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F in The larval development of Hymenosoma orbiculare Desmarest, 1825 (Crustacea: Decapoda: Brachyura: Hymenosomatidae)

F. 3. Hymenosoma orbiculare Desmarest, 1825. Antennule and antenna: (A) first zoea; (B) second zoea; (C) third zoea. Scale: 0.1 mm.

F in The larval development of Hymenosoma orbiculare Desmarest, 1825 (Crustacea: Decapoda: Brachyura: Hymenosomatidae)

F. 2. Hymenosoma orbiculare Desmarest, 1825. Setation of ventral carapace margin: (A) first zoea; (B) second zoea; (C) third zoea. Scale: 0.1 mm.

F in The larval development of Hymenosoma orbiculare Desmarest, 1825 (Crustacea: Decapoda: Brachyura: Hymenosomatidae)

F. 6. Hymenosoma orbiculare Desmarest, 1825. First maxilliped: (A) first zoea; (B) second zoea; (C) third zoea. Scale: 0.1 mm.

F in The larval development of Hymenosoma orbiculare Desmarest, 1825 (Crustacea: Decapoda: Brachyura: Hymenosomatidae)

F. 4. Hymenosoma orbiculare Desmarest, 1825. Maxillule: (A) first zoea; (B) second zoea; (C) third zoea. Scale: 0.1 mm.

F in The larval development of Hymenosoma orbiculare Desmarest, 1825 (Crustacea: Decapoda: Brachyura: Hymenosomatidae)

F. 7. Hymenosoma orbiculare Desmarest, 1825. Second maxilliped: (A) first zoea; (B) second zoea; (C) third zoea. Scale: 0.1 mm.

Density-by-diet interactions during larval development shape adult life-history trait expression and fitness in a polyphagous fly

Habitat quality early in life determines individual fitness, with possible long-term evolutionary effects on groups and populations. In holometabolous insects, larval ecology plays a major role in determining the expression of traits in adulthood, but how ecological conditions during larval stage interact to shape adult life-history and fitness, particularly in non-model organisms, remains subject to scrutiny. Consequently, our knowledge of the interactive effects of ecological factors on insect development is limited. Here, using the polyphagous fly Bactrocera tryoni, we conducted a fully-factorial design where we manipulated larval density and larval diet (protein-rich, standard, and sugar-rich) to gain insights into how these ecological factors interact to modulate adult fitness. As expected, a protein-rich diet resulted in faster larval development, heavier and leaner adults that were more fecund compared with standard and sugar-rich diets, irrespective of larval density. Females from the protein-rich larval diet had overall higher reproductive rate (i.e., eggs per day) than females from other diets, and reproductive rate decreased linearly with density for females from the protein-rich but non-linearly for females from the standard and sugar-rich diets over time. Surprisingly, adult lipid reserve increased with larval density for adults from the sugar-rich diet (as opposed to decreasing, as in other diets), possibly due to a stress-response to an extremely adverse condition during development (i.e., high intraspecific competition and poor nutrition). Together, our results provide insights into how ecological factors early in life interact and shape the fate of individuals through life-stages in holometabolous insects.

opencc-by-4.0Dec 2021View details →

Scripts and data for the PARASO Geoscientific Model Development paper figures

Scripts and data for reproducing all figures from the PARASO model description paper. <ul> <li> <code>*.tex</code> sources generate Tikz pdf figures calling <code>pdflatex <input.tex></code>. they require a working LaTeX installation with some standard libraries (e.g. Tikz and others). </li> <li> <code>*.py</code> are python scripts generating figures. They require standard python libraires such as matplotlib, numpy, cartopy... </li> </ul> Model description: Pelletier, C., Fichefet, T., Goosse, H., Haubner, K., Helsen, S., Huot, P.-V., Kittel, C., Klein, F., Le clec'h, S., van Lipzig, N. P. M., Marchi, S., Massonnet, F., Mathiot, P., Moravveji, E., Moreno-Chamarro, E., Ortega, P., Pattyn, F., Souverijns, N., Van Achter, G., Vanden Broucke, S., Vanhulle, A., Verfaillie, D., and Zipf, L.: PARASO, a circum-Antarctic fully coupled ice-sheet–ocean–sea-ice–atmosphere–land model involving f.ETISh1.7, NEMO3.6, LIM3.6, COSMO5.0 and CLM4.5, Geosci. Model Dev., 15, 553–594, <a href="https://doi.org/10.5194/gmd-15-553-2022">10.5194/gmd-15-553-2022</a>, 2022. Source code (no COSMO): Pelletier, Charles, Klein, François, Zipf, Lars, Haubner, Konstanze, Mathiot, Pierre, Pattyn, Frank, Moravveji, Ehsan, & Vanden Broucke, Sam. (2021). PARASO source code (no COSMO) (v1.4.3). Zenodo. <a href="https://doi.org/10.5281/zenodo.5576201">10.5281/zenodo.5576201</a> Input data: Pelletier, Charles, Klein, François, Zipf, Lars, Vanden Broucke, Sam, Haubner, Konstanze, & Helsen, Samuel. (2021). Input data for PARASO, a circum-Antarctic fully-coupled 5-component model (v1.4.3) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.5588468">10.5281/zenodo.5588468</a> Forcings: Pelletier, Charles, & Helsen, Samuel. (2021). PARASO ERA5 forcings (1.4.3) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.5590053">10.5281/zenodo.5590053</a> Acknowledgements <ol> <li> The ERA5 data (Hersbach, 2019) was downloaded on 01-09-2019 from the Copernicus Climate Change Service (C3S) Climate Data Store. The results contain modified Copernicus Climate Change Service information 2020. Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains. Reference: Hersbach, H., Bell, B., Berrisford, P., Biavati, G., Horányi, A., Muñoz Sabater, J., Nicolas, J., Peubey, C., Radu, R., Rozum, I., Schepers, D., Simmons, A., Soci, C., Dee, D., Thépaut, J-N. (2018): ERA5 hourly data on single levels from 1979 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). (Accessed on 01-SEP-2019), <a href="https://doi.org/10.24381/cds.adbb2d47">10.24381/cds.adbb2d47</a>. </li> <li> The sea-ice index (NSIDC-G02315) was downloaded on 01-09-2019 from the National Snow & Ice Data Center. Reference: Fetterer, F., K. Knowles, W. N. Meier, M. Savoie, and A. K. Windnagel. 2017, updated daily. Sea Ice Index, Version 3. Daily Antarctic. Boulder, Colorado USA. NSIDC: National Snow and Ice Data Center. <a href="https://doi.org/10.7265/N5K072F8">10.7265/N5K072F8</a>. Accessed on 01-SEP-2019. </li> <li> The World Ocean Atlas 2018 (WOA18): Reference: Boyer, Tim P.; Garcia, Hernan E.; Locarnini, Ricardo A.; Zweng, Melissa M.; Mishonov, Alexey V.; Reagan, James R.; Weathers, Katharine A.; Baranova, Olga K.; Seidov, Dan; Smolyar, Igor V. (2018). World Ocean Atlas 2018. Statistical means of temperature and salinity on $0.25^\circ$ grid.. NOAA National Centers for Environmental Information. Dataset. <a href="https://accession.nodc.noaa.gov/NCEI-WOA18">https://accession.nodc.noaa.gov/NCEI-WOA18</a>. Accessed 01-SEP-2020. </li> <li> Ice-shelf melt rates observations: Reference: Rignot, E., Jacobs, S., Mouginot, J., & Scheuchl, B. (2013). Ice-shelf melting around Antarctica (Supplementary Material) Science, 341(6143), 266-270. <a href="https://doi.org/10.1126/science.1235798">10.1126/science.1235798</a>. Reference: Adusumilli, Susheel; Fricker, Helen A.; Medley, Brooke C.; Padman, Laurie; Siegfried, Matthew R. (2020). Data from: Interannual variations in meltwater input to the Southern Ocean from Antarctic ice shelves. UC San Diego Library Digital Collections. <a href="https://doi.org/10.6075/J04Q7SHT">10.6075/J04Q7SHT</a> </li> <li> JRA-55 reanalysis: Reference: Kobayashi, S., Y. Ota, Y. Harada, A. Ebita, M. Moriya, H. Onoda, K. Onogi, H. Kamahori, C. Kobayashi, H. Endo, K. Miyaoka, and K. Takahashi , 2015: The JRA-55 Reanalysis: General specifications and basic characteristics. J. Meteor. Soc. Japan, 93, 5-48, <a href="https://doi.org/10.2151/jmsj.2015-001">10.2151/jmsj.2015-001</a> </li> <li> BedMachine Antarctic topography: Reference: Morlighem, M., Rignot, E., Binder, T. et al. Deep glacial troughs and stabilizing ridges unveiled beneath the margins of the Antarctic ice sheet. Nature Geoscience 13, 132–137 (2020). <a href="https://doi.org/10.1038/s41561-019-0510-8">10.1038/s41561-019-0510-8</a> Reference: Morlighem, M. 2020. MEaSUREs BedMachine Antarctica, Version 2. Ice-sheet thickness, surface elevation and mask. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. doi: <a href="https://doi.org/10.5067/E1QL9HFQ7A8M">10.5067/E1QL9HFQ7A8M </a>(accessed 01-FEB-2020). </li> </ol>

opencc-by-4.0Dec 2021View details →

Clear-sky profile database for the development of Land Surface Temperature algorithms

This dataset includes clear sky atmospheric profiles from the European Centre for Medium Range Forecast (ECMWF) version-5 reanalysis (ERA5), specially selected to support the development of algorithms of Land Surface Temperature (LST) retrieval from Earth observation (EO) data. The profiles were re-sampled from an ERA5 dataset covering the 2009-2019 period, with a 1x1 degree spatial resolution, hourly sampling and using the full vertical resolution (137 model levels). The re-sampling technique is based on a dissimilarity criterion applied to profiles of temperature and specific humidity, in order to obtain regular distributions of atmospheric variables of relevance for LST retrieval in the Thermal Infrared (TIR) spectral range. The database is limited to clear-sky conditions over land, being therefore suitable for the development of satellite land products relying on optical and thermal infrared imagery in general, despite targeting especially LST. Dataset description: The dataset is divided in multiple netCDF4 files based on the range of skin temperature (Tskin; Kelvin) and the range of total column water vapour (TCWV; mm). Each file includes the following variables: <ul> <li>Time</li> <li>Longitude</li> <li>Latitude</li> <li>2-m temperature (t2m)</li> <li>Surface pressure (sp)</li> <li>Total cloud cover (tcc)</li> <li>Total column water vapour (tcwv)</li> <li>Skin temperature (skt)</li> <li>Surface emissivity (emis)</li> <li>Land cover classification (lcc)</li> <li>Temperature profile (t)</li> <li>Specific humidity profile (q)</li> <li>Ozone profile (o3)</li> <li>Pressure profile (p)</li> </ul> All profiles are provided on model levels. For each profile, 6 values of skin temperature and 25 values of emissivity are provided (see publication for details). Emissivity values correspond to the wavelengths of ~11 and ~12 µm. Credit: To use this data please cite this dataset and the respective journal publication: Ermida, S.L.; Trigo, I.F. (2022) A Comprehensive Clear-Sky Database for the Development of Land Surface Temperature Algorithms. Remote Sens., 14, 2329. <a href="https://doi.org/10.3390/rs14102329">https://doi.org/10.3390/rs14102329</a>    Access: Currently, Zenodo does not provide a simple way to download datasets with a large number of files. We recomend trying the <a href="https://zenodo.org/record/3676567#.YnJAxtPMJhE">Zenodo_get</a> to simplify the download.

Supplementary material 1 from: Muraro M, Romagnoli S, Barzaghi B, Falaschi M, Manenti R, Ficetola GF (2021) Invasive predators induce plastic and adaptive responses during embryo development in a threatened frog. NeoBiota 70: 69-86. https://doi.org/10.3897/neobiota.70.65454

Geographic coordinates of the monitored sites and the significance of the independent variables in the three parental investment mixed models.

opencc-by-4.0Dec 2021View details →

Poly(I:C) exposure during in vitro fertilization disrupts first cleavage of mouse embryos and subsequent blastocyst development

The data of the study about: Poly(I:C) exposure during in vitro fertilization disrupts first cleavage of mouse embryos and subsequent blastocyst development.

opencc-by-4.0Jul 2021View details →

The Development of the !trumpet [attached video]

Video attached to the article by Nicolas Collins The Development of the !trumpet

Raw data for Urine DNA (uDNA) as a non-lethal method for endoparasite biomonitoring: development and validation

Changes in environmental conditions alter host-parasite interactions, raising the need for effective epidemiological surveillance. Developing operational, accurate, and cost-effective methods to assess individual infection status and potential for pathogen spread is a prerequisite to anticipate future disease outbreaks in wild populations. For endoparasites, effective detection of infections usually relies on host-lethal approaches, which are barely compatible with wildlife conservation objectives. Here, we used the brown trout (Salmo trutta) - Tetracapsuloides bryosalmonae host-parasite system to develop a non-lethal method for endoparasite infection detection, hereafter called "uDNA" for urine DNA. The uDNA diagnostic test is based on the amplification of endoparasite DNA from host urine. We sampled wild fish (N = 111) from eight sites, let them excrete in individual buckets filled with mineral water and performed parasite DNA amplification from water filtration. We compared the results of the uDNA diagnostic test for host infection status and parasite load to those from kidney samples (the current standard method). uDNA was sensitive in determining host infection status (even for infected hosts showing no sign of the disease), since up to 90% of fish individuals were correctly assigned to their infection status. The quantity of uDNA detected from the hosts depended on the sampling sites, suggesting a spatial variation in the parasite spread. uDNA was positively, but weakly correlated with parasite load in the kidney. This correlation depended on the severity of macroscopic lesions caused by the disease, and was negative in fish with severely damaged kidney, likely due to impaired urine excretion. The uDNA approach provides novel avenues to non-lethally infer infection parameters from wildlife populations at large spatial scales. By targeting parasite transmission stage, uDNA is also valuable to get insights on the parasite fitness and the ecological and evolutionary dynamics of this host-parasite interaction.

Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions

Living birds (Aves) have bodies dramatically modified from the ancestral reptilian condition. The avian pelvis in particular experienced dramatic changes during the transition from early archosaurs to living birds. This stepwise transformation is well documented by an excellent fossil record; however, the ontogenetic alterations that underly it are less well-understood. We used embryological imaging techniques to examine the morphogenesis of avian pelvic tissues in three dimensions, allowing direct comparison with the fossil record. Many ancestral dinosaurian features (e.g., forward-facing pubis, short ilium, pubic 'boot') are transiently present in the early morphogenesis of birds and arrive at their typical 'avian' form after transitioning through a prenatal developmental sequence that mirrors phylogeny. We quantitatively demonstrate that avian pelvic ontogeny closely parallels the dinosaur-to-avian transition and provide evidence for an evolutionary module within the pelvis that is conserved across Archosauria. The presence of ancestral states in avian embryos may stem from this conserved modular relationship. These are further indications that the avian pelvis evolved via terminal addition—a mechanism whereby ancestral states shift to derived states during late development, resulting in retention of ancestral character states. This phenotypic modularity suggests a previously unrecognized mechanism for the promotion of terminal addition, hinting that the retention of ancestral states in development may be common across evolutionary transitions.

opencc-zeroJan 2022View details →

Effects of embryo energy, egg size and larval food supply on the development of asteroid echinoderms

Organisms have limited resources available to invest in reproduction, causing a tradeoff between the number and size of offspring. One consequence of this tradeoff is the evolution of disparate egg sizes and, by extension, developmental modes. In particular, echinoid echinoderms (sea urchins and sand dollars) have been widely used to experimentally manipulate how changes in egg size affect development. Here we test the generality of the echinoid results by 1) using laser ablations of blastomeres to experimentally reduce embryo energy in the asteroid echinoderms (sea stars), Pisaster ochraceus and Asterias forbesi and 2) comparing naturally produced, variably-sized eggs (1.7 fold volume difference between large and small eggs) in A. forbesi. In P. ochraceus and A. forbesi there were no significant differences between juveniles from both experimentally reduced embryos and naturally produced eggs of variable size. However, in both embryo reduction and egg size variation experiments, simultaneous reductions in larval food had a significant and large effect on larval and juvenile development. These results indicate that 1) food levels are more important than embryo energy or egg size in determining larval and juvenile quality in sea stars and 2) the relative importance of embryo energy or egg size to fundamental life history parameters (time-to and size-at metamorphosis), does not appear to be consistent within echinoderms.

opennotspecifiedDec 2021View details →

FIGURE5. Panonychus caglei, female, A. leg I, B. leg II, C. leg III, D., leg IV, the red arrow refers to the excessive seta (l') observed on genu IV in few specimens. Right side. in -Redescription-of-Panonychus caglei Mellott,-1968,- with-ontogenetic-development- (Acari:-Tetranychidae)-

FIGURE5. Panonychus caglei, female, A. leg I, B. leg II, C. leg III, D., leg IV, the red arrow refers to the excessive seta (l') observed on genu IV in few specimens. Right side.

opennotspecifiedDec 2021View details →

FIGURES2–4. Panonychus caglei, female, 2. peritremes, 3. palptarsus, 4. venter of posterior idiosoma. in -Redescription-of-Panonychus caglei Mellott,-1968,- with-ontogenetic-development- (Acari:-Tetranychidae)-

FIGURES2–4. Panonychus caglei, female, 2. peritremes, 3. palptarsus, 4. venter of posterior idiosoma.

opencc-zeroJan 2022View details →

Impact of water resources development on connectivity and primary productivity across a tropical river floodplain

1. Floodplain wetlands provide an important subsidy for riverine food webs as sites of high algal production. However, this subsidy depends on the degree of landscape connectivity during flood pulses, which provides the opportunity for movement of higher order consumers between rivers and floodplains to access these productive habitats. Changes in floodplain inundation extent and duration, due to variable wet season flows or water resources development (WRD), can impact landscape connectivity and ultimately the magnitude of the food web subsidy. 2. We explored landscape connectivity using graph theory and derived four new metrics to measure how different flow scenarios can affect connectivity and algal production. We considered a historic scenario with the present level of water resource development in our study area, the Mitchell River, and a WRD scenario with the inclusion of three new dams in the catchment. We generated 240 unique daily spatial graphs, using surface water inundation maps across 40-day flood events to compare a dry year (2006), an average flow year (2001), and a wet year (2009) with and without a WRD scenario. 3. Drier years and WRD scenario resulted in floodplain fragmentation, potentially constraining the movement of higher order consumers. Changes in connectivity due to WRD resulted in predicted reductions of up to 26% of algal production on the floodplain that was otherwise connected to the main river channels. 4. Synthesis and applications. The approach developed in this study provides new metrics to identify how changes in floodplain surface water extent due to water resource development and climatic variation may impact ecosystem function such as connectivity that facilitates access of higher order consumers to primary production in floodplain wetlands. With a direct link to river flow alteration, these metrics can inform catchment planning and management to ensure that the conservation of floodplain ecosystem functions is adequately considered in water resource management decisions.

opencc-by-4.0Jan 2022View details →

Data linked to publication entitled "Biochar derived from Acai agroindustry waste enhances nutritional status and biomass in young Eucalyptus urophylla plants: Evidence connected to root development and leaf performance"

Data linked to publication entitled "Biochar derived from Acai agroindustry waste enhances nutritional status and biomass in young Eucalyptus urophylla plants: Evidence connected to root development and leaf performance"

opencc-by-4.0Aug 2020View details →

Data Associated with Manuscript Titled "Development of a graphical resilience framework to understand a coupled human-natural system in a remote arid highland of Baja California Sur"

This is a dataset in support of analyses of water chemistry and social networks described and interpreted in the associated manuscript titled "Development of a graphical resilience framework to understand a coupled human-natural system in a remote arid highland of Baja California Sur"