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MAPS 3A–D in Synopsis of the Snakes of the Philippines A Synthesis of Data from Biodiversity Repositories, Field Studies, and the Literature

MAPS 3A–D. Geographic range maps for Philippine records of (A) Ahaetulla prasina suluensis; (B) Aplopeltura boa; (C) Boiga angulata; (D) Boiga cynodon.

MAPS 2A–D in Synopsis of the Snakes of the Philippines A Synthesis of Data from Biodiversity Repositories, Field Studies, and the Literature

MAPS 2A–D. Geographic range maps for Philippine records of (A) Acrochordus granulatus; (B) Acutotyphlops banaorum; (C) Ahaetulla prasina prasina; (D) Ahaetulla prasina preocularis.

MAPS 11A–D in Synopsis of the Snakes of the Philippines A Synthesis of Data from Biodiversity Repositories, Field Studies, and the Literature

MAPS 11A–D. Geographic range maps for Philippine records of (A) Cyclocorus lineatus alcalai; (B) Cyclocorus lineatus lineatus; (C) Cyclocorus nuchalis nuchalis; (D) Cyclocorus nuchalis taylori.

Reference map illustrating the major Philippine faunal regions as defined by the Pleistocene Aggregate Island Complexes (PAICs). Selected island groups, such as the Babuyans, Batanes, the Romblon Island Group (RIG), and the Sulu Archipelago, are also indicated. in Synopsis of the Snakes of the Philippines A Synthesis of Data from Biodiversity Repositories, Field Studies, and the Literature

Reference map illustrating the major Philippine faunal regions as defined by the Pleistocene Aggregate Island Complexes (PAICs). Selected island groups, such as the Babuyans, Batanes, the Romblon Island Group (RIG), and the Sulu Archipelago, are also indicated.

The unpatterned orange morph of Philippine Boiga cynodon photographed in 2016 in the University of the Philipines at Los Baños Quezon Land Grant Forest Reserve, Municipality of Siniloan, Quezon Province, southeastern Luzon Island, Photo: Rafe M. Brown. in Synopsis of the Snakes of the Philippines A Synthesis of Data from Biodiversity Repositories, Field Studies, and the Literature

The unpatterned orange morph of Philippine Boiga cynodon photographed in 2016 in the University of the Philipines at Los Baños Quezon Land Grant Forest Reserve, Municipality of Siniloan, Quezon Province, southeastern Luzon Island, Photo: Rafe M. Brown.

The Philippine Archipelago, with major landmasses and other geographical features indicated. Prepared by Jeffrey L. Weinell. in Synopsis of the Snakes of the Philippines A Synthesis of Data from Biodiversity Repositories, Field Studies, and the Literature

The Philippine Archipelago, with major landmasses and other geographical features indicated. Prepared by Jeffrey L. Weinell.

opencc-zeroJul 2024View details →

dryad40/100

Data from: A sedimentary eDNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem

The hadopelagic environment remains highly understudied due to the inherent difficulties in sampling at these depths. The use of sediment eDNA can overcome some of these restrictions as settled and preserved DNA represent an archive of the biological communities. We use sediment eDNA to assess changes in the community within one of the world's most productive open ocean ecosystems: the Atacama Trench. The ecosystems around the Atacama Trench have been intensively fished and are affected by climate oscillations, but the understanding of potential impacts on the marine community is limited. We sampled five sites using sediment cores at water depths from 2400 to ~8000m. The chronologies of the sedimentary record were determined using 210Pbex. Environmental DNA was extracted from core slices and metabarcoding was used to identify the eukaryote community using two separate primer pairs for different sections of the 18S rDNA gene (V9 and V7) effectively targeting pelagic taxa. The reconstructed communities were similar among markers and mainly composed of chordates and members of the Chromista kingdom. Alpha-diversity was estimated for all sites in intervals of 15 years (from 1842 to 2018), showing a severe drop in biodiversity from 1970 to 1985 that aligns with one of the strongest known El Niño events. We argue that the harsh adverse ENSO events potentially combined with extensive fishing efforts during this period of time resulted in a distinct reduction of marine biodiversity. Fish and cnidarian read abundance was examined separately to determine if fishing had a direct impact, but no direct relation was found. These results demonstrate that sediment eDNA can be a valuable emerging tool providing insight in historical perspectives on ecosystem developments. This study constitutes one of the first steps toward an improved understanding of the importance of environmental and anthropogenic drivers in affecting open and deep ocean communities.

opencc-by-4.0Jul 2024View details →

Data study "The Impact of Augmented Reality on Biodiversity Learning in a Pedagogical Scenario Based on Analogical Reasoning: An Experimental Study"

This data was collected in 2023 as part of a study on the impact of location-based AR on biodiversity education.

opencc-by-4.0Apr 2018View details →

20 GB in 10 minutes: Data linking across major biodiversity databases: Data supplements

This supplementary data publication contains: links-globi-wd-ott.tsv.gz: aggregate list of taxon graphs from Open Tree of Life Taxonomy (OTT), GloBI and Wikidata. This tab separated two column table, describe the taxonomic identifiers (e.g., NCBI:9606) that map into OTT, GloBI and Wikidata. For instance, the line "NCBI:9689{tab}WD:Q140" indicates that wikidata links their lion (Panthera leo, https://www.wikidata.org/wiki/Q140) to NCBI's lion (Panthera leo, https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9689). wikidata-taxon-info20171227.tsv.gz: a terse 5 column file in tab-separated format of taxon objects extracted from WikiData. (2018). Wikidata dump 2017-12-27 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1211767 . The columns contain the following: <ol> <li>wikidata taxon item id (e.g., Q140 or https://www.wikidata.org/wiki/Q140)</li> <li>scientific name of taxon item id (e.g., Panthera leo, Mammalia)</li> <li>rank id of the taxon item id (e.g., Q7432 species or https://www.wikidata.org/wiki/Q7432). To retrieve a full list of wikidata taxon rank ids and their common names, you can use sparql to query wikidata (e.g., <a href="https://github.com/globalbioticinteractions/nomer/blob/c3a1f5a2ebfb87ffc67e3bace19b82d96c0d25e8/nomer/src/main/java/org/globalbioticinteractions/nomer/util/WikidataTaxonRankLoader.java">Nomer's WikidataTaxonRankLoader</a> ). </li> <li>parent ids if taxon item id using pipes "|" as separators if there's multiple parents.  Please note that some taxon items have multiple parents (e.g., https://www.wikidata.org/wiki/Q774014).</li> <li>external taxonomic identifiers that taxon item link to (e.g. "ITIS:162532|EOL:8266|GBIF:2960|WORMS:125440") . If muliple are present, pipes "|" are used to separate the links. Only a selection of taxonomic schemes was used, namely: NCBI, GBIF, ITIS, WORMS, FISHBASE, IF (index fungorum) and EOL.</li> </ol> The datasets can be recreated by scripts in https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata or <a href="https://doi.org/10.5281/zenodo.1428949">https://doi.org/10.5281/zenodo.1428949</a> .

Figure 5 in Biodiversity, DNA barcoding data and ecological traits of caddisflies (Insecta, Trichoptera) in the catchment area of the Mediterranean karst River Cetina (Croatia)

Figure 5. Maximum likelihood phylogram based on a fragment of COI (DNA barcode region) showing the related relationships of the genus Glossosoma. The bootstrap values (BS) are marked on the branches in the order NJ/ML. BS values less than 80 are not shown. The groups delineated by ABGD approach are shown on the right side of the tree. Specimens which genomic DNA was extracted in this study are written in bold letter.

Figure 1 in Biodiversity, DNA barcoding data and ecological traits of caddisflies (Insecta, Trichoptera) in the catchment area of the Mediterranean karst River Cetina (Croatia)

Figure 1. Map of the study area with sampling stations. Names and corresponding abbreviations of the stations are listed in Table 1.

Figure 3 in Biodiversity, DNA barcoding data and ecological traits of caddisflies (Insecta, Trichoptera) in the catchment area of the Mediterranean karst River Cetina (Croatia)

Figure 3. MDS analysis of caddisfly fauna similarity at stations on the Cetina, the Ruda, the Grab and the Rumin rivers.

Figure 2 in Biodiversity, DNA barcoding data and ecological traits of caddisflies (Insecta, Trichoptera) in the catchment area of the Mediterranean karst River Cetina (Croatia)

Figure 2. Cluster analysis of caddisfly fauna similarity at stations on the rivers Cetina, Ruda, Grab and Rumin.

opencc-by-4.0May 2023View details →

Data archive for 'Convolutional neural networks facilitate river barrier detection and evidence severe habitat fragmentation in the Mekong River biodiversity hotspot'

This repository contains the code and databases used in the paper 'Convolutional neural networks facilitate river barrier detection and evidence severe habitat fragmentation in the Mekong River biodiversity hotspot'.  The 'Mekong River Barrier Database (MRBD)' folder contains the basin-scale barrier database developed in this study. This database contains more than 13,000 unique barriers, which were identified by using the convolutional neural networks-based object detection method from Google Earth’s satellite imagery. The 'FCOS' folder contains the barrier detection model (FCOS ResNext-101-FPN), trained for detecting river barriers from remotely sensed images within the MMDetection framework. The 'FCOS_x101_v2' folder contains the enhanced FCOS model. The 'R_script' folder contains R files used in the paper. Coordinate.R was used to extract coordinates from bounding boxes in each TIF image. CAFI.R was used to calculate the CAFI index in each sub-catchment. The 'Barrier image training set' folder contains over 10,000 river barrier satellite images and their associated JSON files, forming the 'training, validation, and test datasets' used during the model training process. This dataset is made available to the user community in raw, in the hope that others will contribute to its future development, thereby enhancing its use and utility. For more information on the MMDetection framework, refer to the following GitHub repository: <a href="https://github.com/open-mmlab/mmdetection">https://github.com/open-mmlab/mmdetection</a>

FIG. 14 in New data on the biodiversity of Solenogastres (Mollusca, Aplacophora) in the Mediterranean Sea: findings from the program "Our Planet Reviewed" Corsica 2019-2022

FIG. 14. — Histological sections of A, Unciherpia hirsuta (MNHN-IM-2019-18279): circumpharyngeal glands and B, Dorymenia vagans (MNHN-IM-2019-18271): copulatory stylets; C-E, Anamenia gorgonophila (MNHN-IM-2019-18270): C, anterior foregut region; D, radular region; D', detail of the radula, radular sac and ventrolateral foregut glands; E, oblique section of posterior region with abdominal spicules visible on the animal's right side. Abbreviations: see Material and methods. Scale bars: 100 µm.

FIG. 11 in New data on the biodiversity of Solenogastres (Mollusca, Aplacophora) in the Mediterranean Sea: findings from the program "Our Planet Reviewed" Corsica 2019-2022

FIG. 11. — Histological sections of the anterior region of Pruvotina impexa (Pruvot, 1890) (MNHN-IM-2019-1746): A-D, atrial cavity; E-H', region between the atrial opening and the mouth; H´, detail of the ventral region between the opening of the atrium and the mouth, without cuticular layer. Abbreviations: see Material and methods. Scale bars: 100 µm.

FIG. 7 in New data on the biodiversity of Solenogastres (Mollusca, Aplacophora) in the Mediterranean Sea: findings from the program "Our Planet Reviewed" Corsica 2019-2022

FIG. 7. — SEM images of the sclerites of A-D, Nematomenia banyulensis (Pruvot, 1890) (MNHN-IM-2019-1747); E, Tegulaherpia cf. myodoryata (MNHN-IM-2019-16176); F, Simrothiella margaritacea (Koren & Danielssen, 1877) (MNHN-IM-2019-18280); G, H, Dorymenia vagans (Kowalevsky & Marion, 1887) (MNHN-IM-2019-18274); I, Anamenia gorgonophila (Kowalevsky, 1880) (MNHN-IM-2019-18270). Scale bars: 20 µm.

FIG. 9 in New data on the biodiversity of Solenogastres (Mollusca, Aplacophora) in the Mediterranean Sea: findings from the program "Our Planet Reviewed" Corsica 2019-2022

FIG. 9. — Sclerites of A-E, Eleutheromenia sierra (Pruvot, 1890) (MNHN-IM-2019-1749): A, light microscopy image of the cuticle (the dorsal keel); B, general view of the sclerites in the dorsal region of the body; C, closer view of the hook-shaped sclerites and acicular sclerites in the dorsal region of the body (arrow, thin sclerites; star: longer and thicker sclerites); D, detail of the hook-shaped sclerites; E, acicular sclerites in the ventral region of the body; F-I, Unciherpia hirsuta (MNHN-IM-2019-18279): F, hook-shaped and harpoon-shaped sclerites (star, harpoon-shaped sclerites); G, acicular sclerites in the ventral region of the body; H, I, hook-shaped sclerites. Scale bars: A, 200 µm, B-I, 20 µm.

FIG. 6 in New data on the biodiversity of Solenogastres (Mollusca, Aplacophora) in the Mediterranean Sea: findings from the program "Our Planet Reviewed" Corsica 2019-2022

FIG. 6. — SEM images of the sclerites of Dondersia festiva (Pruvot, 1890) (MNHN-IM-2019-16170): A, layer of oval-shaped scales (many are broken) with palletshaped scales among them; B, oval-shaped scales; C, short pallet-shaped scales with a long stem; D, short pallet-shaped scales with a short stem; E-G, distal end of long pallet-shaped scales. H, long pallet-shaped scales with a long stem; I, long pallet-shaped scales with a short stem.; J, striated acicular sclerites; K, detail of the striated acicular sclerites; L, pallet-shaped scales of the anterior region. Scale bars: 20 µm. Symbols: arrows, oval-shaped scales from the basal layer.

FIG. 5 in New data on the biodiversity of Solenogastres (Mollusca, Aplacophora) in the Mediterranean Sea: findings from the program "Our Planet Reviewed" Corsica 2019-2022

FIG. 5. — Habitus of Pruvotina impexa (Pruvot, 1890): A, MNHN-IM-2019-18281 (photo of the preserved specimen); A', MNHN-IM-2019-18281 (photo of the living animal); A'', detail of the atrio-buccal region of MNHN-IM-2019-18281, arrow indicates the muscular ridge separating the atrium and pedal pit; B, MNHN-IM-2019-1746 (photo of the living animal); C, MNHN-IM-2019-1748 (photo of the living animal); D, MNHN-IM-2019-1745 (photo of the preserved specimen); E, MNHN-IM-2019-18285 (photo of the preserved specimen); F, MNHN-IM-2019-18273 (photo of the living animal and expelled gut contents); G, MNHN-IM-2019-16179 (photo of the preserved specimen). Scale bar: 1 mm. Symbols: stars, the anterior end of the animals.