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FIGURE 5 in Evolutionary history of species of the fireFly subgenus Hotaria (Coleoptera, Lampyridae, Luciolinae, Luciola) inferred from DNA barcoding data
FIGURE 5 Distributional patterns (collection sites) for terminal taxa of Luciola unmunsana (LU), L. papariensis (LP), and L. tsushimana (LT) constructed using BEAST. Red dotted line indicates the approximate location of the "Bekdudaegan" mountains. Yellow dotted line indicates the approximate location of the "Hannam-Geumbuk Jeongmaeck" mountains. Green dotted line denotes the approximate location of the "Nakdong Jeongmaeck" mountains. The map was extracted from Google Earth.
FIGURE 3 Majority-rule consensus tree from a in Evolutionary history of species of the fireFly subgenus Hotaria (Coleoptera, Lampyridae, Luciolinae, Luciola) inferred from DNA barcoding data
FIGURE 3 Majority-rule consensus tree from a Bayesian analysis (BI) of 128 samples of 14 morphospecies based on COI barcode sequences. The numbers at each node indicate Downloadedposteriorfrom Brill. probabilities com 12. /12/ Weakly 2023 03 sup-:05:57PM ported nodes (posterior via probabilityOpen below Access. 0.95) Thisareis an shownopenin red. access article distributed under the terms of the CC-BY 4.0 License. https://creativecommons.org/licenses/by/4.0/
FIGURE 2 in Evolutionary history of species of the fireFly subgenus Hotaria (Coleoptera, Lampyridae, Luciolinae, Luciola) inferred from DNA barcoding data
FIGURE 2 Maximum likelihood (ML) tree of 128 samples of 14 morphospecies based on COI barcode sequences. The numbers at each node indicate support (%). Weakly supported nodes (below 70%) are shown in red. Downloaded from Brill.com 12/12/2023 03:05:57PM via Open Access. This is an open access article distributed under the terms of the CC-BY 4.0 License. https://creativecommons.org/licenses/by/4.0/
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs.
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet.
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation.
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime.
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction.
Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period.
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day.
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays.
Figure 8 in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Figure 8. – Egg production as a function of age. These results were obtained from the number of eggs laid throughout the breeding season divided by the number of females that laid. The same bloodstocks (born in captivity in 2008) were used for 9 years. The maximum production was obtained at 6 years. The number of females was 17 at the beginning and 2 at the end (Tab. II).
Figure 2. – Z. asper eggs. A in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Figure 2. – Z. asper eggs. A: Mature ovum on the right and immature ovum on the left. B: Extraction of milt, this operation is done first. C: A low pressure from the abdomen towards the anus with the index finger allows the ova to be extracted. D: The yellow colour of the ova is a good indicator of their good quality. E: Water can only be added when everything is well mixed.
Linked collectors and determiners for: Collection of various insect orders, Natural History Museum, University of Oslo.
Natural history specimen data linked to collectors and determiners held within, "Collection of various insect orders, Natural History Museum, University of Oslo". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418">https://bionomia.net/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418">https://gbif.org/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Hymenoptera collection, Natural History Museum, University of Oslo.
Natural history specimen data linked to collectors and determiners held within, "Hymenoptera collection, Natural History Museum, University of Oslo". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/a4e7ff0a-f9c0-481a-88ed-5986ec86b24a">https://bionomia.net/dataset/a4e7ff0a-f9c0-481a-88ed-5986ec86b24a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/a4e7ff0a-f9c0-481a-88ed-5986ec86b24a">https://gbif.org/dataset/a4e7ff0a-f9c0-481a-88ed-5986ec86b24a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Diptera collection, Natural History Museum, University of Oslo.
Natural history specimen data linked to collectors and determiners held within, "Diptera collection, Natural History Museum, University of Oslo". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/bb39604c-3731-49ce-a9dc-f3617d3d0d15">https://bionomia.net/dataset/bb39604c-3731-49ce-a9dc-f3617d3d0d15</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/bb39604c-3731-49ce-a9dc-f3617d3d0d15">https://gbif.org/dataset/bb39604c-3731-49ce-a9dc-f3617d3d0d15</a>. Formatted as a Frictionless Data package.
Data from: Distribution, ecology, and natural history of the recently rediscovered and critically endangered Santa Marta Sabrewing
<div><strong>Description for "RawData&media_Cphainopeplus" dataset.</strong></div> <div> </div> <div>Data from: Distribution, ecology, and natural history of the recently rediscovered and critically endangered Santa Marta Sabrewing</div> <div>MS bioRxiv ID: </div> <div>Article DOI:</div> <div> </div> <div>Please address questions to:</div> <div> </div> <div>Esteban Botero D., Dr.Sc.</div> <div>Director of Conservation Science</div> <div>SELVA: Research for Conservation in the Neotropics</div> <div>http://www.selva.org.co</div> <div>https://www.selva.org.co/integrantes/esteban-botero-delgadillo/</div> <div>e-mail: eboterod@gmail.com; esteban.botero@selva.org.co</div> <div> </div> <div>=====================================================================================</div> <div>=====================================================================================</div> <div> </div> <div> </div> <div><strong>General information:</strong></div> <div> </div> <div>The whole dataset contains information on Santa Marta Sabrewing, a critically endangered (CR) hummingbird species endemic to the Sierra Nevada de Santa Marta, northern Colombia. Part of the data are of public access and consist of historical geographic records, while another part contains data collected from a focal study population of Santa Marta Sabrewing inhabiting along the La Macana stream, in the Guatapurí River Basin, Cesar Department. No exact coordinates from the focal population were included in this dataset or related documents/materials to protect these locations.</div> <div> </div> <div>The data set is comprised by an Excel file (four spreadsheets) and two short video files that are explained below.</div> <div> </div> <div>*************************************************************************************</div> <div> </div> <div><strong>Excel file "RawData_Cphainopeplus.xlsx" (created 12-02-2024)</strong></div> <div> </div> <div> </div> <div>********** Spreadsheet "1. ConfirmedLoc" **********</div> <div>This spreadsheet contains metadata for the only five records of Santa Marta Sabrewing with confirmatory evidence.</div> <div> </div> <div>The matrix contains the following variables:</div> <div> </div> <div>VARIABLE DESCRIPTION</div> <div> </div> <div>Locality: Name of the locality as described in museums or public databases.</div> <div>Department: Name of department where the locality is found.</div> <div>Latitude: Latitude in decimal degrees.</div> <div>Longitude: Longitude in decimal degrees.</div> <div>Record status: Confirmed (with confirmatory evidence) or unconfirmed (without or needing further examination).</div> <div>Evidence: Evidence available to confirm the record.</div> <div>Source: Source of the record.</div> <div>Observations: Additional information for each row.</div> <div> </div> <div> </div> <div>********** Spreadsheet "2. PointCountDat" **********</div> <div>This spreadsheet contains information from bird counts aimed at detecting Santa Marta Sabrewing.</div> <div> </div> <div>The matrix contains the following variables:</div> <div> </div> <div>VARIABLE DESCRIPTION</div> <div> </div> <div>ID: Point-count station ID.</div> <div>Elevation: Elevation in m.</div> <div>Native: Proportion (0–1) of native vegetation 100 m around the point coordinates.</div> <div>Transformed: Proportion (0–1) of transformed vegetation 100 m around the point coordinates.</div> <div>R1: First point-count replicate, with 0 = absence and 1 = presence.</div> <div>R2: Second point-count replicate, with 0 = absence and 1 = presence.</div> <div>R3: Third point-count replicate, with 0 = absence and 1 = presence.</div> <div>R4: Fourth point-count replicate, with 0 = absence and 1 = presence.</div> <div> </div> <div> </div> <div>********** Spreadsheet "3. Behav" **********</div> <div>This spreadsheet contains information from ad libitum observations to characterize habitat associations and general behaviour of Santa Marta Sabrewing.</div> <div> </div> <div>The matrix contains the following variables:</div> <div> </div> <div>VARIABLE DESCRIPTION</div> <div> </div> <div>Date: Date (day/month/year).</div> <div>Hour: Hour in 24h format.</div> <div>Elevation: Elevation in m.</div> <div>No. Indiv.: No. of individuals of Santa Marta Sabrewing recorded.</div> <div>Behaviour: Simple categories describing sabrewing behaviour.</div> <div>Habitat: Simple categories describing habitat type where sabrewing was recorded.</div> <div> </div> <div> </div> <div>********** Spreadsheet "4. HabitatNeu" **********</div> <div>This spreadsheet contains estimated quantities for estimating Neu´s habitat proportions for Santa Marta Sabrewing. </div> <div> </div> <div>The matrix contains the following variables:</div> <div> </div> <div>VARIABLE DESCRIPTION</div> <div> </div> <div>Habitat: Simple categories describing habitat type where sabrewing was recorded.</div> <div>Obs. Count: No. of Santa Marta Sabrewing records in each habitat type.</div> <div>Hab. Prop.: Proportional area (0–1) of each habitat type in study area.</div> <div>Expected Use: Expected No. of records based on each habitat's proportional area.</div> <div>Sel. Ratio: Ratio between observed count and expected use.</div> <div>Standard. Ratio: Standardized selection ratio (0–1).</div> <div> </div> <div>*************************************************************************************</div> <div> </div> <div><strong>Video file "Campylopterus_threat.mp4" (modified 09-02-2024)</strong></div> <div> </div> <div>A slow-motion (~0.1 x) video showing a perching male Santa Marta Sabrewing involved in a persecution flight with a conspecific male aggressor. <span>Footage was taken along the course of La Macana stream, near Chemesquemena village (Cesar Department, northern Colombia). </span>Video: Elquin Toro © (reproduced with permission).</div> <div> </div> <div>*************************************************************************************</div> <div> </div> <div><strong>Video file "Campylopterus_fight.mp4" (modified 09-02-2024)</strong></div> <div> </div> <div>A lek-attending male Santa Marta Sabrewing vocalizing in a perch and subsequently adopting a threatening body posture with wing and tail feathers extended towards a conspecific male intruder. <span>Footage was taken along the course of La Macana stream, near Chemesquemena village (Cesar Department, northern Colombia). </span>Video: Elquin Toro © (reproduced with permission).</div> <div> </div> <div> </div> <div>=====================================================================================</div> <div> </div> <div> </div> <div><strong>Methodological information (for more details, please see the related manuscript):</strong></div> <div> </div> <div>We conducted a thorough revision of scientific literature, international public databases, digital collections, and museum international/national bird collections in search of geographical records of Santa Marta Sabrewing.</div> <div> </div> <div>Aside from the locality where the focal population was found (along the La Macana stream, near the Chemesquemena village, Cesar department), we also conducted three 4–7-day field expeditions to three other localities where Santa Marta Sabrewing could stably occur: San Lorenzo ridge (Magdalena Department); the upper Rioancho River basin, in Dibulla (La Guajira Department); Aracataca (Magdalena Department).</div> <div> </div> <div>We projected Santa Marta Sabrewing's extent of occurrence (EOO) and area of occupancy (AOO). Our EOO and AOO projections were compared with the threshold values given under the IUCN’s criteria B1 and B2 (IUCN 2022). To this end, we delimited suitable habitat in ArcGIS Desktop 10 (ESRI 2011) using a vegetation layer from the CORINE Land Cover Methodology from Colombia, 2018, at 1:100,000 scale (IDEAM 2021), and a layer of biomes compiled in the public-access portal of the Land-use Planning Geographic Information System (SIG-OT) of the “Agustín Codazzi” Geographic Institute of Colombia (https://geoportal.igac.gov.co).</div> <div> </div> <div>We conducted bird counts from September to December 2022 to estimate local abundance along the course of La Macana stream, near Chemesquemena village. Bird surveys were carried out using 20 georeferenced point-count stations (30 m radius), in which one observer searched for Santa Marta Sabrewing for 15 min. One count per station was conducted every month between 07:00 to 11:00s. Detection histories were analysed using the <em>occu</em> function in the <em>unmarked</em> package (Fiske and Chandler 2011) in R 4.0.2 (R Core Team 2020).</div> <div> </div> <div>In the same locality, we also conducted ad libitum observations from July 2022 to October 2023 to describe different aspects of the species’ natural history. We conducted 2–3-day monthly visits to monitor individuals and territories year-round. We described feeding habits and aspects of social or breeding behaviour, including territorial and lekking displays, vocal activity, and lek conformation.</div> <div> </div> <div>Lastly, we performed acoustic analysis focused on a description of Santa Marta Sabrewing territorial calls based on three males. We selected and analyzed a single high-quality recording per male of 20 seconds each. We used a Zoom H6 recorder coupled with a Rode NTG4 phantom-powered shotgun microphone. We visualized and analyzed the recordings using the Seewave package (Sueur et al. 2008) in R.</div> <div> </div> <div> </div> <div><strong>References:</strong></div> <div> </div> <div>ESRI (2011). ArcGIS Desktop: Release 10. Redlands, CA, USA: Environmental Systems Research Institute.</div> <div> </div> <div>Fiske, I., and Chandler, R. (2011). “unmarked”: an R package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance. J. Stat. Soft. 43: 1–23.</div> <div> </div> <div>IDEAM (2021). Leyenda nacional de coberturas de la tierra. Metodología CORINE Land Cover adaptada para Colombia escala 1:100.000 (período 2018). Bogotá, Colombia: Instituto de Hidrología, Meteorología y Estudios Ambientales (IDEAM).</div> <div> </div> <div>IUCN Standards and Petitions Committee (2022). Guidelines for using the IUCN Red List Categories and Criteria. Version 15. Prepared by the Standards and Petitions Committee. https://www.iucnredlist.org/documents/RedListGuidelines.pdf</div> <div> </div> <div>R Core Team. (2020). R: a language and environment for statistical computing, version 4.0.2. R Foundation for Statistical Computing, Vienna, Austria, http://www.R.project.org</div> <div> </div> <div>Sueur, J., Aubin, T., and Simonis, C. (2008). Seewave: a free modular tool for sound analysis and synthesis. Bioacoustics 18: 213–226.</div> <div> </div> <div>=====================================================================================</div> <div>=====================================================================================</div> <p> </p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by John Maconochie, <a href="http://www.wikidata.org/entity/Q21339335">http://www.wikidata.org/entity/Q21339335</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Hippolit Mikhailovich Krascheninnikov, <a href="http://www.wikidata.org/entity/Q5898435">http://www.wikidata.org/entity/Q5898435</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Pál Kitaibel, <a href="http://www.wikidata.org/entity/Q583036">http://www.wikidata.org/entity/Q583036</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.