Find research datasets worth reusing

opencc-by-4.0Oct 2017View details →

COMMENTS.— Although not breeding in the Mediterranean, the species forages in Libyan waters (van Dijk et al. 2014). In addition to the single beached record, an individual was pulled from nearshore waters of the Tajura coast in 1996 and died in the rehabilitation facility of the Marine Biology Research Centre (MBRC) at Tajura, where it was subsequently taxidermied at the MBRC Museum (Hamza 2010). Capra's (1949) records were based on a report in "L'Idea Coloniale" for 2 May 1927 (Mongàr) and an unspecified specimen in the Museo Civico di Storia Naturale di Trieste (Sella). IUCN THREAT STATUS.— Vulnerable A2bd. MAP 3. Distribution of Dermochelys coriacea in Libya showing stranding site records. in Atlas of the Reptiles of Libya

COMMENTS.— Although not breeding in the Mediterranean, the species forages in Libyan waters (van Dijk et al. 2014). In addition to the single beached record, an individual was pulled from nearshore waters of the Tajura coast in 1996 and died in the rehabilitation facility of the Marine Biology Research Centre (MBRC) at Tajura, where it was subsequently taxidermied at the MBRC Museum (Hamza 2010). Capra's (1949) records were based on a report in "L'Idea Coloniale" for 2 May 1927 (Mongàr) and an unspecified specimen in the Museo Civico di Storia Naturale di Trieste (Sella). IUCN THREAT STATUS.— Vulnerable A2bd. MAP 3. Distribution of Dermochelys coriacea in Libya showing stranding site records.

opencc-by-4.0Dec 2023View details →

Figure 2. – Mean abundance per 750 m2 in Changes in distribution patterns of two vulnerable fish species (Epinephelus marginatus and Sciaena umbra) in the Scandola marine reserve (Corsica, NW Mediterranean): a possible effect of increased boat tourism

Figure 2. – Mean abundance per 750 m2 (± SE) of the dusky grouper Epinephelus marginatus (A) and the brown meagre Sciaena umbra (B) according to protection level at Scandola in 2012 and 2018. IR: integral reserve, BZ: buffer zone, UP: unprotected zone. Interannual difference are indicated for each protection level, *: significant at p <0.05, ns: not significant.

opencc-by-4.0Dec 2023View details →

Figure 1 in Changes in distribution patterns of two vulnerable fish species (Epinephelus marginatus and Sciaena umbra) in the Scandola marine reserve (Corsica, NW Mediterranean): a possible effect of increased boat tourism

Figure 1. – Location of sites surveyed for dusky grouper and brown meagre populations inside and outside the Scandola MNR (Corsica, NW Mediterranean), according to protection status in summer 2012 and 2018. Dark blue arrows = integral reserve (IR), light blue arrows = buffer zone (BZ), red arrows = unprotected zones (UP). Blue stars = surveyed only in 2012, red star = site surveyed only in 2018.

opencc-by-4.0Dec 2023View details →

Figure 5 in Changes in distribution patterns of two vulnerable fish species (Epinephelus marginatus and Sciaena umbra) in the Scandola marine reserve (Corsica, NW Mediterranean): a possible effect of increased boat tourism

Figure 5. – Size structure of Epinephelus marginatus and Sciaena umbra at Scandola in 2012 and 2018. Size classes = 10 cm for the dusky grouper and 5 cm for the brown meagre.

opencc-zeroJan 2024View details →

Linked collectors and determiners for: A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov..

Natural history specimen data linked to collectors and determiners held within, "A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9c423299-73fd-4c27-b497-fa7b98850ed9">https://bionomia.net/dataset/9c423299-73fd-4c27-b497-fa7b98850ed9</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9c423299-73fd-4c27-b497-fa7b98850ed9">https://gbif.org/dataset/9c423299-73fd-4c27-b497-fa7b98850ed9</a>. Formatted as a Frictionless Data package.

Fig. 4 in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species

Fig. 4. Multidimensional Scaling (MDS) plot (stress: 0.0045) performed using average pairwise TN93 (Tamura & Nei, 1993) distances among investigated Lutrogale perspicillata groups created according to the country of origin of samples (modern + museum DNA and GenBank entries).

Fig. 3. A in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species

Fig. 3. A, Lutrogale perspicillata network computed using haplotypes (h) from the 305 bp-long sequence alignment (modern + museum DNA and GenBank entries). A scale to infer the number of sequences for each pie (i.e., haplotype) was provided together with a length bar to compute the number of mutational changes. The colour of each country and the number of each haplotype are indicated. See Table S1 for more details. B, Mismatch Distributions (MD) of the mtDNA pairwise differences (dotted: observed; line: expected) calculated for South East Asia haplogroup (Fig. 3A). Estimates of FS and R2 statistics (with related P values), r (raggedness index) and the outcome of SSD and SSD* test under a model (H0) of sudden demographic and spatial population expansion, respectively, are provided.

Fig. 2 in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species

Fig. 2. Photos of MNHN-ZM-MO-2001-350, L. p. perspicillata holotype resident in the mammal collection of the National Museum of Natural History of Paris, France. A, right side, lateral view (bar length = 20 cm); B, left forelimb, lateral view; C, basement, in French "Lutra perspicillata = Lutra leptonix Horsf., loutre de Java par m Diard, mai 1821, la tête est au lab d'anatomie", which can be translated into and interpreted as: "Lutra perspicillata = Lutra leptonix (Horsfield, 1824), Java otter from M. Diard, May 1821, skull is in the lab of anatomy" (see also Material and Methods). Photos courtesy and copyright: © MNHN - RECOLNAT - Laura Flamme - 2014.

Fig. 1 in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species

Fig. 1. Lutrogale perspicillata distribution (in yellow; see insets for Iraq and Pakistan) including sampling localities of modern (white circles) and museum (green squares) individuals. As far as the latter are concerned, we reported only sites for which samples were successfully investigated (see Table S1 for the entire sample size of this study; symbol "?" stands for unknown locality). The white stars indicate, in Iraq, the locality (TaqTaq, Kurdistan) where the sample of Omer et al. (2012) was collected, in Cambodia/Thailand and Malaysia, the country/ies of origin of EF472348 and KY117557 GenBank sequence, respectively. In Iraq, Pakistan, and supposedly Java, Indonesia, the green squares indicate localities (when known) of L. p. maxwelli, L. p. sindica, and L. p. perspicillata museum holotypes, respectively. Finally, Naga Hills at the border between Myanmar and India as well as Bahoo-Kalat River Basin between Iran and Pakistan are indicated (see text for more details). The species' geographic range was adapted from IUCN (International Union for Conservation of Nature) 2015. Lutrogale perspicillata. The IUCN Red List of Threatened Species 2019-3 was modified using CorelDraw!12 (2003). Digital images (insets) were obtained from Google Earth 7.1.5.1557 (2015 Google Inc.) and Google Earth map data (Data SIO, NOAA, U.S. Navy, NGA, GEBCO - Image Landsat). Please note that thick dotted lines mark out new borders for L. p. sindica and L. p. perspicillata subspecies as established in this study (see text for more details).

opencc-zeroJan 2023View details →

Data for: Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests

Understanding the evolutionary processes that shape the landscape of genetic variation and influence the response of species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across the distribution range of a dominant forest tree, Quercus acutissima, in East Asia, and applied genome-wide analyses to track the evolutionary history and predict the fate of populations under future climate. We found two genetic groups (East and West) in Q. acutissima that diverged during the Pliocene. We also found a heterogeneous landscape of genomic variation in this species, which may have been shaped by population demography and linked selections. Using genotype-environment association analyses, we identified climate-associated SNPs in a diverse set of genes and functional categories, indicating a model of polygenic adaptation in Q. acutissima. We further estimated three genetic offset metrics to quantify genomic vulnerability of this species to climate change due to the complex interplay between local adaptation and migration. We found that marginal populations are under higher risk of local extinction because of future climate change, and may not be able to track suitable habitats to maintain the gene-environment relationships observed under the current climate. We also detected higher reverse genetic offsets in northern China, indicating that genetic variation currently present in the whole range of Q. acutissima may not adapt to future climate conditions in this area. Overall, this study illustrates how evolutionary processes have shaped the landscape of genomic variation, and provides a comprehensive genome-wide view of climate maladaptation in Q. acutissima.

opencc-by-4.0Jan 2023View details →

Supplementary Data and Code: Determinants of range sizes pinpoint vulnerability of groundwater species to climate change: a case study on subterranean amphipods from the Dinarides

Supplementary Data and R code for phylogenetic analyses for manuscript entitled Determinants of range sizes pinpoint vulnerability of groundwater species to climate change: a case study on subterranean amphipods from the Dinarides. The dataset contains beast.tree → data for import into R: maximum credibility phylogeny data_lambert.csv → data for import into R: data on habitat and distribution for 52 Niphargus species morpho.csv → data for import into R: morphometric data (body length) for 52 Niphargus species niphargus_ranges.Rmd → fully reproducible R markdown file niphargus_ranges.html → html output of Rmd file To be able to run the analysis put the data files into folder <data> and run the Rmd script.

FIG. 7 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.

FIG. 7. — Median-joining networks based on trnSGG and rps4-trnS sequences: A, the Ptisana attenuata clade; B, the P. salicina/P. soluta comb. nov., stat. nov./P. smithii clade. The size of each circle is proportional to the haplotype frequency. Undetected intermediate haplotypes on nodes are shown as black circles and hatch marks represent mutational steps separating haplotypes.

FIG. 6 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.

FIG. 6. — Phylogram from the Bayesian phylogenetic analysis of the chloroplast DNA sequence data for Ptisana Murdock. Support values for branches are given in the order of Bayesian inference posterior probability; maximum parsimony bootstrap support; and maximum likelihood bootstrap support. Only values>0.80 PP and 60% BS are shown.

FIG. 4 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.

FIG. 4. — Distribution map for the New Caledonian endemic species of Ptisana attenuata (Labill.) Murdock (), P. rolandi-principis (Rosenst.) Christenh. (Δ), and P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov. (, with unvouchered field observations indicated by a broken outline). Shaded areas are ultramafic substrates. The collecting sites of the sequenced P. attenuata samples are indicated.

FIG. 5 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.

FIG. 5. — The holotype of Ptisana soluta (Compton) Murdock & Perrie, comb. nov., stat. nov. (Compton 1674, Ignambi, 1914, BM[BM000787128]) showing how the lamina transitions from 3-pinnate proximally to 2-pinnate distally. CC BY The Trustees of the Natural History Museum, London.

FIG. 3 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.

FIG. 3. — Ptisana soluta (Compton) Murdock & Perrie, comb. nov., stat. nov., field photos: A, frond with lamina 3-pinnate proximally and 2-pinnate distally. The frond at top-right is P. attenuata (Labill.) Murdock; B, stipes are greenish-brown at a distance; C, abaxial surface of costae and fertile lamina, showing transition from 3-pinnate to 2-pinnate; D, stipe greenish-brown and smooth; E, stipules around stipe bases. Photos: A-D, Leon Perrie from near Nouméa; E, Rémy Amice, from near Nouméa.

FIG. 1 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.

FIG. 1. — Ptisana attenuata (Labill.) Murdock, field photos: A, 3-pinnate frond; B, stipes are dark at a distance; C, abaxial surface of costae and lamina, with synangia; D, stipe dark and wrinkled; E, divided stipules around stipe bases. Photos: Leon Perrie, from near Nouméa.

opencc-zeroSep 2023View details →

Data from: Species-specific ecological traits, phylogeny, and geography underpin vulnerability to population declines for North American birds

Species declines and extinctions characterize the Anthropocene. Determining species vulnerability to decline, and where and how to mitigate threats, are paramount for effective conservation. We hypothesized that species with shared ecological traits also share threats, and therefore may experience similar population trends. Here, we used a Bayesian modeling framework to test whether phylogeny, geography, and 22 ecological traits predict regional population trends for 380 North American bird species. Groups like blackbirds, warblers, and shorebirds, as well as species occupying Bird Conservation Regions at more extreme latitudes in North America, exhibited negative population trends, while groups such as ducks, raptors, and waders, as well as species occupying more inland Bird Conservation Regions, exhibited positive trends. Specifically, we found that in addition to phylogeny and breeding geography, multiple ecological traits contributed to explaining variation in regional population trends for North American birds. Furthermore, we found that regional trends and the relative effects of migration distance, phylogeny, and geography differ between shorebirds, songbirds, and waterbirds. Our work provides evidence that multiple ecological traits correlate with North American bird population trends, but that the individual effects of these ecological traits in predicting population trends often vary between different groups of birds. Moreover, our results reinforce the notion that variation in avian population trends is controlled by more than phylogeny and geography, where closely-related species within one region can show unique population trends due to differences in their ecological traits. We recommend that regional conservation plans, i.e. one-size-fits-all plans, be implemented only for bird groups with population trends under strong phylogenetic or geographic controls. We underscore the need to develop species-specific research and management strategies for other groups, like songbirds, that exhibit high variation in their population trends and are influenced by multiple ecological traits.

publicJan 2023View details →

Data for: Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests

Open the record for dataset details and reuse information.