Find research datasets worth reusing

opencc-by-4.0Jun 2017View details →

Figure 2 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species

Figure 2. Types of molecular genetic data used in published studies examining questions at the species-level, subspecies-level, or undefined taxonomic level for marine mammals. Note that studies may have used more than one data type. Mitochondrial DNA sequence data (MtDNASeq), nuclear DNA sequence data (NuSeq), microsatellites (Msats), morphological data (Morph).

opencc-zeroFeb 2023View details →

MicromAsia: small mammal surveys in Western China and Kyrgyzstan (1994-2014)

This dataset corresponds to surveys carried out in Asia (western China and Kyrgyzstan) between May 1994 and August 2014 as part of the research expeditions of Patrick Giraudoux and his team. It includes: <ul> <li>Traplines set up and small mammal captured. The corresponding collection of skulls, specimens and tissues has been donated to the Museum National d'Histoire Naturelle, Paris since the 22nd of November 2022.</li> <li>Activity index transect walked to provide abundance estimates over a larger range than possible using trapping methods</li> <li>Miscellaneous supplementary files and trapline photos.</li> </ul> Main files <a href="https://zenodo.org/record/7614879/files/Traplines.txt?download=1">Traplines.txt </a> <a href="https://zenodo.org/api/files/17e03137-dc8a-4b79-bd1c-4a9752fe0a9d/Traplines.txt"> </a> This file is a table that describes the 787 traplines or trap clusters or circumstances by which small mammal specimens have been captured. Some traplines can have  no capture. This is a point to consider when trapping success is computed joining the trapline table to the capture table. Those two tables can be joined using the field 'idLine'. For more details about sampling design, trap types, distance between two traps, etc. please refer to the articles published using those data (see references on this web page). <ul> <li>nameStudysite, name of the survey site</li> <li>country, country ISO code</li> <li>countryName, country name</li> <li>province, province name</li> <li>idLine, trapline ID code: digits #1-2 location ID, digits #3-4 year, digits  #5-6 month, digits #7-8 line number. The two latter digits can be coded on numbers 01, 02, 03... or on letters AA, AB, AC,...</li> <li>sLongitude, longitude of the trapline beginning (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')</li> <li>sLatitude, latitude of the trapline beginning (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')</li> <li>eLongitude, longitude of the trapline end</li> <li>eLatitude, latitude of the trapline beginning</li> <li>cLongitude, longitude of the trapline centroid (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')</li> <li>cLatitude, latitude of the trapline beginning (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')</li> <li>altitude, altitude</li> <li>emplacementMethod, way location is recorded: CoordCloserVillage, distance and direction of the nearest village (used on a time when GPS receivers were nor available); GPS, geographical coordinates; unknown</li> <li>distVillage, distance to the nearest village (in m)</li> <li>azimuthVillage, bearing direction to the nearest village</li> <li>habitat, habitat description</li> <li>campagneObs, month and year of the survey</li> <li>campagneObsBegin, date of the beginning of the survey</li> <li>campagneObsEnd, date of the end of the survey</li> <li>traptype, trap type (see e.g. <a href="https://zenodo.org/record/7614879/files/Traptypes.pdf?download=1">Traptypes.pdf</a> for some  illustrations): <ul> <li>INRA, INRA trap</li> <li>sbbt, small break back trap</li> <li>apporté, brought by people</li> <li>apporté (?), possibly brought by people</li> <li>BBBT, big break back trap</li> <li>sSherman, small Sherman trap</li> <li>BSHERMAN, big Sherman trap</li> <li>CAGE, cage trape</li> <li>tong, tong trap</li> <li>attrapé à la main, caught by hand</li> <li>road, found dead along a road</li> <li>trouvés, found</li> <li>assommoir, deadfall trap</li> <li>tong trap, tong trap</li> <li>bbbt, small break back trap</li> <li>child, brought by a child</li> <li>collet, snare</li> <li>BBBT ou jaw, big break back trap or jaw trap</li> <li>jaw, jaw trap</li> </ul> </li> <li>remarks, remarks</li> <li>nbControlNights, number of control nights (traps were set up during the day and controlled every morning)</li> <li>nbTrapsInstal1, number of traps set up</li> <li>nbTrapsRecov1, number of traps recovered on first control</li> <li>nbTrapsRecov2, number of traps recovered on control #2</li> <li>nbTrapsRecov3, number of traps recovered on control #3</li> <li>nbTrapsRecov4, number of traps recovered on control #4</li> <li>nbTrapsRecov5, number of traps recovered on control #5</li> </ul> <a href="https://zenodo.org/records/14246016/files/capturesV2.txt?download=1">CapturesV2.txt</a> This file is a table that describes the 2178 animals captured.  As a  table, it can be joined to the trapline table using the field 'idLine'. Animals with an idMNHN have had their skulls and sometimes other body parts deposited at the Museum National d'Histoire Naturelle in Paris. <ul> <li>country, country ISO code</li> <li>idCapture, Capture ID code: digits #1-8 trapline ID, see field 'idLine' of <a href="https://zenodo.org/record/7614879/files/Traplines.txt?download=1">Traplines.txt</a> for details, digits #9-10 capture ID in the trapline</li> <li>numControlNight, number of the control night</li> <li>dateControlNight, date of the control night</li> <li>labCode, code for the laboratory</li> <li>speciesField, species as identified in the field; for abbreviations see <a href="https://zenodo.org/record/7614879/files/SpeciesNames.txt?download=1">SpeciesNames.txt </a></li> <li>species, species as confirmed in the lab</li> <li>sex, M male; F female.</li> <li>reproducing T true; F False</li> <li>remarks</li> <li>HeadBodyLength, head-body length</li> <li>UterusDiameter (mm)</li> <li>WholeBodyWetmass, body mass (g)</li> <li>EarLength (mm)</li> <li>ToesForelegNb, number of toes (foreleg)</li> <li>ToesHindlegNb, number of toes (hintleg)</li> <li>ClawLength (mm)</li> <li>TailLength (mm)</li> <li>TailQuiffLength (mm)</li> <li>HindFootLength (mm)</li> <li>CristallineLensNb, number of crystalline lens weighed (sometimes only one could be taken)</li> <li>CristallineLensDrymass, dry mass of the crystalline lens weighed (one or two together according to 'CristallineLensNb'</li> <li>TesticleLength (mm)</li> <li>TesticleWidth (mm)</li> <li>SeminalVesicleLength (mm)</li> <li>SeminalVesicleWidth (mm)</li> <li>PlacentaScarsNb, number of placental scares</li> <li>EmbryosNb, number of embryos</li> <li>idLine, ID of the trapline where the animal was caught</li> <li>idMNHN, MNHN ID</li> </ul> <a href="https://zenodo.org/record/7614879/files/Parasites.txt?download=1">Parasites.txt </a> Livers and general cavity were generally examined visually to identify macroparasites such as cestode kysts or nematodes with a particular attention for Echinococcus multilocularis metacestodes. Additionnal informations on parasites might have been reported in the field 'remarks' of <a href="https://zenodo.org/record/7614879/files/Captures.txt?download=1">Captures.txt</a>. As a  table, it can be joined to the capture table using the field 'idCapture' <ul> <li>country, country ISO code</li> <li>idCapture, Capture ID code see field idCapture of <a href="https://zenodo.org/record/7614879/files/Captures.txt?download=1">Captures.txt</a><a href="https://zenodo.org/api/files/17e03137-dc8a-4b79-bd1c-4a9752fe0a9d/Captures.txt"> </a></li> <li>species, parasite species name: "?" or  "99" = unknown (generally a small unidentifiable white dot);  "CH" =  Capillaria hepatica  (sometimes in full "Capillaria hepatica"); "Em"  =  Echinococcus multilocularis (sometimes in full "Echinococcus multilocularis");   "Taenia" ;  "Taenia crassiceps"; "Taenia taeniformis"</li> <li>number</li> </ul> <a href="https://zenodo.org/record/7614879/files/Transects.zip?download=1">Transects.zip </a> Transects were used to sample open habitats such as grassland, arable fields etc., for species that leave conspicuous activity indices on the ground surface, in order to provide abundance estimates over a larger range than possible using trapping methods. For each transect, 10 paces intervals were surveyed with activity indicators identifiable to species or genus level (including foraging corridors, ground holes, earth tumuli and small mammal faeces) recorded. Except for Sary Mogol, Kyrgyzstan, where transect were walked on twenty 10-paces intervals centred on the nodes of a grid, transect routes were selected opportunistically under accessibility constraints in order to cross the largest portion of each habitat patch. They were recorded via Global Positioning System receivers with an approximate 15 m accuracy. The zip file includes the followings: <ul> <li>Transect file descriptions.rtf, the description of the fields of each transect table</li> <li>Transects_Honlong_2007_09.txt, transects walked near HongLong, China, in September 2007</li> <li>Transects_Narati_2006_09.txt, transects walked near Narati, China, in September 2006</li> <li>Transects_Ningxia_2003_09.txt, transects walked in Ningxia, China, in September 2003</li> <li>Transects_SaryMoghul_2012_2014.txt, transects walked near Sary Moghul, Kyrgyzstan, in May 2012 and August 2014</li> <li>Transects_Serxu_2002_07.txt, transects walked near Serxu, China, in July 2002</li> <li>Transects_Tuotuohe_2006_07.txt, transects walked on the way from Xining to Tuotuo He, China, in July 2006</li> </ul> Supplementary files <a href="https://zenodo.org/record/7614879/files/1MapStudyAreas.jpg?download=1">1MapStudyAreas.jpg</a> Map of the main areas surveyed <a href="https://zenodo.org/record/7614879/files/DNA_sequencing.txt?download=1">DNA_sequencing.txt </a>table of the specimens whose DNA has been sequenced <ul> <li>ind_number, Capture ID code: see field 'idCapture' in <a href="https://zenodo.org/record/7614879/files/Captures.txt?download=1">Captures.txt </a></li> <li>ID_lab, lab identification label</li> <li>Species_DNA, species as identified by DNA sequencing</li> <li>laboratory, people and/or lab who performed the analysis</li> <li>ID morphometry/karyotype, species as identified by morphology + karyotype</li> </ul> <a href="https://zenodo.org/record/7614879/files/Photos_traplines.zip?download=1">Photos_traplines.zip</a> Photos of traplines and habitats for the following surveys <ul> <li>Honglong, CN, September 2007</li> <li>Maerkang, CN, September 2005</li> <li>Narati, CN, September 2006</li> <li>Ningxia, CN, September 2003, July 2012</li> <li>Rantang, CN, June 2004</li> <li>Sary Mogol, KG, April 2008</li> <li>Serxu, CN, July 2002</li> </ul> <a href="https://zenodo.org/record/7614879/files/SpeciesNames.txt?download=1">SpeciesNames.txt</a> Abbreviations, latin, English, French names of species <ul> <li>Code, code on 4 digits</li> <li>Nom latin, latin name</li> <li>Nom commun (Anglais), common name (English)</li> <li>Nom commun (Français), common name (French)</li> <li>Remark</li> </ul> <a href="https://zenodo.org/record/7614879/files/Small_mammal_measurements.pdf?download=1">Small_mammal_measurements.pdf</a> Method for small mammal sampling and measurements. <a href="https://zenodo.org/record/7614879/files/TrapLocationCodes.txt?download=1">TrapLocationCodes.txt</a> Codes for the location of traplines <ul> <li>Location, location name</li> <li>Symbol, symbol (first two digits of idLine in <a href="https://zenodo.org/record/7614879/files/Traplines.txt?download=1">Traplines.txt </a></li> <li>Province, province name</li> <li>Trapping, remarks about sampling design</li> </ul> <a href="https://zenodo.org/record/7614879/files/Traptypes.pdf?download=1">Traptypes.pdf</a>  Samples of small and big break back traps, tong trap and INRA trap.

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Small mammal ARTS: Orion receiver data for site radiomapping and vole tracking, and scripts and results for localization and activity estimates

This data set accompanies "An Automated Radio-Telemetry System (ARTS) for Monitoring Small Mammals". The behavior of small fossorial mammals, such as voles, is extremely difficult to observe in natural environments. Small mammals were traditionally studied with labor intensive methods such as trapping and recapture or radio telemetry via homing, which require week/months of work and produce static home range estimates. In pursuit of better understanding natural history and behavioral ecology we implemented an automated radio telemetry system (ARTS) to continuously monitor small mammals. We used an isotropic antenna array coupled with broadband receivers to estimate animal positions with nonlinear least squares, nonparameteric, and Bayesian trilateration methods. We then used Lomb-Scargle periodograms to estimate activity patterns of freely-behaving Prairie voles.

opencc-zeroMar 2022View details →

Fig. 3 in Analysis of biodiversity data suggests that mammal species are hidden in predictable places

Fig. 3. Consensus results of species delimitation analyses. Phylogenetic distribution of hidden diversity estimated from strict consensus of delimitation results (SI Appendix, Table S1). Each silhouette represents a mammalian order with its shadow reflecting the ratio of predicted species to recognized species. Striped silhouettes represent orders with conflicting delimitation results that were not included in the predictive analysis. Phylogeny was adapted from ref. 31.

Fig. 4 in Analysis of biodiversity data suggests that mammal species are hidden in predictable places

Fig. 4. Important predictors of hidden species in mammals. (A) From Top to Bottom, the 50 most important predictive variables (judged by MDA), for the consensus random forest classification model. In both plots, variables are color coded by life history, geographic, climatic, taxonomic, and environmental. (B) Boxplots representing values of the top predictive variables for species included in the consensus model. Values from species identified as hidden are shown at the Bottom of each plot (labeled "H"), and values from species not identified as hidden are shown Above (labeled "NH"). Outliers are excluded from boxplots.

Fig. 1 in Analysis of biodiversity data suggests that mammal species are hidden in predictable places

Fig. 1. Predictive modeling workflow. The framework proposed for identifying named mammal species that are likely to contain hidden diversity utilizes barcoding gene sequences and machine learning models built from environmental, geographic, climatic, taxonomic, and life history variables.

Fig. 2 in Analysis of biodiversity data suggests that mammal species are hidden in predictable places

Fig. 2. Scope of the dataset. Genetic sequences for ∼70% of currently recognized mammalian species were obtained. All mammalian orders are represented, with 23 orders containing sequences from both COI and cytb and 4 having only sequences from cytb. (A) Circle plots reflect species representation for the COI and cytb genes in each order. Dark bars represent the species present in the dataset and light bars represent species for which no genetic data are available. (B) Blue bars represent the proportion of the sequence database represented by each order, and gray bars represent the proportion of recognized species in each order. (C) A total of 3,205,630 geographic occurrence records were obtained for species present in the genetic database.

Fig. 9 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 9. Morphometric parameters of free-living females of S. papillosus: а — body length; b — body width; c — length of esophagus; d — length of intestine; e — length of tail; f — distance to vulva; g — number of eggs; on the ordinate axis — length in µm, on the abscissa axis — species of host (Ch — Capra hircus, Oc — Oryctolagus cuniculus, Cp — Cavia porcellus).

Fig. 8 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 8. Morphometric parameters of S. papillosus males: a — body length; b – body width; c — length of esophagus; d — length of intestine; e — length of the tail; f — length of spicules; on the ordinate axis — length in µm, on the abscissa axis — species of host (Ch — Capra hircus, Oc — Oryctolagus cuniculus, Cp — Cavia porcellus).

Fig. 7 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 7. Free-living female of S. papillosus: a — general view; b — anterior part (the arrowheads indicate the bulbs); c — uterus with eggs (the pointer indicates the genital opening); scale bars 100 µm.

Fig. 5 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 5. Morphometric parameters of L3: а — body length; b — body width; c — length of esophagus; d — length of intestine; e — length of the tail end; on the ordinate axis — length in µm, on the abscissa axis — species of host (Ch — Capra hircus, Oc — Oryctolagus cuniculus, Cp — Cavia porcellus).

Fig. 6 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 6. Mature male of S. papillosus: a — general view; b — anterior part (arrowheads indicate bulbs); c — caudal part with spicules in lateral view; d — caudal part with spicules in dorsal view; scale bars 100 µm.

Fig. 3 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 3. Morphometric parameters of L2 of S. papillosus: а — body length; b — body width; c — length of esophagus; d — length of intestine; e — length of the tail; on the ordinate axis — length in µm, on the abscissa axis – species of host (Ch — Capra hircus, Oc — Oryctolagus cuniculus, Cp — Cavia porcellus).

Fig. 2 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 2. Morphometric parameters of L1 of S. papillosus: а — body length; b — body width; c — length of esophagus; d — length of intestine; e — length of tail; on the ordinate axis — length in µm, on the abscissa axis — species of host (Ch — Capra hircus, Oc — Oryctolagus cuniculus, Cp — Cavia porcellus).

Fig. 4 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 4. Third-stage larva of S. papillosus: a — general view; b — anterior part (the pointer indicates the place where the esophagus joins the intestine); c — posterior part; scale bars 100 µm.

Fig. 1 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 1. Rhabditiform larvae of S. papillosus: a — L1 from C. hircus (arrowheads indicate the bulb-like dilatations on the esophagus and the tail); b — L1 from O. hircus (arrowheads indicate bulb-like dilatations on the esophagus and the tail); c — L2 from C. hircus (arrowheads indicate two bulb-like dilatations); scale bars 100 µm.

opencc-by-4.0Aug 2017View details →

Fig. 2 in Accumulation Of Heavy Metals By Small Mammals The Background And Polluted Territories Of The Urals

Fig. 2. The dendrogram is obtained for element analysis (Cu+Zn+Cd) in small mammals from natural populations in the background zone (Bcg) and polluted territories (Imp). The results of cluster analysis confirmed the statistically significant differences in heavy metals total accumulation in three species of small mammals.

opencc-by-4.0Jun 2017View details →

Fig. 1 in Helminths Of Wild Predatory Mammals Of Ukraine. Nematodes

Fig. 1. Structure of nematode communities in carnivorans of the family Canidae in Ukraine (based on original data). A — red fox; B — wolf; C — raccoon dog. Toxe — Toxascaris leonina; Unst — Uncinaria stenocerhala; Toca — Toxocara canis; Pepl — Pearsonema plica; Euae — Eucoleus aeropilus; Paff — Pterygodermatites affinis; Trvu — Trichuris vulpis; Mopa — Molineus patens; Crvu — Crenosoma vulpis; Casp — Capillaria sp.; Ster — Strongyliodes erschowi; Spar — Spirocerca artica; Splu — S. lupi; Trsp — Trichinella cf. spiralis; Aopu — Aonchotheca putorii; Syag — Sy. agraria; Heum — Heligmosomum sp.; Anca — Ancylostoma caninum.

opencc-by-4.0Jul 2016View details →

Fig. 2 in Helminths Of Wild Predatory Mammals (Mammalia, Carnivora) Of Ukraine. Trematodes

Fig. 2. Structure of the trematode fauna of the racoon dog in Ukraine (original data): ALT — A. alata; MSK — M. skworzowi; EPE — E. perfoliatus; IME — I. melis; ADO — A. donicum.