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opencc-by-4.0Sep 2024View details →

Species diversity and extinction risk of vertebrate pollinators in India

This repository includes the data compiled and used for the study of ‘Species diversity and extinction risk of vertebrate pollinators in India’. If you use these data, please cite them along with our manuscript: <blockquote> Kallivalappil R., Grattarola F., de Alwis Pitts D., Cotter S.C. & Pincheira-Donoso D. (2024). Species diversity and extinction risk of vertebrate pollinators in India. Biodiversity and Conservation. https://doi.org/10.1007/s10531-024-02848-3 </blockquote>   <h2>Abstract</h2> Animal pollinators underpin the functioning and persistence of ecosystems globally. However, the vital role of pollination is being progressively eroded by the worldwide decline of pollinator species caused by human-induced environmental degradation, resulting in rising costs to biodiversity, agriculture, and economy. Most studies quantifying pollinator diversity and declines have focused on insects, whereas vertebrate pollinators remain comparatively neglected. Here, we present the first comprehensive study quantifying the macroecological patterns of species richness and extinction risk of bird and mammal pollinators in India, a region of extremely high biodiversity and increasing anthropogenic pressure. Our results reveal that hotspots of mammal pollinator diversity are restricted to the south of the Western Ghats, whereas bird pollinator diversity hotspots are scattered throughout the country. Analyses of hotspots of threatened species (based on the IUCN Red List) show that only mammal pollinators are currently classified as threatened in India, whereas multiple hotspots of population declines were observed for birds, and primarily in the Southwest for mammal pollinators. Our analyses failed to identify a role for species traits as drivers of these patterns, whereas most pollinators appear to be threatened by agriculture, logging and hunting for food, and medicinal purposes. Pollinator endangerment has widescale ecological and economic implications such as reduced food production, plant extinction, loss of functional and genetic diversity, and economic damage. We suggest protection of vertebrate pollinators should be emphasised in active conservation agendas in India.   <h2>Files</h2> <h3>Spatial</h3> <ul> <li><code>india.gpkg</code></li> <li><code>birds.gpkg</code></li> <li><code>mammals.gpkg</code></li> <li><code>how_to_read_gpkg_data.R</code></li> </ul> <h3>Phylogenetic</h3> <ul> <li><code>PGLS_phylogeny_birds.nex</code></li> <li><code>PGLS_phylogeny_mammals.nex</code></li> </ul> <h3>Tables</h3> <ul> <li><code>all_bird_traits.csv</code></li> <li><code>all_mammals_traits.csv</code></li> <li><code>threatened_mammals_traits.csv</code></li> <li><code>plant_pollinator_dataset.csv</code></li> <li><code>pollinator_plant_dataset.csv</code></li> <li><code>references.txt</code></li> </ul>

opencc-by-4.0Jul 2022View details →

Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»

Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.

opencc-by-4.0Jul 2021View details →

Ensemble projections (+ uncertainties) of contemporary (2012-2031) and future (2081-2100) mean annual plankton/phytoplankton/zooplankton species diversity (and species turn-over in time) for the global surface open ocean.

Gridded spatial fields (raster objects) containing the species distribution models (SDMs) projections of mean annual plankton total plankton, phytoplankton and zooplankton species diversity from Benedetti et al. (2021). The present .grd file ('rasterStack' object in R) contain the fields of mean annual surface plankton/phytoplankton/zooplankton species diversity for the contemporary (2012-2031) and future (2081-2100) conditions of the global open ocean (i.e., data underlying those maps in Figure 1 and Figure 3 of Benedetti et al., 2021). Layers quantifying the uncertainty (i.e., the variablity across models projections estimated through the standard deviation) in ensemble projections were also added (i.e., data underlying the maps in Supplementary Figure 4). See the Methods section of Benedetti et al. (2021) for a full description of the methodology and the ensemble SDMs forecasting framework. The raster layers follow the 1°x1° cell grid of the World Ocean Atlas (https://www.ncei.noaa.gov/). In short, we empirically modelled the monthly and mean annual diversity patterns stemming from the distribution of 860 plankton species (336 phytoplankton, 524 zooplankton) spanning 13 phyla, 71 orders and 324 genera through an ensemble approach based on SDMs. The considered species cover a wide range of traits and functions, representing 10 major plankton functional groups (PFGs; three phytoplankton and seven zooplankton groups). We compiled the species occurrence records from various data sources (available here: https://zenodo.org/record/5101349#.YO7Dqm469lM) and aggregated them onto a monthly-resolved 1°x1° grid, excluding observations from regions where the seafloor is shallower than 200 m. We matched these binned open ocean records with observation-based climatologies of environmental predictors (temperature, dissolved oxygen concentration, solar irradiance, macronutrients concentration, chlorophyll a concentration) that reflect the climatic and biogeochemical conditions of the surface open ocean. Four types of SDMs (generalized linear models, generalized additive models, artificial neural networks, and random forests) were fitted to model the species’ current environmental habitat suitability patterns. For each SDMs, we used four alternative pools of predictors. Assuming niche conservatism, we projected each of the 16 resulting species-level habitat suitability models into the future using outputs from five ESMs belonging to the Coupled Model Intercomparison Project 5 (CMIP5) that were forced by the Representative Concentration Pathway 8.5 (RCP8.5) scenario of high greenhouse gas concentrations. To this end, we first computed the modelled monthly climatologies of the selected predictors for the 2012-2031 and 2081-2100 periods, and derive the future monthly anomalies from the differences between these two time periods. These anomalies were added to the observation-based monthly climatologies (i.e., those used to train the SDMs) to estimate the future environmental conditions of the ocean, and projected the SDMs in these future conditions. Finally, we estimated the mean annual present and future alpha diversity (species richness; SR) and beta diversity (species turnover through time) patterns for both trophic levels, for each cell, from the ensemble of SDMs. SR ensembles are estimated as the sum of all species’ habitat suitability patterns averaged across all 80 possible combinations (i.e., "ensemble members") of SDMs (n = 4), ESMs (n = 5) and predictor pools (n = 4). To assess the uncertainties of our diversity projections based on the ensemble members, we compute the interquartile range of the 80 ensemble members SR projections. We calculate species turnover as the change in mean annual species composition between present and future time based on Jaccard’s dissimilarity index and by decomposing this total turnover into the true species turnover (ST, also known as species replacement) and the nestedness (SR change) components. Numerous tests are conducted to ensure the robustness of the results with regard to the spatially and temporally highly uneven sampling effort as well as with regard to the relative role of different predictors. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862923. This output reflects only the author’s view, and the European Union cannot be held responsible for any use that may be made of the information contained therein.

opencc-by-4.0Dec 2020View details →

Data from: Moth species richness and diversity decline in a 30-year time series in Norway, irrespective of species' latitudinal range extent and habitat

Data from: Burner, R., V. Selås, S. Kobro, R. Jacobsen, A. Sverdrup-Thygeson. 2021. Moth species richness and abundance decline in a 30-year time series, irrespective of species’ latitudinal range extent and habitat. Journal of Insect Conservation   Current contact info for corresponding author: Ryan C. Burner, rburner[at]usgs.gov   These data consist of a 30-year time series (1984 to 2013) of moth captures from a single site in southeast Norway, along with trait data for many of the species and climate data for the site. The moths were collected and identified by Sverre Kobro for the entire 30-year period and we are grateful for his efforts.    Abstract from manuscript: Introduction Insects are reported to be in decline around the globe, but long-term datasets are rare. The causes of these trends are elusive, with land use change and climate change among the top candidates. Yet if species traits can predict rates of population change, this can help identify underlying mechanisms. If climate change is important, for example, northern species may decline as southern species expand. Land use changes, however, may impact species that rely on certain habitats. Aims and Methods We present 30 years of moth captures (comprising 85,149 individuals of 885 species) from a site in southeastern Norway to test for population trends that are correlated with species traits. We use time series analyses and joint species distribution models combined with local climate and habitat data. Results and Discussion Species richness and abundance declined by 10.1% and 13.8% per decade, respectively. Capture rates declined for 19% of species during this time as well, though 6% have increased. Annual summer weather is correlated with annual rates of abundance change for many species. But, opposite to a general expectation, many species in our study responded negatively to increasing summer temperatures. Surprisingly, neither species’ northern range limits nor the habitat in which their primary food plants grow are strong predictors of their rates of change, or their responses to climatic factors. However, species with more southerly distributions are less likely to be declining. Complex and indirect effects of both land use and climate change may play a role in these declines. Implications for insect conservation Our results provide additional evidence for long-term declines in insect abundance. The multifaceted causes of population changes may limit the ability of species traits to reveal which species are most at risk.     ACKNOWLEDGEMENTS Thanks to J. Fjelddalen, who helped with geometrid moth identifications. This project was supported by internal funding from the Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences.

openOpenNov 2005View details →

N-fixation rate and leaf N content in two species of Alnus and their relationship to diversity of symbiotic Frankia

This study investigated patterns of nitrogen (N) fixation rates, leaf N content, and geographic diversity in the N-fixing bacterium Frankia occurring in symbiosis with Alnus incana ssp. tenuifolia and A. viridis ssp. fruticosa in early and late successional habitats on the Tanana river floodplain and surrounding uplands in the Bonanza Creek Experimental Forest. Frankia diversity was estimated via polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the nifD-K spacer region, a non-coding region in the nitrogenase-encoding operon. Specific N-fixation rate was measured with a 15N2 uptake assay and leaf N content via mass spectrometry. Additional parameters measured were soil temperature and moisture, leaf del 15N, and specific leaf area.

Fall 2000 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at GCE LTER sampling sites 1, 3, 4, 5, and 6

Grasshopper abundance and species diversity were investigated at five sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2000. Visual surveys were conducted along 10 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2002 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2002. Visual surveys were conducted along 10 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2005 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2005. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2006 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in July-August 2006. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2007 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in July-August 2007. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2008 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2008. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2009 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2009. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2010 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2010. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2011 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in July 2011. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2012 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2012. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

Fall 2001 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites

Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2001. Visual surveys were conducted along 10 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.

FIG. 8 in Unexpected diversity of the genus Collarina Jullien, 1886 (Bryozoa, Cheilostomatida) in the NE Atlantic-Mediterranean region: new species and reappraisal of C. balzaci (Audouin, 1826) and C. fayalensis Harmelin, 1978

FIG. 8. — Outlines of orifice, apertural bar, avicularium and portion of costate shield and gymnocyst: A, Collarina gautieri Harmelin, n. sp.; B, C. macaronensis Harmelin, n. sp.; C, C. speluncola Harmelin, n. sp. Scale bar: 100 µm (orifices), 50 µm (avicularia).

FIG. 5 in Unexpected diversity of the genus Collarina Jullien, 1886 (Bryozoa, Cheilostomatida) in the NE Atlantic-Mediterranean region: new species and reappraisal of C. balzaci (Audouin, 1826) and C. fayalensis Harmelin, 1978

FIG. 5. — Collarina fayalensis Harmelin, 1978: A-C, non-ovicelled and ovicelled autozooids showing the structure and limited extent of the costate shield, orifice dimorphism, small spines and relatively narrow avicularia; D, non-ovicelled zooid, for marginal pores; E, drawing from Harmelin (1978: fig. 9); F, distal part of a non-ovicelled zooid from a colony edge; G, proximal half of costate shield, note the distribution of pelmata and the shape of the basal intercostal spaces. Origin: Azores - Saô Miguel, Vila Franca Is., 15 m (A-C, F, G); Formigas Is., 15 m, 'Jean Charcot' Biaçores 1971, P.43 (D); Faial, 'Jean Charcot' Biaçores 1971, P.11 (E). Scale bars: A, 200 µm; B-D, 100 µm, F, 50 µm; G, 25 µm.

FIG. 3 in Unexpected diversity of the genus Collarina Jullien, 1886 (Bryozoa, Cheilostomatida) in the NE Atlantic-Mediterranean region: new species and reappraisal of C. balzaci (Audouin, 1826) and C. fayalensis Harmelin, 1978

FIG. 3. — Collarina balzaci (Audouin, 1826), NW Mediterranean: A, B, ovicelled and non-ovicelled zooids, note the abundance of large pseudopores (pelmata) on both the spinocyst and the ooecium; C, distal portion of a non-ovicelled zooid with no adventitious avicularia; D, distal portion of an ovicelled zooid, note the broader orifice, the shape of the apertural bar and the position of the adventitious avicularium; E, structure of the costate shield and the peripheral gymnocyst; F, adventitious avicularium with rostrum finely serrated, slightly hooked tip, and broad, rounded opesia; G, ancestrula with five spines, partly covered by filamentous microphyte. Origin: Marseille, Planier Islet, on Posidonia leaf. Scale bars: A, 200 µm; B, G, 100 µm; C-E, 50 µm; F, 25 µm.

FIG. 10 in Unexpected diversity of the genus Collarina Jullien, 1886 (Bryozoa, Cheilostomatida) in the NE Atlantic-Mediterranean region: new species and reappraisal of C. balzaci (Audouin, 1826) and C. fayalensis Harmelin, 1978

FIG. 10. — Collarina gautieri Harmelin, n. sp., NE Atlantic: A, Lepralia punctata Hassall, 1841: Busk 1854, pl. 96, fig. 3; B, C, ovicelled and non-ovicelled autozooids, note the typically curved spines associated with ovicells, the orientation of the avicularia and the respective extent of costate shield and gymnocyst; D, part of a young colony including the ancestrula (right) and the colony edge with 2 ovicelled zooids (left); E, non-ovicelled zooid (right) and fertile zooid with an early stage of the ooecium formation (middle), note the typical shape of the orifices and the structure of the costate shield with large marginal pelmata; F, ancestrula. Origin: B, Devon, coll. by JDB; C, NHMUK 1973.4.6.1, Raasay Sound, Scotland: Species A, Bishop (1986); D, Galicia, Malpica; E, Galicia, Ferrol; F, Algarve, coll. by JS. Scale bars: B, D, 200 µm; E, F, 100 µm.