Species-level divergences in multiple functional traits between the two endemic subspecies of Blue Chaffinches Fringilla teydea in Canary Islands

Background: One of the biggest challenges in avian taxonomy is the delimitation of allopatric species because their reproductive incompatibility cannot be directly studied in the wild. Instead, reproductive incompatibility has to be inferred from multiple, divergent character sets that indicate a low likelihood of allopatric populations amalgamating upon secondary contact. A set of quantitative criteria for species delimitation has been developed for avian taxonomy. Results: Here, we report a broad multi-trait comparison of the two insular subspecies of the Blue Chaffinch Fringilla teydea, endemic to the pine forests of Tenerife (ssp. teydea) and Gran Canaria (ssp. polatzeki) in the Canary Islands. We found that the two taxa were reciprocally monophyletic in their whole mitogenomes and two Z chromosome introns. The genetic distance in mitogenomes indicates around 1 Mya of allopatric evolution. There were diagnostic differences in body morphometrics, song and plumage reflectance spectra, whose combined divergence score (=11) exceeds the threshold level (=7) set for species delimitation by Tobias et al. (Ibis 152:724–746, 2010). Moreover, we found a marked divergence in sperm lengths with little range overlap. Relatively long sperm with low intra- and intermale CV compared to other passerines suggest a mating system with high levels of sperm competition (extrapair paternity) in these taxa. Conclusion: The large and diagnostic divergences in multiple functional traits qualify for species rank, i.e., Tenerife Blue Chaffinch (Fringilla teydea) and Gran Canaria Blue Chaffinch (Fringilla polatzeki). We encourage a wider use of sperm traits in avian taxonomy because sperm divergences might signal reproductive incompatibility at the postcopulatory prezygotic stage, especially in species with sperm competition

An Improved and Homogeneous Altimeter Sea Level Record from the ESA Climate Change Initiative

Sea Level is a very sensitive index of climate change since it integrates the impacts of ocean warming and ice mass loss from glaciers and the ice sheets. Sea Level has been listed as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS). During the past 25 years, the sea level ECV has been measured from space by different altimetry missions that have provided global and regional observations of sea level variations. As part of the Climate Change Initiative (CCI) program of the European Space Agency (ESA) (established in 2010), the Sea Level project (SL_cci) aimed at providing an accurate and homogeneous long-term satellite-based sea level record. At the end of the first phase of the project (2010-2013), an initial version (v1.1) of the sea level ECV has been made available to users (Ablain et al., 2015). During the second phase (2014-2017), improved altimeter standards have been selected to produce new sea level products (called SL_cci v2.0) based on 9 altimeter missions for the period 1993-2015 (https://doi.org/10.5270/esa-sea_level_cci-1993_2015-v_2.0-201612). Corresponding orbit solutions, geophysical corrections and altimeter standards used in this v2.0 dataset are described in details in Quartly et al. (2017). The present paper focuses on the description of the SL_cci v2.0 ECV and associated uncertainty and discusses how it has been validated. Various approaches have been used for the quality assessment such as internal validation, comparisons with sea level records from other groups and with in-situ measurements, sea level budget closure analyses and comparisons with model outputs. Compared to the previous version of the sea level ECV, we show that use of improved geophysical corrections, careful bias reduction between missions and inclusion of new altimeter missions lead to improved sea level products with reduced uncertainties at different spatial and temporal scales. However, there is still room for improvement since the uncertainties remain larger than the GCOS requirements. Perspectives for subsequent evolutions are also discussed

Exploitation of error correlation in a large analysis validation: GlobCurrent case study

An assessment of variance in ocean current signal and noise shared by in situ observations (drifters) and a large gridded analysis (GlobCurrent) is sought as a function of day of the year for 1993–2015 and across a broad spectrum of current speed. Regardless of the division of collocations, it is difficult to claim that any synoptic assessment can be based on independent observations. Instead, a measurement model that departs from ordinary linear regression by accommodating error correlation is proposed. The interpretation of independence is explored by applying Fuller's (1987) concept of equation and measurement error to a division of error into shared (correlated) and unshared (uncorrelated) components, respectively. The resulting division of variance in the new model favours noise. Ocean current shared (equation) error is of comparable magnitude to unshared (measurement) error and the latter is, for GlobCurrent and drifters respectively, comparable to ordinary and reverse linear regression. Although signal variance appears to be small, its utility as a measure of agreement between two variates is highlighted. Sparse collocations that sample a dense (high resolution) grid permit a first order autoregressive form of measurement model to be considered, including parameterizations of analysis-in situ error cross-correlation and analysis temporal error autocorrelation. The former (cross-correlation) is an equation error term that accommodates error shared by both GlobCurrent and drifters. The latter (autocorrelation) facilitates an identification and retrieval of all model parameters. Solutions are sought using a prescribed calibration between GlobCurrent and drifters (by variance matching). Because the true current variance of GlobCurrent and drifters is small, signal to noise ratio is near zero at best. This is particularly evident for moderate current speed and for the meridional current component

A regional characterization of the GlobCurrent ocean surface current analysis

Observations of extreme conditions, characterized by high heat flux, rapidly changing surface salinity, or strong ocean current, are rare. Although analyses provide estimates of these conditions, because there are few observations to begin with, it is difficult to separately characterize (in terms of calibration and validation) extreme and typical conditions using independent observations. This requirement of independence may not be so dire, however, if we acknowledge that the impact of observations on an analysis is generally local, as is the propagation of errors in space and time. We propose that temporal extrapolation from outside a typical analysis window permits a calibration and validation by triple collocation (e.g., using only an analysis and available in situ observations; cf. Stoffelen 1998). We seek evidence of analysis performance improvement (as expected) using the calibrations that can be derived. We also seek to validate the GlobCurrent ocean current analysis across an entire current speed range, including at both the low (0.1ms-1) and high (1ms-1) ends

A large geometric distortion in the first photointermediate of rhodopsin, determined by double-quantum solid-state NMR

Double-quantum magic-angle-spinning NMR experiments were performed on 11,12-C-13(2)-retinylidene-rhodopsin under illumination at low temperature, in order to characterize torsional angle changes at the C11-C12 photoisomerization site. The sample was illuminated in the NMR rotor at low temperature (similar to 120 K) in order to trap the primary photointermediate, bathorhodopsin. The NMR data are consistent with a strong torsional twist of the HCCH moiety at the isomerization site. Although the HCCH torsional twist was determined to be at least 40A degrees, it was not possible to quantify it more closely. The presence of a strong twist is in agreement with previous Raman observations. The energetic implications of this geometric distortion are discussed

Using detergent to enhance detection sensitivity of African trypanosomes in human CSF and blood by Loop-Mediated Isothermal Amplification (LAMP)

<p><b>Background:</b> The loop-mediated isothermal amplification (LAMP) assay, with its advantages of simplicity, rapidity and cost effectiveness, has evolved as one of the most sensitive and specific methods for the detection of a broad range of pathogenic microorganisms including African trypanosomes. While many LAMP-based assays are sufficiently sensitive to detect DNA well below the amount present in a single parasite, the detection limit of the assay is restricted by the number of parasites present in the volume of sample assayed; i.e. 1 per µL or 103 per mL. We hypothesized that clinical sensitivities that mimic analytical limits based on parasite DNA could be approached or even obtained by simply adding detergent to the samples prior to LAMP assay.</p> <p><b>Methodology/Principal Findings:</b> For proof of principle we used two different LAMP assays capable of detecting 0.1 fg genomic DNA (0.001 parasite). The assay was tested on dilution series of intact bloodstream form Trypanosoma brucei rhodesiense in human cerebrospinal fluid (CSF) or blood with or without the addition of the detergent Triton X-100 and 60 min incubation at ambient temperature. With human CSF and in the absence of detergent, the LAMP detection limit for live intact parasites using 1 µL of CSF as the source of template was at best 103 parasites/mL. Remarkably, detergent enhanced LAMP assay reaches sensitivity about 100 to 1000-fold lower; i.e. 10 to 1 parasite/mL. Similar detergent-mediated increases in LAMP assay analytical sensitivity were also found using DNA extracted from filter paper cards containing blood pretreated with detergent before card spotting or blood samples spotted on detergent pretreated cards.</p> <p><b>Conclusions/Significance:</b> This simple procedure for the enhanced detection of live African trypanosomes in biological fluids by LAMP paves the way for the adaptation of LAMP for the economical and sensitive diagnosis of other protozoan parasites and microorganisms that cause diseases that plague the developing world.</p&gt

Ocean Virtual Laboratory: A new way to explore multi-sensor synergy demonstrated over the Agulhas region

Ocean Virtual Laboratory is an ESA-funded project to prototype the concept of a single point of access for all satellite remote-sensing data with ancillary model output and in situ measurements for a given region. The idea is to provide easy access for the non-specialist to both data and state-of-the-art processing techniques and enable their easy analysis and display. The project, led by OceanDataLab, is being trialled in the region of the Agulhas Current, as it contains signals of strong contrast (due to very energetic upper ocean dynamics) and special SAR data acquisitions have been recorded there. The project also encourages the take up of Earth Observation data by developing training material to help those not in large scientific or governmental organizations make the best use of what data are available. The website for access is: http://ovl-project.oceandatalab.com

Progress in satellite remote sensing for studying physical processes at the ocean surface and its borders with the atmosphere and sea-ice

Physical oceanography is the study of physical conditions, processes and variables within the ocean, including temperature-salinity distributions, mixing of the water column, waves, tides, currents, and air-sea interaction processes. Here we provide a critical review of how satellite sensors are being used to study physical oceanography processes at the ocean surface and its borders with the atmosphere and sea-ice. The paper begins by describing the main sensor types that are used to observe the oceans (visible, thermal infrared and microwave) and the specific observations that each of these sensor types can provide. We then present a critical review of how these sensors and observations are being used to study i) ocean surface currents, ii) storm surges, iii) sea-ice, iv) atmosphere-ocean gas exchange and v) surface heat fluxes via phytoplankton. Exciting advances include the use of multiple sensors in synergy to observe temporally varying Arctic sea-ice volume, atmosphere- ocean gas fluxes, and the potential for 4 dimensional water circulation observations. For each of these applications we explain their relevance to society, review recent advances and capability, and provide a forward look at future prospects and opportunities. We then more generally discuss future opportunities for oceanography-focussed remote-sensing, which includes the unique European Union Copernicus programme, the potential of the International Space Station and commercial miniature satellites. The increasing availability of global satellite remote-sensing observations means that we are now entering an exciting period for oceanography. The easy access to these high quality data and the continued development of novel platforms is likely to drive further advances in remote sensing of the ocean and atmospheric systems

Mesoscale Eddies Are Oases for Higher Trophic Marine Life

Mesoscale eddies stimulate biological production in the ocean, but knowledge of energy transfers to higher trophic levels within eddies remains fragmented and not quantified. Increasing the knowledge base is constrained by the inability of traditional sampling methods to adequately sample biological processes at the spatio-temporal scales at which they occur