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opencc-by-4.0Aug 2024View details →

Mobilising marine biodiversity data: a new malacological dataset of Italian records (Mollusca)

The location and palaeoceanographic history of the Mediterranean Sea make it a biodiversity hotspot, prompting extensive studies in this region. However, despite the marine biodiversity of this area is apparently widely studied, a large amount of distributional data for Mediterranean taxa is still unpublished or scattered in various sources and formats, causing severe limitations to their potential reuse. This emerges as a particularly thorny issue for highly biodiverse and neglected taxa, such as invertebrates. The mobilisation of these frozen data through a process of standardisation and georeferencing could potentially support biodiversity research and conservation. The aim of this work is to provide a standardised pipeline to integrate these dispersed data, focusing on the Italian waters of the Mediterranean Sea and using molluscs as target taxa. Data were gathered from two main sources: published literature and Natural History Collections. The harmonisation process involved three key steps: 1) terminology and structure standardisation, 2) taxonomy updating and 3) georeferencing. Our efforts yielded over 44000 standardised records of mollusc species from Italian seawaters. These records encompassed primary biodiversity data from newly digitised specimens owned by 11 different institutions and private collectors, as well as secondary biodiversity data extracted from 311 published studies.

opencc-by-4.0Dec 2024View details →

A legacy of submarine slope failure in seismic reflection data along the active Hikurangi Margin, Aotearoa New Zealand

We present a database that documents mass transport deposits (MTDs) in 32 marine geophysical surveys, encompassing >38,000 line-km of 2D seismic profiles. We map and characterise 737 MTDs, showing variations in size, location and style of failure, which we attribute to changes in geomorphic setting from north to south. MTDs in the northern Hikurangi margin, characterised by a high taper wedge and seamount subduction, show a broad range in size, with the highest proportion of MTDs displaying blocky or intact internal architecture. The central margin, characterised by lower wedge taper, hosts the most MTDs (51%), albeit with the thinnest (on average) and clustering within interridge basins. The southern Hikurangi margin hosts widespread submarine canyons and the largest (on average) MTDs, based on area and thickness. We demonstrate the importance of seismic archives in providing new insights into MTD preservation and discuss the bias between seafloor geomorphology and subseafloor seismic data in quantifying MTD occurrence. Our findings support the interrogation of the varied and complex causes of submarine landslides along active margins generally, as well as regions prone to cascading geohazards and landslide-induced tsunami.

opencc-by-4.0Nov 2024View details →

Bees of the IMBE collection in Marseille: new data for southeastern France (Hymenoptera)

Version 2 (18 Dec. 2024) Some Nomada had their identification corrected by Eric Dufrêne. Nomenclatural changes requalified as Bombus mastrucatus specimens previously identified as Bombus wurflenii, and corrected the spelling of Hoplitis mocsaryi. The dataset now includes 2181 specimens belonging to 246 species. Version 1 (14 Nov. 2024) We provide distribution data on 2180 specimens belonging to 244 species of bees, mainly from Mediterranean France. For each specimen, the following columns are given, with names from the Darwin-core system of the Blobal Biodiversity Information Facility (GBIF). Coding is UTF-8. Beware : some locality names and comments contain an quotation mark ('), which should be taken into account when reading the data with R or other statistical systems. All specimens are stored at the Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE, Marseille, France).

opencc-by-4.0Jan 2024View details →

The data for new theoretical Fe II templates for bright quasars

The compressed '.tar.gz' files contain new theoretical Fe II templates that can be used for fitting UV to near-IR (1000-10000 Angstrom) spectra of quasars. The templates were developed using the latest Fe II atomic database of <a href="http://doi.org/10.1093/mnras/sty3198">Smyth et al. (2019)</a> within the CLOUDY C23.0 photoionization code with the following set of parameters. <ul> <li>H-ionizing photons flux: 17 ≤ log ΦH (cm−2 s−1) ≤ 22, and</li> <li>Gas density: 9≤ log nH (cm−3) ≤ 14, </li> <li>Step size: 0.25 on log scale.</li> <li>A fixed Hydrogen column density: 10^24 cm−2 </li> <li>Abundance: solar </li> <li>SED shapes:</li> </ul> (1) Standard "agn.sed", a continuum similar to <a href="https://ui.adsabs.harvard.edu/abs/1987ApJ...323..456M/abstract/">Mathews & Ferland (1987)</a> (2) Intermediate SED of (<a href="https://ui.adsabs.harvard.edu/abs/2012MNRAS.425..907J/abstract/">Jin et al., 2012</a>)                          <ul> <li>The Fe II template is available for the microturbulence values 0, 20, 50 and 100 km/s.</li> </ul> (Note: The Fe II templates are also available in the GitHub link: https://github.com/Ashwani-88/Fe2_template) Each tar.gz file consists of Fe II templates for different SED shapes.  For each SED shape; The new Fe II templates are available in the directory "Templates_including_only_total_Fe2".  Additionally, we provide templates for the outward and inward Fe II emissions in the directory "Templates_including_outward_Fe2" The directory for Fe II templates for a microturbulence velocity is named as turb_vn where n is the microturbulence velocity in km/s.  The files within each directory are named as follows: phia_nHb_mc.dat where  a =  log value of the H-ionizing photon flux in cm−2 s−1, b = log value of the Hydrogen gas density in cm−3, and c =  the value of microturbulence in km/s. <h2>Each template file in ``Templates_including_only_total_Fe2'' has two columns  </h2>   First column: wavelength in Angstrom with 2 Angstrom binning     Second column: Fe II line intensity (in erg cm-2 s-1 A-1) <h2>Templates in ``Templates_including_outward_Fe2'' has four columns.</h2> First column: wavelength in Angstrom with 1000 logarithmic bins, each ~ 584 km/s wide,  between 1000 and 7000 Angstrom.      Second column: Total Fe II line intensity (in erg cm-2 s-1 A-1)       Third column:  Inward Fe II line intensity (in erg cm-2 s-1 A-1)        Fourth column: Outward Fe II line intensity (in erg cm-2 s-1 A-1)        The Fe II line intensity includes a covering factor of 30 % and is scaled for our test object RM 102.

opencc-by-4.0Aug 2024View details →

Source data to create the figures of the study "Rising greenhouse gas emissions embodied in the global bioeconomy supply chain" using REX3 with new GHG extension including LULUCF

This repository contains the source data to create the figures of the study <a href="https://doi.org/10.1038/s43247-025-02144-0">Rising greenhouse gas emissions embodied in the global bioeconomy supply chain</a> published in Communications Earth & Environment. The results were calculated with the REX3 database in Version 3.2 of this repository and the GHG extension and matlab codes in Version 3.4 of this repository. Figure 1, and 3–5 were created in Rstudio with the attached Rcode Bioeconomy_GHG_sankeys.R Figure 2 was created in tableau with an <a href="https://public.tableau.com/app/profile/livia.cabernard/vizzes">interactive data visualizer</a> that allows to zoom into the global bioeconomy supply chain.

Fig. 1 in A new Diplura species from Georgia caves, Plusiocampa (Plusiocampa) imereti (Diplura, Campodeidae), with morphological and molecular data

Fig. 1. Distribution map of cave-adapted diplurans in the Black Sea region: Plusiocampa (Plusiocampa) isterina Condé, 1993 (red circle), Plusiocampa (Dydimocampa) evallonychia Silvestri, 1949 (red triangles), Plusiocampa (Plusiocampa) imereti Sendra & Barjadze sp. nov. (red stars), Plusiocampa (Plusiocampa) aff. dublanskii Sendra & Turbanov, 2020 (red rhombus), Plusiocampa (Dydimocampa) euxina Condé, 1996 (black square), Plusiocampa (Plusiocampa) dublanskii Sendra & Turbanov, 2020 (black circle). Yellow = karst areas (source: Chen et al. 2017); orange = deserts (source: Olson & Dinerstein 2002); blue = ice cover and permafrost extent during the Last Glacial Maximum (sources: Ehlers et al. 2011; Lindgren et al. 2016).

Figs 14–18. 14–16. Entrances. 17–18 in A new Diplura species from Georgia caves, Plusiocampa (Plusiocampa) imereti (Diplura, Campodeidae), with morphological and molecular data

Figs 14–18. 14–16. Entrances. 17–18. Plans of the studied caves. 14. Datvis Cave. 15. Melouri Cave. 16. Shvilobisa Cave. 17. Plan of the Melouri Cave (Tatashidze et al. 2009a). 18. Plan of the Shvilobisa Cave (Tatashidze et al. 2009a). Black dots = locations where the specimens of the new species were sampled; E = entrance.Scale bares: 14–16 = 1 m.

Fig. 13 in A new Diplura species from Georgia caves, Plusiocampa (Plusiocampa) imereti (Diplura, Campodeidae), with morphological and molecular data

Fig. 13. Maximum likelihood (ML) tree of Diplura obtained from CO1 data. Only bootstrap support values above 70 are shown.

Figs 2–6 in A new Diplura species from Georgia caves, Plusiocampa (Plusiocampa) imereti (Diplura, Campodeidae), with morphological and molecular data

Figs 2–6. Plusiocampa (Plusiocampa) imereti Sendra & Barjadze sp. nov., ♀, holotype (IZISU- TD-T-00001). 2. Thoracic nota. 3. Frontal process. 4. Detail of mesonotum. 5. Detail of mesonotum at high magnification. 6. Detail of metanotum.

Fig. 6 in Pseudoleucochloridium ainohelicis nom. nov. (Trematoda: Panopistidae), a Replacement for Glaphyrostomum soricis Found from Long-Clawed Shrews in Hokkaido, Japan, with New Data on its Intermediate Hosts

Fig. 6. The egg of Pseudoleucochloridium ainohelicis nom. nov. in the gravid adult. The left end is an operculum. An arrow indicates the notch of eggshell. A miracidium is visible inside. Scale bar 10 µm.

Fig. 4 in Pseudoleucochloridium ainohelicis nom. nov. (Trematoda: Panopistidae), a Replacement for Glaphyrostomum soricis Found from Long-Clawed Shrews in Hokkaido, Japan, with New Data on its Intermediate Hosts

Fig. 4. The cercaria and metacercaria of Pseudoleucochloridium ainohelicis nom. nov. from Ainohelix editha. Both of the drawings are in ventral view. A) Cercaria. Scale bar 100 µm; B) Metacercaria. Scale bar 500 µm.

Fig. 1 in Pseudoleucochloridium ainohelicis nom. nov. (Trematoda: Panopistidae), a Replacement for Glaphyrostomum soricis Found from Long-Clawed Shrews in Hokkaido, Japan, with New Data on its Intermediate Hosts

Fig. 1. Frequencies of cox1 haplotypes and their statistical parsimony network in Pseudoleucochloridium ainohelicis nom. nov. All of the twelve isolates were collected in Asahikawa. The size of circles indicates the frequency of the haplotypes. Small circles show hypothetical haplotypes. The shaded circle represents the hypothetical ancestor.

Fig. 5 in Pseudoleucochloridium ainohelicis nom. nov. (Trematoda: Panopistidae), a Replacement for Glaphyrostomum soricis Found from Long-Clawed Shrews in Hokkaido, Japan, with New Data on its Intermediate Hosts

Fig. 5. The adult of Pseudoleucochloridium ainohelicis nom. nov. from Sorex unguiculatus. The drawing is in ventral view. The large suckers, M-shaped configuration of uterus, and terminally-positioned genital pore are characteristic of the genus. Scale bar 500 µm.

FIG. 8. — Paragiopagurus schnauzer n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 8. — Paragiopagurus schnauzer n. sp., ♂ holotype 3.3 mm, BIOGEOCAL, stn CP 214, New Caledonia (MNHN-Pg 7615): A, propodus and dactyl of left fourth pereopod, lateral; B, propodus and dactyl of left fifth pereopod, lateral; C, thoracic region, ventral; D, anterior and posterior lobes of thoracic sternite XII (third pereopods), ventral; E, uropods and telson, dorsal; F, left first pleopod, mesial; G, left second pleopod, anterior. Scale bars: A-D, F, G, 1 mm; E, 0.5 mm.

FIG. 3. — Oncopagurus conicus n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 3. — Oncopagurus conicus n. sp., ♂ holotype 2.0 mm, HALIPRO 1, stn C 858, New Caledonia (MNHN-Pg 7612): A, left second pereopod, lateral; B, dactyl of same, mesial; C, left third pereopod, lateral; D, dactyl of same, mesial; E, propodus and dactyl of left fourth pereopod, lateral; F, propodus and dactyl of left fifth pereopod, lateral. Scale bars: A-D, 1 mm; E, F, 0.20 mm.

FIG. 4. — Oncopagurus conicus n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 4. — Oncopagurus conicus n. sp., ♂ holotype 2.0 mm, HALIPRO 1, stn C 858, New Caledonia (MNHN-Pg 7612); A, thoracic region, ventral;B, anterior and posterior lobes of thoracic sternite XII (third pereopods), ventral; C, uropods and telson, dorsal; D, left first pleopod, mesial; E, left second pleopod, anterior. Scale bars: A, 0.50 mm; B, D, E, 0.20 mm; C, 0.25 mm.

FIG. 9 in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 9. — Right ocular peduncle and cornea (stippling indicates weakly calcified portion): A-C, Typhlopagurus foresti de Saint Laurent, 1972, ♂ 3.7 mm, SALOMON 1, stn CP 1781 (USNM 1084207, ex MNHN-Pg 6706); D, Sympagurus acinops Lemaitre, 1989, ♂ paratype 3.2 mm, Tongue of the Ocean, Bahamas, 1438 m (USNM 231834); E, Parapagurus saintlaurentae Lemaitre, 1999, ♂ paratype 12.8 mm, N of Madagascar, 4810 m (USNM 276123); A, D, E, lateral; B, mesial; C, ventral. Scale bars: A-D, 0.25 mm; E, 1 mm.

FIG. 7. — Paragiopagurus schnauzer n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 7. — Paragiopagurus schnauzer n. sp., ♂ holotype 3.3 mm, BIOGEOCAL, stn CP 214, New Caledonia (MNHN-Pg 7615): A, right second pereopod, lateral; B, dactyl of same, mesial; C, right third pereopod, lateral; D, dactyl of same, mesial. Scale bar: 1 mm.

FIG. 1. — Oncopagurus conicus n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 1. — Oncopagurus conicus n. sp., New Caledonia: A, ♀ paratype 2.0 mm, HALIPRO 1, stn C 858 (MNHN-Pg 7613); B-D, F-J, ♂ holotype 2.0 mm, HALIPRO 1, stn C 858 (MNHN-Pg 7612); E, ovig. ♀ paratype 2.1 mm, BIOGEOCAL, stn CP 214 (MNHN-Pg 7614); A, gill lamella; B, shield and cephalic appendages, dorsal (stippling indicates weakly calcified portion); C, right ocular peduncle and cornea, lateral; D, epistome, dorsolateral (es, epistomial spine; ls, labral spine); E, anterior portion of shield and cephalic appendages, dorsal; F, right antennal peduncle, lateral; G, right cheliped, dorsal; H, chela of same, lateral; I, same, mesial; J, left cheliped, dorsal. Scale bars: A, 0.10 mm; B, 0.50 mm; C-F, 0.25 mm; G-J, 1 mm.

FIG. 6. — Paragiopagurus schnauzer n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 6. — Paragiopagurus schnauzer n. sp., ♂ paratype 3.2 mm, HALIPRO 2, stn BT 105, Loyalty Islands (MNHN-Pg 6705), left mouthparts, internal: A, mandible; B, maxillule; C, maxilla; D, first maxilliped; E, second maxilliped; F, third maxilliped. Scale bars: 0.25 mm.