multilabel experiments and provides a means for studying the influence of the biological environment on nonlinear excitation

Stream and slope weathering effects on organic-rich mudstone geochemistry and implications for hydrocarbon source rock assessment: a Bowland Shale case study

This study contributes to the exploration and quantification of the weathering of organic-rich mudstones under temperate climatic conditions. Bowland Shales, exposed by a stream and slope, were sampled in order to develop a model for the effects of weathering on the mudstone geochemistry, including major and trace element geochemistry, Rock-Eval pyrolysis and δ13Corg. Four weathering grades (I – IV) are defined using a visual classification scheme; visually fresh and unaltered (I), chemically altered (II, III) and ‘paper shale’ that typifies weathered mudstone on slopes (IV). Bedload abrasion in the stream exposes of visually fresh and geochemically unaltered mudstone. Natural fractures are conduits for oxidising meteoric waters that promote leaching at the millimetre scale and/or precipitation of iron oxide coatings along fracture surfaces. On the slope, bedding-parallel fractures formed (and may continue to form) in response to chemical and/or physical weathering processes. These fractures develop along planes of weakness, typically along laminae comprising detrital grains, and exhibit millimetre- and centimetre-scale leached layers and iron oxide coatings. Fracture surfaces are progressively exposed to physical weathering processes towards the outcrop surface, and results in disintegration of the altered material along fracture surfaces. Grade IV, ‘paper shale’ mudstone is chemically unaltered but represents a biased record driven by initial heterogeneity in the sedimentary fabric. Chemically weathered outcrop samples exhibit lower concentrations of both ‘free’ (S1) (up to 0.6 mgHC/g rock) and ‘bound’ (S2) (up to 3.2 mgHC/g rock) hydrocarbon, reduced total organic carbon content (up to 0.34 wt%), reduced hydrogen index (up to 58 mgHC/gTOC), increased oxygen index (up to 19 mgCO + CO2/gTOC) and increased Tmax (up to 11 °C) compared with unaltered samples. If analysis of chemically weathered samples is unavoidable, back-extrapolation of Rock-Eval parameters can assist in the estimation of pre-weathering organic compositions. Combining Cs/Cu with oxygen index is a proxy for identifying the weathering progression from fresh material (I) to ‘paper shale’ (IV). This study demonstrates that outcrop samples in temperate climates can provide information for assessing hydrocarbon potential of organic-rich mudstones

Using Touchscreen Electronic Medical Record Systems to Support and Monitor National Scale-Up of Antiretroviral Therapy in Malawi

Gerry Douglas and colleagues describe the rationale and their experience with scaling up electronic health records in six antiretroviral treatment sites in Malawi