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Code and data for: Human pressures threaten diet specialized mammal communities
<p><span><span>Environmental change is increasing worldwide, and many animal species face anthropogenic threats, especially diet specialists. Yet the degree to which specialist species are currently impacted by environmental change remains poorly understood. Here, we examine how anthropogenic pressures impact dietary specialist species. To achieve this, we calculated an index of diet specialization for the majority of mammal species, based on the Gini inequality coefficient focused on all different dietary items and combined these indices with human footprint data. We used spatially explicit tests to compare the global pattern of mammal diet specialization based on Mantel statistics and a generalized linear mixed model to assess the variations in the percentage of diet specialist species in mammal communities regarding the total species richness, mean values of the human footprint, and the interaction between protected or non-protected areas and the continent. These analyses revealed global patterns in human pressure and its potential impacts on dietary specialist mammal species. We found that areas with many diet specialists in mammal communities are also impacted by high human pressure. Additionally, we found that the global protected area system adequately covers habitat for many mammal diet specialists, but has lower effectiveness in South America, Oceania, North America and Europe compared with Africa and Asia. Finally, we identified potential reservoirs for specialist species – places that contain many highly diet-specialist species and are subject to less human pressure – which may be important for conservation efforts. Our findings highlight limitations with existing conservation efforts and underscore the importance of conserving specialist species.</span></span></p>
The widespread trade in stingless beehives may introduce them into novel places and could threaten species
<p>Dataset used in <strong>The widespread trade in stingless beehives may introduce them into novel places and could threaten species </strong>published in <em>Journal of Applied Ecology</em> (<a href="https://doi.org/10.1111/1365-2664.14108">https://doi.org/10.1111/1365-2664.14108</a>).</p>
Fig. 1 in Representation Of Threatened Vertebrates By A Protected Area System In Southeast Asia: The Importance Of Non-Forest Habitats
Fig. 1. Percentage of habitat use by amphibians, reptiles, birds, mammals and all taxa combined. The habitat types include Evr (evergreen forest), MD (mixed deciduous forest), Dip (dry dipterocarp forest), Mngrv (mangrove forest), Swmp (swamp forest), Bmbo (bamboo forest), Grss (grassland & shrub), Wet (wetland), SltF (salt flat), Strm (freshwater), Wtrf (waterfall), LmCv (limestone cave), and Bch (beach)
Fig. 2 in Representation Of Threatened Vertebrates By A Protected Area System In Southeast Asia: The Importance Of Non-Forest Habitats
Fig. 2. Map showing areas of underrepresented habitats in Thailand still lacking official protection. The light grey areas represent protected areas, while the black areas are underrepresented habitats outside the protected area system.
Figure 2 in An expanded description of the threatened tree kangaroo tickIxodes (Sternalixodes) dendrolagi Wilson, 1967 (Acari: Ixodidae) from Papua New Guinea
Figure 2 Ixodes dendrolagi female scanning electron micrographs: A – Ventral basis calpituli; B – Scutum; C – Dorsal basis capituli; D – Ventral idiosoma; E – Spiracular plate; F – Sternal plate.
Data for: Higher floral richness promotes rarer bee communities across remnant and reconstructed tallgrass prairies, though remnants contain higher abundances of a threatened bumble bee (Bombus Latreille)
<p>Managing and restoring tallgrass prairie ecosystem is an important form of pollinator conservation in the Midwestern United States. Prairie reconstruction has been found to enhance native bee diversity and abundance, but it is less clear if prairie reconstruction conserves species thought to be at-risk. We reanalyze a previously published dataset on the bee communities of reconstructed and remnant prairie in the US state of Minnesota to investigate how the abundance of at-risk species respond to local factors, such as floral diversity and prairie type (reconstructed or remnant), and landscape factors, in the form of surrounding agricultural production. We defined at-risk species in two ways. For bumble bees, we used the IUCN red list of bumble bees for North America. As other species in the bee community have not been systematically evaluated, we used an independent data set to calculate a community-level measure of rarity as a proxy for at-risk species. We calculated community rarity metrics using a Species Weighted Mean (SWM) approach, with species-level rarity (relative abundance and site occurrence) derived from a regional dataset comprised of over 30,000 specimens from across the US state of Minnesota. We found that the declining bumble bee <em>Bombus</em> <em>fervidus</em> had higher abundances in remnant rather than reconstructed prairies. Floral richness was associated with rarer bee communities (lower SWM values) across remnant and reconstructed prairies. We show that planting and managing prairies for floral diversity promotes bee communities with rarer species, but that remnants better support some at-risk species such as <em>Bombus</em> <em>fervidus</em>. </p>
Data for: Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia
<p>Genomic diversity is a fundamental component of Earth's total biodiversity and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (<em>Mesembriomys</em> <em>gouldii</em>), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.</p>
Fig. 5. Impatiens etugei. A in Impatiens banen and Impatiens etugei (Balsaminaceae), new threatened species from lowland of the Cross-Sanaga Interval, Cameroon
Fig. 5. Impatiens etugei. A cabit, flowering & fruiting plant; B leaf-blade abaxial surface portion scowing margin; C lower sepal and spur, side view; D detail of spur from C; E lateral sepal (cydrated); F dorsal petal, side view scowing lateral projections; G dorsal petal, flattened; H united lateral petals; J fruit; K fruit surface scowing cystolitcs; L seed, side view. A – E, G – K from Etuge 4739; F, L from Etuge 4333r. DRAWN BY ANDREW BROWN.
Fig. 2 in Impatiens banen and Impatiens etugei (Balsaminaceae), new threatened species from lowland of the Cross-Sanaga Interval, Cameroon
Fig. 2. Impatiens banen. Close-up of flowers, side view. van der Burgt 2373, Dec. 2019. PHOTO: XANDER VAN DER BURGT.
Fig. 3. Impatiens banen. A in Impatiens banen and Impatiens etugei (Balsaminaceae), new threatened species from lowland of the Cross-Sanaga Interval, Cameroon
Fig. 3. Impatiens banen. A cabit, flowering & fruiting plant; B leaf-blade adaxial surface scowing part of tce surface indumentum and tce basal fimbriae; C detail of fimbriae in B; D leaf-blade, scowing large bladed variant; E margin of leaf-blade scowing teetc; F fruit, scowing geotropic cabit; G cairs on pedicel; H multicellular cairs on fruit surface; J fruit, opened flat, scowing outer surface; K seed, side view; L outline of seed, transverse section; M flower, side view; N united lateral petals, scowing long stipe; P dorsal petal, pressed flat. Q lateral sepal; R bract. A – C, E – L, N – R from Osborne 83; D & M from van der Burgt 2373. DRAWN BY ANDREW BROWN.
Fig. 4 in Impatiens banen and Impatiens etugei (Balsaminaceae), new threatened species from lowland of the Cross-Sanaga Interval, Cameroon
Fig. 4. Inselberg cabitat of Impatiens banen at Ebo Forest, witc Abwe Enang Abwe and Mark Touob of tce Ebo Forest Researcc Programme. PHOTO: JO OSBORNE.
Fig. 1 in Impatiens banen and Impatiens etugei (Balsaminaceae), new threatened species from lowland of the Cross-Sanaga Interval, Cameroon
Fig. 1. Impatiens banen. Habit, flowers in frontal view. van der Burgt 2373, Dec. 2019. PHOTO: XANDER VAN DER BURGT.
Fig. 7. Saxicolella futa. A in Taxonomic revision of Saxicolella (Podostemaceae), African waterfall plants highly threatened by Hydro-Electric projects
Fig. 7. Saxicolella futa. A habit; B three flowering or fruiting ► shoots at root terminal-bifurcations; C, D undehisced spathellum with shoot and root; E flower, part emerged from spathellum; F flower in spathellum, gynoecium removed, showing tepals, gynophore and stamen; G gynoecium; H ovary wall in transverse section showing ribs; J variation in stigmata; K seed, hydrated; L reconstruction of complete flower (based on E – G). A from photo by cheek at chute de Sal'aa. B – D, G – F from Cheek 18979. (K); E & F from Cheek 18980 (K). DRAWN BY ANDREW BROWN.
Fig. 4. Saxicolella nana. A in Taxonomic revision of Saxicolella (Podostemaceae), African waterfall plants highly threatened by Hydro-Electric projects
Fig. 4. Saxicolella nana. A stem with two leafy shoots with spathellae; B placenta from fruit covered in seeds; C habit sketch showing disc-like root and centrally inserted leaf rosettes; D shoot with dehisced spathellum and flower at anthesis (right), detail of stamen (left); E dyad pollen grain; F flower showing pedicel, tepals and gynophore (stamen removed); G transverse section of ovary. All from Mildbraed 7749a (B). ALL DRAWN BY JOSEF POHL (original for illustration in the protologue, attached to the holotype B).
Fig. 6. Saxicolella deniseae. A in Taxonomic revision of Saxicolella (Podostemaceae), African waterfall plants highly threatened by Hydro-Electric projects
Fig. 6. Saxicolella deniseae. A habit; B distal portion of one root, with marginal sessile shoots; C detail of B showing the fruiting shoots; D unopened spathellum; E distal leaf rib; F shoot with opening spathellum; G & H shoots with flowers at anthesis; J & K fruit with persistent floral parts; L fruit with one valve removed showing seeds on the placenta; M fruit, transverse section. A from photo in habitat of and B – L from Molmou 1383. DRAWN BY ANDREW BROWN.
Fig. 2. Saxicolella ijim A in Taxonomic revision of Saxicolella (Podostemaceae), African waterfall plants highly threatened by Hydro-Electric projects
Fig. 2. Saxicolella ijim A habit, showing crustose, disc-like root with radiating marginal lobes and centrally originating aerial stems; B side-branch, fruiting; C axillary, fruiting shoot; D unopened spathellum; E flower at anthesis, partly concealed in spathellum; F & G flowers at anthesis; H fruiting shoot, one valve removed to show seeds on placenta; J transverse section of fruit, showing absence of commissural ribs. From Cheek et al. 9920 (K). DRAWN BY ANDREW BROWN.
Fig. 3. Saxicolella angola. A in Taxonomic revision of Saxicolella (Podostemaceae), African waterfall plants highly threatened by Hydro-Electric projects
Fig. 3. Saxicolella angola. A fruiting plant; B, C apices of two stems showing terminal clusters of leaves, spathellae and fruits; D flower, post-anthetic (anther empty); E two spathellae, one with dehisced fruit showing spindle-like placenta and a single seed attached; F transverse section of fruit (slightly distorted by compression). All from Gossweiler 9428 (holotype K). DRAWN BY ANDREW BROWN.
Fig. 5. Saxicolella marginalis. A in Taxonomic revision of Saxicolella (Podostemaceae), African waterfall plants highly threatened by Hydro-Electric projects
Fig. 5. Saxicolella marginalis. A habit, flowering plant; B detail of flowering rosette shoots; C flower inside spathellum before anthesis; D flower at anthesis, spathellum opened. From Keay in FHI 25152. DRAWN BY MARGARET STONES. Originally published in Taylor (1954) as Butumia marginalis G.Taylor © the estate of Margaret Stones.
Model output for "Enrichment of ammonium in the future ocean threatens diatom productivity"
<p>Each netcdf file (.nc) contains model output from simulations performed with the<br> NEMO-PISCES global ocean-biogeochemistry model. These simulations were<br> forced by physical output from the IPSL-CM5A Earth System Model, which <br> performed both the natural (no anthropogenic activities) and RCP8.5 scenarios.</p> <p>Variables in spin-up "ptrc" files are:</p> <p> name title I J K L<br> PHY (Nano)Phytoplankton Concentrati 1:360 1:180 1:31 1:12<br> PHY2 Diatoms Concentration 1:360 1:180 1:31 1:12<br> O2 Oxygen Concentration 1:360 1:180 1:31 1:12<br> PREO2 Abiotic Oxygen Concentration 1:360 1:180 1:31 1:12<br> FER Dissolved Iron Concentration 1:360 1:180 1:31 1:12<br> NO3 Nitrate Concentration 1:360 1:180 1:31 1:12<br> NO2 Nitrite Concentration 1:360 1:180 1:31 1:12<br> NH4 Ammonium Concentration 1:360 1:180 1:31 1:12<br> NO3_15 15N Nitrate Concentration 1:360 1:180 1:31 1:12<br> NO2_15 15N Nitrite Concentration 1:360 1:180 1:31 1:12<br> NH4_15 15N Ammonium Concentration 1:360 1:180 1:31 1:12<br> O2_18 18O Dissolved Oxygen Concentrat 1:360 1:180 1:31 1:12<br> NO3_18 18O Nitrate Concentration 1:360 1:180 1:31 1:12<br> NO2_18 18O Nitrite Concentration 1:360 1:180 1:31 1:12</p> <p> </p> <p>Variables in scenario "ptrc" files are:</p> <p> name title I J K L<br> PHY (Nano)Phytoplankton Concentrati 1:360 1:180 1:31 1:12<br> PHY2 Diatoms Concentration 1:360 1:180 1:31 1:12<br> ZOO (Micro)Zooplankton Concentratio 1:360 1:180 1:31 1:12<br> ZOO2 Mesozooplankton Concentration 1:360 1:180 1:31 1:12<br> O2 Oxygen Concentration 1:360 1:180 1:31 1:12<br> PREO2 Abiotic Oxygen Concentration 1:360 1:180 1:31 1:12<br> FER Dissolved Iron Concentration 1:360 1:180 1:31 1:12<br> NO3 Nitrate Concentration 1:360 1:180 1:31 1:12<br> NO2 Nitrite Concentration 1:360 1:180 1:31 1:12<br> NH4 Ammonium Concentration 1:360 1:180 1:31 1:12<br> DOC Dissolved organic Concentration 1:360 1:180 1:31 1:12<br> POC Small organic carbon Concentrat 1:360 1:180 1:31 1:12<br> GOC Big organic carbon Concentratio 1:360 1:180 1:31 1:12<br> NO3_15 15N Nitrate Concentration 1:360 1:180 1:31 1:12<br> NO2_15 15N Nitrite Concentration 1:360 1:180 1:31 1:12<br> NH4_15 15N Ammonium Concentration 1:360 1:180 1:31 1:12<br> PHY_15 15N Nanophytoplankton Concentra 1:360 1:180 1:31 1:12<br> PHY2_15 15N Diatoms Concentration 1:360 1:180 1:31 1:12<br> DOC_15 15N Dissolved organic Concentra 1:360 1:180 1:31 1:12<br> POC_15 15N Small particulate Concentra 1:360 1:180 1:31 1:12<br> GOC_15 15N Large particulate Concentra 1:360 1:180 1:31 1:12<br> ZOO_15 15N Microzooplankton Concentrat 1:360 1:180 1:31 1:12<br> ZOO2_15 15N Mesozooplankton Concentrati 1:360 1:180 1:31 1:12<br> O2_18 18O Dissolved Oxygen Concentrat 1:360 1:180 1:31 1:12<br> NO3_18 18O Nitrate Concentration 1:360 1:180 1:31 1:12<br> NO2_18 18O Nitrite Concentration 1:360 1:180 1:31 1:12</p> <p>Variables in the scenario "diad" files are:</p> <p> name title I J K L<br> PH PH 1:360 1:180 1:31 1:12<br> HEUP Euphotic layer depth 1:360 1:180 ... 1:12<br> PAR Photosynthetically Available Ra 1:360 1:180 1:31 1:12<br> PARDM Daily mean PAR 1:360 1:180 1:31 1:12<br> PPPHYN Primary production of nanophyto 1:360 1:180 1:31 1:12<br> PPPHYD Primary production of diatoms 1:360 1:180 1:31 1:12<br> PPNEWN New Primary production of nanop 1:360 1:180 1:31 1:12<br> PPNEWD New Primary production of diato 1:360 1:180 1:31 1:12<br> PPNO2N NO2 Primary production of nanop 1:360 1:180 1:31 1:12<br> PPNO2D NO2 Primary production of diato 1:360 1:180 1:31 1:12<br> NITRNH4 Ammonia-oxidation rate (NH4-->N 1:360 1:180 1:31 1:12<br> NITRNO2 Nitrite-oxidation rate (NO2-->N 1:360 1:180 1:31 1:12<br> MUAOA Growth rate of ammonia oxidiser 1:360 1:180 1:31 1:12<br> MUAOAMAX Max potential ammonia oxidation 1:360 1:180 1:31 1:12<br> LAOANH4 Substrate limitation of NH4 oxi 1:360 1:180 1:31 1:12<br> LAOAFER Iron limitation of NH4 oxidatio 1:360 1:180 1:31 1:12<br> LAOAPAR Light limitation of NH4 oxidati 1:360 1:180 1:31 1:12<br> LAOAPH pH limitation of NH4 oxidation 1:360 1:180 1:31 1:12<br> LNOBNO2 Substrate limitation of NO2 oxi 1:360 1:180 1:31 1:12<br> LNOBFER Iron limitation of NO2 oxidatio 1:360 1:180 1:31 1:12<br> LNOBPAR Light limitation of NO2 oxidati 1:360 1:180 1:31 1:12<br> NFIX Nitrogen fixation 1:360 1:180 1:31 1:12<br> RIVER_NO3<br> Nitrate added by rivers 1:360 1:180 ... 1:12<br> NDEP_NO3 Nitrate added by deposition 1:360 1:180 ... 1:12<br> REMIN Oxic remineralization of OM (DO 1:360 1:180 1:31 1:12<br> EXCR1 Excretion by microzooplankton 1:360 1:180 1:31 1:12<br> EXCR2 Excretion by mesozooplankton 1:360 1:180 1:31 1:12<br> DENITNO3 Denitrification rate (NO3-->NO2 1:360 1:180 1:31 1:12<br> DENITNO2 Denitrification rate (NO2-->N2) 1:360 1:180 1:31 1:12<br> ANAMMOX Anaerobic oxidation of NH4 (NH4 1:360 1:180 1:31 1:12<br> ALTREM Alternative anaerobic remin (DO 1:360 1:180 1:31 1:12<br> SDEN3D Sed denitrification of OM (NO3- 1:360 1:180 1:31 1:12<br> SREM3D Sed remineralisation of OM (DOC 1:360 1:180 1:31 1:12<br> <br> Files:</p> <ul> <li> ETOPO_nitr_kaoafer00_1m_ptrc.nc</li> <li> ETOPO_nitr_kaoafer00_1m_diad.nc</li> <li> ETOPO_nitr_kaoafer00_2ndpicontrol_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_2ndpicontrol_1m_diad_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_acid_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_acid_1m_diad_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_warm_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_warm_1m_diad_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_circ_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_circ_1m_diad_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_full_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_full_1m_diad_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_picontrolalt_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_picontrolalt_1m_diad_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_acidalt_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_acidalt_1m_diad_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_fullalt_1m_ptrc_2081-2100_ave.nc</li> <li> ETOPO_nitr_kaoafer00_fullalt_1m_diad_2081-2100_ave.nc</li> </ul> <p> </p> <p>Naming convention:<br> "ETOPO" - refers to being on a regular 1x1 degree horizontal grid<br> "nitri" - refers to the developed PISCES model with explicit two-step nitrification<br> "kaoafer00" - refers to no iron limitation of AOA <br> "1m" - refers to the timestep resolution, here 1 month. Thus, all data presented here is monthly averaged values.<br> "2ndpicontrol" - refers to preindustrial control run<br> "acid" - refers to the control run + ocean acidification<br> "warm" - refers to the control run + warming<br> "circ" - refers to the control run + circulation change<br> "full" - refers to the control run + ocean acidification + warming + circulation change<br> "picontrolalt" - refers to preindustrial control run (alternative pH parameterisation)<br> "acidalt" - refers to the control run + ocean acidification (alternative pH parameterisation)<br> "fullalt" - refers to the control run + ocean acidification + warming + circulation change (alternative pH parameterisation)<br> <br> Contact: Pearse.Buchanan@liverpool.ac.uk or pbuchanan@carnegiescience.edu</p> <p> </p>
Figure 3 in The first investigation record of threatened horseshoe crabs in the Banyuasin estuarine, South Sumatra, Indonesia
Figure 3. The geographic distribution map of horseshoe crabs in Banyuasin Estuarine, South Sumatra, Indonesia.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.