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opencc-by-4.0Dec 2022View details →

Estimated densities of activity from: Characterising diel activity patterns to design conservation measures: Case study of European bat species

Estimated densities of activity calculated in "Characterising diel activity patterns to design conservation measures: case study of European bat species" (see Materials and Methods for more information on these calculations). The files named "densitiyAllYear" correspond to the estimated densities based on our entire dataset. The files named "densitiySpring" correspond to the estimated densities based on a subset of our dataset comprising only monitoring carried out between 1 March and 21 June. The files named "densitiySummer" correspond to the estimated densities based on a subset of our dataset comprising only monitoring carried out between 22 June and 21 August. The files named "densitiyAutumn" correspond to the estimated densities based on a subset of our dataset comprising only monitoring carried out between 22 August and 31 October. The first column of each file ("PercentageNight") corresponds to the percentage of the night elapsed (0 % = sunset time, 100 % =  sunrise time), the second to the estimated activity density ("Density").

opencc-zeroDec 2022View details →

Floristic composition, structure and diversity of riparian forests in southwestern Nigeria: Conservation is inevitable

The Nigerian riparian forest ecosystems had declined in extent and distribution and this had been attributed mainly to land use change. This study intended to provide an understanding of the links between plant diversity, composition, structures, and disturbances both anthropogenic and natural processes inducing the vegetation dynamics. Nine study sites were used for this study, within each site, five (5) plots (0.25 ha in size) were marked out and placed systematically at an interval of 10 m along the transect. A complete enumeration of plant species was carried out and identified at the species level. Diversity indices and structural parameters were determined and anthropogenic activities were ranked. A total number of 233 plant species were identified, belonging to 80 families; out of which, Euphorbiaceae and Apocynaceae were dominant families The density and basal area ranged from 2,200-6,000 ha-1 and 2.59-17.58 m2 ha-1 respectively across the study sites. Pterocarpus santalinoides, Alchornea cordiflora, Chassalia kolly, Tetracera spp, Fimbristylis, Bambusa vulgaris and Cyrtosperma senegalense were the dominant species. The Shannon diversity index ranged from (1.38-3.49), Simpson (0.66-0.97), and Evenness diversity (0.43-0.84). Fisher alpha (10.03-30.21) and Whittaker beta diversity (0.36-0.89) values were highest in Ipetumodu (site VIII) and lowest in Ilesha (site II). Seventy-three (73%) of the species in this study had a low important value index (IVI). The dominance of some lianas and herbaceous species in the riparian forest sites showed disturbances, stages of ecological succession, and regeneration of the vegetation. Conservation is inevitable towards maintaining and protecting species diversity, ecosystem roles, and services of these forests in Nigeria.

opencc-by-4.0Dec 2022View details →

Local knowledge, exploitation, and conservation of the African golden cat Caracal aurata in Central Cameroon

The data contains the responses from a questionnaire survey. Data were collected in local communities in Cameroon using Kobocollect, to assess the knowledge of the locals on the African golden cat. The questions are listed in the first row and the following rows contain the answers of each participant. The first 13 columns contain socio-demographic questions and the remaining contain specific questions related to the African golden cat knowledge and exploitation. No abbreviation is used in the dataset except YCF (Council Forest of Yoko); MDNP (Mpem et Djim National park); 1 (Yes), 0(NO)

opencc-zeroDec 2022View details →

Evolutionary conservation and diversification of auditory neural circuits that process courtship songs in Drosophila

Acoustic communication signals diversify even on short evolutionary time scales. To understand how the auditory system underlying acoustic communication could evolve, we conducted a systematic comparison of the early stages of the auditory neural circuit involved in song information processing between closely-related fruit-fly species. Male Drosophila melanogaster and D. simulans produce different sound signals during mating rituals, known as courtship songs. Female flies from these species selectively increase their receptivity when they hear songs with conspecific temporal patterns. Here, we first confirmed interspecific differences in temporal pattern preferences; D. simulans preferred pulse songs with longer intervals than D. melanogaster. Primary and secondary song-relay neurons, JO neurons and AMMC-B1 neurons, shared similar morphology and neurotransmitters between species. The temporal pattern preferences of AMMC-B1 neurons were also relatively similar between species, with slight but significant differences in their band-pass properties. Although the shift direction of the response property matched that of the behavior, these differences are not large enough to explain behavioral differences in song preferences. This study enhances our understanding of the conservation and diversification of the architecture of the early-stage neural circuit which processes acoustic communication signals.

opencc-zeroDec 2022View details →

Drawing on local knowledge and attitudes for the conservation of critically endangered rhino rays in Goa, India

In the context of marine species declines in data-limited regions, local ecological knowledge (LEK) is a valuable source of information on species ecology and historical trends. LEK can also help understand how threatened species exist within a local culture, in terms of their uses and values, and reveal attitudes toward their conservation. Rhino rays (guitarfish and wedgefish) are highly threatened by overfishing with most species Critically Endangered, yet poorly studied in countries like India that fish them the most. We drew on LEK to understand the socio-ecological status of rhino rays in Goa, on the west coast of India. We investigated their habitat use and seasonality, interaction with fisheries, socio-economic uses, and relational values. We also explored attitudes of fishers towards rhino rays and their conservation. A combination of semi-structured interviews and key informant interviews (88 in total) were conducted with fishers at multiple sites. Local knowledge suggests that nearshore habitats around river mouths form important nursery grounds for some rhino rays, and provided insights into their seasonality and breeding. Rhino rays appeared to be targeted historically but are entirely bycaught at present, with the highest catches in gillnets and in the South Goa district, during September and October. LEK indicated that taxa like sawfish (Pristis spp.) and wedgefish (Rhynchobatus spp.) have severely declined or disappeared from this region. We coded different relational values, from recreation (rhino rays are consumed and enjoyed with alcohol) to symbolic values (rhino rays are considered lucky). All key informants expressed positive attitudes towards rhino ray conservation and stated that a ban on landing these species would have little to no impact on fisher earnings. The usefulness of LEK suggests it should be brought into the scientific mainstream to support development of more equitable and socially-appropriate management plans. Fostering relational values can reinforce fishers' positive attitudes, thereby enhancing rhino ray conservation. Their low commercial value and potentially high post-capture survival suggest that using norm-based approaches to promote live release may be successful. Further research on rhino ray ecology and human dimensions can support the development of appropriate conservation interventions.

Post-translocation dynamics of black-tailed prairie dogs (Cynomys ludovicianus): A successful conservation and human-wildlife conflict mitigation tool

Prairie dogs have declined by 98% throughout their range in the grasslands of North America. Translocations have been used as a conservation tool to reestablish colonies of this keystone species and to mitigate human-wildlife conflict. Understanding the behavioral responses of prairie dogs to translocation is of utmost importance to enhance the persistence of the species and for species that depend on them, including the critically endangered black-footed ferret. In 2017 and 2018, we translocated 658 black-tailed prairie dogs on the Lower Brule Indian Reservation in central South Dakota, USA, a black-footed ferret recovery site. Here, we describe and evaluate the effectiveness of translocating prairie dogs into augered burrows and soft released within presumed coteries to reestablish colonies in previously occupied habitat. We released prairie dogs implanted with passive integrated transponders (PIT tags) and conducted recapture events approximately 1-month and 1-year post-release. We hypothesized that these methods would result in a successful translocation and that prairie dogs released as coteries would remain close to where they were released because of their highly social structure. In support of these methods leading to a successful translocation, 69% of marked individuals were captured 1-month post-release, and 39% were captured 1-year post-release. Furthermore, considerable recruitment was observed with 495 unmarked juveniles captured during the 1-year post-release trapping event, and the reestablished colony had more than doubled in area by 2021. Contrary to our hypothesis, yet to our knowledge a novel finding, there was greater initial movement within the colony 1-month post-release than expected based on recapture locations compared to published average territory size; however, 1-year after release most recaptured individuals were captured within the expected territory size when compared to capture locations 1-month post-release. This research demonstrates that while translocating prairie dogs may be socially disruptive initially, it is an important conservation tool.

Conservation measures or hotspots of disease transmission? Agri-environment schemes can reduce disease prevalence in pollinator communities

Insects are under pressure from agricultural intensification. To protect pollinators, conservation measures such as the EU agri-environment schemes (AES) promote planting wildflowers along fields. However, this can potentially alter disease ecology by serving as transmission hubs or by diluting infections. We tested this by measuring plant-pollinator interactions and virus infections (DWV-A, DWV-B and ABPV) across pollinator communities in agricultural landscapes over a year. AES had a direct effect on DWV-B, reducing prevalence and load in honeybees, with a tentative general dilution effect on load in early summer. DWV-A prevalence was reduced both under AES and with increasing niche overlap between competent hosts, likely via a dilution effect. In contrast, AES had no impact on ABPV; its prevalence was driven by the proportion of bumblebees in the community. Epidemiological differences were also reflected in the virus phylogenies, with DWV-B showing recent rapid expansion, while DWV-A and ABPV showed slower growth rates and geographic population structure. Phylogenies indicate that all three viruses freely circulate across their host populations. Our study illustrates how complex interactions between environmental, ecological and evolutionary factors may influence wildlife disease dynamics. Supporting pollinator nutrition can mitigate the transmission of important bee diseases, providing an unexpected boost to pollinator conservation.

Genetic restoration of black rhinoceroses in South Africa: conservation implications

Globally, wildlife populations are becoming increasingly small and isolated. Both processes contribute to an elevated risk of extinction, notably due to genetic factors related to inbreeding depression and a loss of adaptive potential. Wildlife translocation is a valuable conservation tool to reintroduce species to previously occupied areas, or augment existing populations with genetically divergent animals, thereby improving the viability of endangered populations. However, understanding the genetic implications of mixing gene pools is key to avoid the risk of outbreeding depression, and to maximise translocation effectiveness. In this study we used mitochondrial and microsatellite DNA collected from 110 black rhinoceroses (Diceros bicornis minor) in Kruger National Park, South Africa, to determine levels of genetic diversity, inbreeding and relatedness. We compared this diversity with the two source populations (KwaZulu-Natal, South Africa and Zambezi River, Zimbabwe) using data from previously published studies, and assessed changes in the relative contribution of source lineages since their reintroduction in the 1970s. Our results show that Kruger's black rhinoceroses are genetically more diverse than those from KwaZulu-Natal, with levels closer to those from the Zambezi Valley. Furthermore, our findings indicate a relative increase in the Zimbabwean lineage since reintroduction, suggesting a possible selective advantage. From a conservation perspective, our results demonstrate the benefits of mixing multiple source populations to restore gene flow, improve genetic diversity and thereby help protect small, isolated populations from extinction.

Botanic records from the forest reserves of south west Ghana: Plant species distribution data with checklist and conservation assessments from 114 vegetation plots

South west Ghana is a biodiversity hotspot within the western African lowland tropical rainforest region, supporting many endemic and restricted range plant species. This dataset comprises botanic records from five forest reserves of south west Ghana (Ankasa, Boi Tano, Tano Nimri, Jema Assemkron, Nini Suhein). Vascular plant species distribution data (12,232 records) from 114 vegetation plot samples are presented, surveyed between 1981 and 2015. A plant species checklist including conservation assessments for each species is included. Nomenclature is current as of 2016. The dataset is linked to the publication Marshall et al, 2023, Implications for conservation assessment from flux in the botanical record over 20 years in south west Ghana, Ecology and Evolution <a href="https://doi.org/10.1002/ece3.9775">https://doi.org/10.1002/ece3.9775</a>. The dataset is also used in Marshall et al, 2022, Predictors of plant endemism in two west African forest hotspots, Frontiers in Ecology and Evolution 10:980660 <a href="https://doi.org/10.3389/fevo.2022.980660">https://doi.org/10.3389/fevo.2022.980660</a>.

Media portrayal of the illegal trade in wildlife: The case of turtles in the US and implications for conservation

News media framing of instances of illegal wildlife trade provides a window into understanding public perceptions of trade dynamics and potential support for conservation actions. Here, we used 54 known cases of illegal turtle trade in the United States occurring between 1998–2021 as a case study to investigate news media framing of illegal wildlife trade. We synthesized information from these cases and qualitatively analyzed how they were framed in 217 associated news articles. The 54 cases involved the illegal trade of at least 24,000 freshwater turtles of 34 different species; box turtles (Terrapene spp.) were traded the most. Of the known species involved, 23 were listed under one of the CITES Appendices, and 12 were considered threatened by the IUCN. Trade occurred in at least 43 US states and 6 countries. Despite the multifaceted nature of these cases, problem and solution framing was relatively unvarying. Media coverage framed foreign demand, particularly from Asia for high-value pet turtles, as a main driver of illegal trade. Solutions focused on regulations and enforcement which follow global trends in illegal wildlife trade discourses. However, we also found that articles neutralized illegal turtle trade in several ways, reflecting a lack of perceived legitimacy of and necessity for trade rules and enforcement. Without acknowledging longstanding and formerly legal practices in wildlife trading, conservation efforts which focus on regulations and enforcement may be undermined by a lack of normative compliance.

Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)

To establish the microtubule cytoskeleton, the cell must tightly regulate when and where microtubules are nucleated. This regulation involves controlling the initial nucleation template, the γ-tubulin ring complex (γTuRC). Although γTuRC is present throughout the cytoplasm, its activity is restricted to specific sites including the centrosome and Golgi. The well-conserved γ-tubulin nucleation activator (γTuNA) domain has been reported to increase the number of microtubules (MTs) generated by γTuRCs. However, previously we and others observed that γTuNA had a minimal effect on the activity of antibody-purified Xenopus γTuRCs in vitro (Thawani et al., eLife, 2020; Liu et al., 2020). Here we instead report, based on improved versions of γTuRC, γTuNA, and our TIRF assay, the first real-time observation that γTuNA directly increases γTuRC activity in vitro, which is thus a bona fide γTuRC activator. We further validate this effect in Xenopus egg extract. Via mutation analysis, we find that γTuNA is an obligate dimer. Moreover, efficient dimerization as well as γTuNA's L70, F75, and L77 residues are required for binding to and activation of γTuRC. Finally, we find that γTuNA's activating effect opposes inhibitory regulation by stathmin. In sum, our improved assays prove that direct γTuNA binding strongly activates γTuRCs, explaining previously observed effects of γTuNA expression in cells and illuminating how γTuRC-mediated microtubule nucleation is regulated.

Data from: Reconciling diverse viewpoints within systematic conservation planning

<ol> <li>Conservation encompasses numerous alternative viewpoints on what to value (features such as biodiversity, ecosystem services or socio-economic benefits) and how to convert these values into conservation policies that deliver for nature and people. Reconciling these differing values and viewpoints in policy development and implementation is a perennial challenge.</li> <li>Balancing differing stakeholder viewpoints within a single conservation plan risks some viewpoints overshadowing others. This can occur as some dominant viewpoints may lead to more marginal views being suppressed, and also through social biases during the planning process.</li> <li>Here we develop four separate 'caricature' conservation viewpoints, and spatially quantify each of them in order to test different approaches to equitable reconciliation. Each viewpoint prioritises different locations, dependent on the extent to which they deliver a variety of different biodiversity, well-being and economic goals.</li> <li>We then show how these different viewpoints can be reconciled using numeric methods. We find that a pluralist approach, which accounts for the spatial similarities and differences between viewpoints, is able to deliver equitably for multiple conservation features. This pluralist approach provides a coherent spatial conservation strategy with the capacity to satisfy advocates of quite divergent approaches to conservation.</li> </ol>

opencc-zeroFeb 2023View details →

Niche dynamics of Memecylon in Sri Lanka: distribution patterns, climate change effects, and conservation priorities

Aim: Recent climate projections have shown that the distribution of organisms in island biotas is highly affected by climate change. Here, we present the results of the analysis of niche dynamics of a plant group, Memecylon on Sri Lanka, an island, using species occurrences and climate data. We aim to determine which climate variables explain current distribution, model how climate change impacts the availability of suitable habitat for Memecylon, and determine conservation priority areas for Sri Lankan Memecylon. Location: Sri Lanka Methods: We used georeferenced occurrence data of Sri Lankan Memecylon to develop ecological niche models and assess both current and future potential distributions under six climate change scenarios in 2041-2060 and 2061-2080. We also overlaid land-cover, and protected area maps and performed a gap analysis to understand the impacts of land-cover changes on Memecylon distributions and propose new areas for conservation. Results: Differences among suitable habitats of Memecylon were found to be related to patterns of endemism. Under varying future climate scenarios, endemic groups were predicted to experience habitat shifts, gains, or losses. The narrow endemic Memecylon restricted to the montane zone were predicted to be the most impacted by climate change. Projections also indicated that changes in species' habitats can be expected as early as 2041-2060. Gap analysis showed that while narrow endemic categories are considerably protected as demonstrated by their overlap with protected areas, more conservation efforts in Sri Lankan forests containing wide endemic and non-endemic Memecylon are needed. Main conclusions: This research helped clarify general patterns of responses of Sri Lankan Memecylon to global climate change. Data from this study are useful for designing measures aimed at filling the gaps in forest conservation on this island.

opencc-by-nc-4.0Nov 2022View details →

Figure 4 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit

Figure 4. Camponotus cillae recorded for the RPPN Botujuru: (A) front view; (B) dorsal view; (C) side view. regeneration of the older areas provides resources to Another important factor is the potential of conservation those species with more specialized habits. units to discover new species, mainly invertebrates (Liu We underscore the presence of two species, a pos- et al., 2022), a group that lacks inventory data. sible new species of Octostruma Forel, 1912, recorded They also emphasize the need to advance in the idenin the areas with an understory, and Camponotus cillae tification of recorded morphospecies, increase sampling Forel, 1912 (Fig. 4) recorded in Brazil only by the type se- efforts, use other collection techniques to better underries in the state of São Paulo (Botucatu) by Forel in 1912 stand the diversity of ants and other faunal and floristic (Forel, 1912). Data on their biology is scarce in the liter- groups in the RPPN. Moreover, these results also underature. This new record highlights the importance of new score the need for the creation of measures aiming at studies on biodiversity to our comprehension of the dis- preserving the area, given that the urbanization process tribution of species (Janicki et al., 2016). has been intense in the vicinity of the conservation unit. In addition, our results show the potential of RPPN Botujuru; the occurrence of C. cillae and the possible species of Octostruma in the Botujuru RPPN emphasizes the CONCLUSION importance of conservation units for threatened biomes. Fragments of Atlantic Forest found in conservation units The diversity of ants evaluated in this first work, carare important for the preservation of biodiversity, acting ried out with only one collection campaign, indicates as refuge areas for species that suffer from anthropo- that the natural regeneration process is having positive genic pressures such as deforestation and urban growth effects in abandoned areas. The fragments that compose (Gardner et al., 2009; Pardini et al., 2009; Lima et al., 2020), the RPPN Botujuru may prove to be very representative providing resources, even for those rarely collected. of the Alto Tietê region regarding the conservation of the

opencc-by-nc-4.0Nov 2022View details →

Figure 3 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit

Figure 3. Non-metric multidimensional scaling (NMDS) Bray-Curtis type for the areas with 1-4 years (grey), 7-12 years (light green), and 14 years (dark green). (Anosim = 0,0001).

opencc-by-nc-4.0Nov 2022View details →

Figure 2 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit

Figure 2. The number of occurrences of trophic guilds along the regeneration gradient in areas of Eucalyptus sp.: 1-4 years (no understory), located in the buffer zone of RPPN Botujuru – Serra do Itapety; 7-12 years (with an understory composed of shrubby vegetation), and 14 years (with an understory displaying both shrubby and arboreal vegetation).

opencc-by-4.0Feb 2023View details →

Supplementary Information for "Mapping potential conflicts between global agriculture and terrestrial conservation"

This archive contains supplementary figures from mapping potential conflicts between global agriculture and terrestrial conservation in 2010 and 2070. Please see the captions of these figures below. Supplementary Figure 3. Distribution of regional land use by agricultural commodity and conservation priority (CP) index intervals (48 x 3 sub-figures). Supplementary Figure 4. Distribution of regional land use (left) and global land use (right) of 48 agricultural commodities (48 x 3 sub-figures). The x-axis is the land use as a proportion of the total global production area. Supplementary Figure 5. Comparison of the distribution of regional land use for 48 agricultural commodities between 2010 and 2070 scenarios (48 x 7 x 2 sub-figures). Supplementary Figure 6. Comparison of land use and conservation conflict between national and global levels. The y-axis refers to the land use as a proportion of the total global production area. There are 48 agricultural commodities for 197 countries (197 x 48 x 3 sub-figures). Supplementary Figure 7. Comparison of the land use distribution of top producers for 48 agricultural commodities between 2010 and 2070 scenarios (48 x 10 x 2 sub-figures). Supplementary Figure 8. Spatial distribution maps of production areas for 48 agricultural commodities (48 x 3 maps). Supplementary Figure 9. Conflict between conservation priority sites and (non-)domestic land use for 42 agricultural commodities associated with consumption in 197 countries (197 x 42 x 3 sub-figures). Supplementary Figure 10. Land use maps of 42 agricultural commodities linked to consumption in 197 countries (197 x 42 x 3 maps). Supplementary Figure 11. Conservation priority index and export rate of selected agricultural commodity for primary production cells (land use of each agricultural commodity > 10% of cell area). a) Current status in 2010. b) Shifts of conservation priority in 2070 (RCP 8.5). Triangles point-up and point-down to indicate increased and decreased CP, respectively. Density plots on top and right show cell densities corresponding to export rate and CP index, respectively. Supplementary Figure 12. Maps of global conservation priority index in 2010 and 2070. Supplementary Figure 13. a, Performance curves for prioritization per scenario 2010, 2070-RCP2.6, and 2070-RCP8.5). Curves show the average fraction of species' range covered in each scenario weighted by each species weight, divided by the total weight of species (y-axis), by a given fraction of the landscape (x-axis). b, Histograms and boxplots of all CP map pixels. Each jittered point in boxplots represents a map pixel.

opencc-by-4.0Nov 2022View details →

Dataset I related to the publication: In silico Evaluation of the Thr58-associated Conserved Water with KRAS Switch-II Pocket Binders

WaterMaps results related to the publication: Leini R, Pantsar T: In Silico Evaluation of the Thr58-Associated Conserved Water with 2 KRAS Switch-II Pocket Binders. J. Chem. Inf. Model. [accepted] https://doi.org/10.1021/acs.jcim.2c01479 <ul> <li>Individual .zip files contain the WaterMap results for each structure.</li> </ul> Additional notes: there is a typo in the 5v90 file name (it is the 5v9o structure). Related datasets: 10.5281/zenodo.7341954 and 10.5281/zenodo.7342311

opencc-by-4.0Feb 2023View details →

Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)"

Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)" alignments: alignments used for BEAST ("bayes") and PopArt ("popart"). The "popart" folder also has a traits file per each species. bayesian_plots: TSVs ("tsv") and PDF files ("ogs") generated by BEAST. The "tsv" folder also has the scripts for plotting the results in R. easysfs: scripts, population file and results from the VCF to SFS conversione done by easySFS. fineRADstructure: fineRADstructure input files and output PDF plots ("plots") for C. formosanus ipyrad and Stacks ("stacks") data.  logs: logs for ipyrad, ModelTest, PGDspider, PopArt ("popart") and Stacks ("stacks"). The "popart" folder also have the generated networks in a TXT file. The "stacks" folder also has ODS files for calculating the amount of loci per each M/n fixed value. snapclust: STR files used with R for snapclust. Scripts included. stairway_plot: input (blueprint files) and outputs for Stairway Plot 2 analyses. The C. formosanus folder ("chordodes") also has scripts for R plotting. vcfs: VCF and HDF5 files used in this study. Also scripts for filtering/converting data and plotting the PCA with ipyrad (activate python first!) for C. formosanus. "acutogordius" = A. taiwanensis "chordodes" = C. formosanus "gordius" = G. chiashanus