Find research datasets worth reusing

opennotspecifiedMay 2020View details →

FIGURE 1 in Evolution, characterization and phylogenetic utility of ITS2 gene in Orthoptera and some Polyneoptera: Highly variable at the order level and highly conserved at the species level

FIGURE 1. Secondary structure of ITS2 in Polyneoptera taxa (conserved motifs of helix III showed in dashed boxes and U-U mismatch of helix II in dotted boxes; A—Blatella germanica, B—Mantis religiosa, C—Coptotermes formosanus, D—Oligotoma sp., E—Timema cristinae).

Conservation genetics of native and European-introduced Chinese Water Deer (Hydropotes inermis)

The Chinese water deer (Hydropotes inermis) belongs to a relatively early-divergence lineage of Cervidae and is thought to have retained some ancestral features of the group. This species is classified as Vulnerable on the IUCN Red List (accessed 2020), and populations in its native range have declined drastically in recent years. However, a number of individuals were introduced to the UK about a century ago; these have flourished and now make up over 40% of global numbers. To infer the population genetic structure and genetic diversity of Chinese water deer both in their native China and in populations introduced to the UK and France, mitochondrial DNA sequence variation was investigated (control region and cytochrome B) for near 100 individuals. The distribution of haplotypes among the regions shows distinct geographic structure, and only one cytochrome B haplotype was common to both China and European populations. Our results reveal lower levels of genetic diversity in the British populations, differentiation between native and introduced populations, and that the source population of British deer is likely to be extinct. Some recommendations are made for the conservation of different populations.

Conservation status of a plant family with high endemism, the Primulaceae, in China

Primroses, ca 1000 species from the family Primulaceae, are mostly distributed in high mountains and attract people's attention with their high ornamental value. However, they are increasingly threatened by human activities and climate change in recent decades. China harbors more than half of global primrose species, most of which are endemic. To strengthen studies on their conservation, we established a distribution database for primroses in China, including 12 genera and 535 speceies. Based on this database, we explored the geographic pattern of the richness of primrose species in relation to environmental factors and identified conservation priority areas. The results showed that the primrose richness was highest in the mountain areas from the eastern Himalayas to the Hengduan Mountains, with habitat heterogeneity and temperature seasonality together shaping that pattern. Furthermore, the richnesses of endemic and threatened primroses were strongly affected by the long-term climate stability since the Last Glacial Maximum. On average, national nature reserves (NNRs) covered 29.6% of the distribution areas of primroses. By analyzing less protected species, we proposed that nature reserves need to be established in several conservation gaps mainly located in Southwest China to protect the primrose species in China.

opencc-zeroDec 2019View details →

Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status

Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (Crotalus oreganus) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.

opencc-by-4.0Aug 2020View details →

Data and code for Chapter 1: An expanded scope of biodiversity in urban agriculture, with implications for conservation.

Data and code for Chapter 1: An expanded scope of biodiversity in urban agriculture, with implications for conservation, in Urban Agroecology: Interdisciplinary Research and Future Directions (Monika Egerer and Hamutahl Cohen eds). CRC Press, Taylor & Francis, Abingdon, UK

Data from: Conservation concern among Australian undergraduates is associated with childhood socio-cultural experiences

Fostering widespread concern for conservation problems requires a robust understanding of the life experiences that positively contribute to an individual's conservation attitudes and behaviours. However, few studies have assessed a comprehensive range of social and experiential predictors of conservation concern. Using survey responses from 391 undergraduate students enrolled in various course disciplines across Australia, we describe the relationship between five major constructs of early-life experiences and two measures of conservation concern: a preference for conservation career, and positive conservation attitudes. We find that conservation career preferences are positively associated with childhood preferences for nature-related books, movies and school subjects, biospheric family value orientations and environmental volunteering. Conseravtion attitudes were postitively associated with biospheric family value orientations and environmental volunteering. Both constructs were negatively associated with egoistic family values, and childhood experiences in nature were not a significant factor in either of our models. This suggests that limited nature experiences do not necessarily impede the development of conservation concern in young Australians, which was strongly related to the values of their immediate family and their experiences with environmental organisations, nature-related storylines and school subjects.

opennotspecifiedMay 2019View details →

FIGURE 3 in First record and conservation status of Allobates algorei (Anura: Aromobatidae) in Colombia

FIGURE 3. Phylogenetic relationships for some Allobates species in North of South America. The numbers at the nodes indicate maximum likelihood ultrafast-bootstrap values.

opennotspecifiedMay 2019View details →

FIGURE 2 in First record and conservation status of Allobates algorei (Anura: Aromobatidae) in Colombia

FIGURE 2. Illustration of the morphological characteristics of A. algorei (MCNUP-H 0521). (A) plantar view of the right foot and (B) lateral view of the head. Illustration: O. Armesto.

opencc-by-4.0Aug 2020View details →

Datasets of the study: "Describing variability in pig genes involved in coronavirus infections: towards a One Health perspective in conservation of animal genetic resources"

Dataset description Sequencing data (*.bam files) of four pig genes (ACE2, ANPEP, DPP4 and TMPRSS2) that can serve as receptors or protease for priming the infection of coronaviruses. The datasets are related to 22 European pig breeds and wild boars (Alentejana, AL; Apulo-Calabrese, AC; Basque, BA; Bísara, BI; Black Slavonian, BS; Casertana, CA; Cinta Senese, CS; Gascon, GA; Kr&scaron;kopolje, KR; Lithuanian Indigenous Wattle, LIW; Lithuanian White Old Type, LWOT; Majorcan Black, MB; Mora Romagnola, MR; Moravka, MO; Nero Siciliano, NS; Sarda, SA; Schwäbisch-Hällisches Schwein, SHS; Swallow-Bellied Mangalitsa, SBMA; Turopolje, TU; Italian Duroc, IDU; Italian Large White, ILW; Italian Landrace, ILA; Wild Boar, WB). This work took advantage of a study design developed within the Horizon 2020 TREASURE project. Each folder contains *.bam files and the related indexes *.bai. The name of the investigated breed and gene is part of the file name (e.g. ILW.ACE2.bam identifies the sequencing data related to the ACE2 gene in the Italian Large White pig breed). Details of sequencing and the bioinformatic pipeline are below reported. Sequencing data A total of 22 DNA pools were constructed from the European pig breeds and one DNA pool was constructed from European wild boars, including in each pool 30 or 35 individual DNA samples pooled at equimolar concentration. For the 22 DNA pools, libraries were prepared and fed into an Illumina HiSeq X Ten sequencer for paired-end sequencing, obtaining 150 bp length reads. The wild boar DNA pool was sequenced from 250 bp fragment libraries, with 100 bp long paired-end reads, on the BGISeq 500 platform, following the provider’s procedures. Data processing Reads that were obtained from the sequenced libraries were cleaned by removing adapter sequences and filtering out sequences presenting more than 10% unknown bases (N) and/or containing low-quality bases (Q ≤ 5) over 50% of the total sequenced bases. Then, filtered high-quality reads were mapped on the latest version of the Sus scrofa reference genome (Sscrofa11.1; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.fna.gz) using the BWA-MEM algorithm v.0.7.17 and the parameters for paired-end data. Picard v.2.1.1 (https://broadinstitute.github.io/picard/) was used to remove duplicated reads. Whole sequence data are available in the EMBL-EBI European Nucleotide Archive (ENA) repository (http://www.ebi.ac.uk/ena), under the study accession PRJEB36830.  Reads covering the four genes (ACE2: NC_010461.5:12094853-12156275; ANPEP: NC_010449.5:55346083-55378881; DPP4: NC_010457.5:68655849-68748818; TMPRSS2: NC_010455.5:204871561-204907561) were extracted with samtools v.1.7 and exported as aligned, sorted and indexed *.bam files. Gene length includes UTRs and flanking regions of 5 kbp upstream [flanking (5’-UTR)] and downstream [flanking (3’-UTR)].

opencc-zeroDec 2019View details →

Extreme mobility of the world's largest flying mammals creates key challenges for management and conservation

Background: Effective conservation management of highly mobile species depends upon detailed knowledge of movements of individuals across their range; yet, data are rarely available at appropriate spatiotemporal scales. Flying-foxes (Pteropus spp.), are large bats that forage by night on floral resources and rest by day in arboreal roosts that may contain colonies of many thousands of individuals. They are the largest mammals capable of powered flight, and they are highly mobile, which makes them key seed and pollen dispersers in forest ecosystems. However, their mobility also facilitates transmission of zoonotic diseases and brings them in conflict with humans, and so require a precarious balancing of conservation and management concerns throughout their Old World range. Here we analyse the Australia-wide movements of 201 satellite-tracked individuals, providing unprecedented detail on the inter-roost movements of three flying-fox species: Pteropus alecto, P. poliocephalus, and P. scapulatus across jurisdictions over up to five years. Results: Individuals were estimated to travel long distances among a network of 755 roosts, with P. alecto reaching more than 1,800 kilometers a year, P. poliocephalus up to 2,500 kilometers a year and P. scapulatus up to 6,000 kilometers a year, but with little uniformity among their directions of travel. This indicates that flying-fox populations are composed of extremely mobile individuals that move nomadically and at species-specific rates. Individuals of all three species exhibited very low fidelity to roosts, resulting in very high estimated colony turnover rates. This indicates that flying-fox roosts form nodes in a vast continental network of 'staging posts' through which highly mobile individuals travel far and wide across their species range. Conclusions: The extreme inter-roost mobility reported here demonstrates the extent of the ecological linkages that nomadic flying-foxes provide across Australia's contemporary fragmented landscape, with profound implications for the ecosystem services and zoonotic dynamics of flying-fox populations. In addition, the extreme mobility of the species means that impacts from local management actions can readily reverberate across jurisdictions throughout the species ranges; therefore, local management actions need to be assessed with reference to actions elsewhere and hence require national coordination. These findings underscore the need for sound understanding of animal movement dynamics to support evidence-based, transboundary conservation and management policy, tailored to the unique movement ecologies of species.

Diversity and conservation of saproxylic beetles in 42 European tree species: an experimental approach using early successional stages of branches

Correction: In the original version of this dataset, the non‐native Prunus serotina was incorrectly interchanged with the native Prunus padus, and eight individuals of saproxylic beetles were incorrectly removed from the data when splitting beetles in saproxylic and non‐saproxylic species. The correct tree species is Prunus serotina, and results refer to a total of 113 species of saproxylic beetles and 30,550 individuals. 1. Tree species diversity is important to maintain saproxylic beetle diversity in managed forests. However, knowledge about the conservational importance of single tree species and implications for forest management and conservation practices are lacking. 2. We exposed freshly cut branch-bundles of 42 tree species, representing tree species native and non-native to Europe, under sun-exposed and shaded conditions for one year. Afterwards, communities of saproxylic beetles were reared ex-situ for two years. We tested for the impact of tree species and sun exposure on alpha-, beta-, and gamma diversity as well as composition of saproxylic beetle communities. 3. Tree species had a lower impact on saproxylic beetle communities compared to sun exposure. The diversity of saproxylic beetles varied strongly among tree species, with highest alpha- and gamma-diversity found in Quercus petraea. Red-listed saproxylic beetle species occurred ubiquitously among tree species. We found distinct differences in the community composition of broadleaved and coniferous tree species, native and non-native tree species as well as sun-exposed and shaded deadwood. 4. Our study enhances the understanding of the importance of previously understudied and non-native tree species for the diversity of saproxylic beetles. To improve conservation practices for saproxylic beetles and especially red-listed species, we suggest a stronger incorporation of tree species diversity and sun exposure into forest management strategies, including the enrichment of deadwood from native tree species and with a specific focus on locally rare or silvicultural less important tree species.

Data from: Taxonomic delimitation of species complexes: a challenge for conservation, first steps with Abarema cochliacarpos complex

Taxonomic and ecological knowledge of plant species complexes informs their conservation status. Poorly delimited species boundaries can lead to incorrect assessments of biodiversity, and a rare species might have its distribution range overestimated if considering other closely related taxa as the same one. The present study investigates the level of morphometric variation within the Abarema cochliacarpos complex, throughout its entire distribution range in Brazilian Atlantic Forest and Caatinga vegetation, and considers the drivers of this variation. A morphometric study using cluster, PERMANOVA, and NMDS analyses was conducted. We analyzed patterns of trait variation among and within populations, and their relationship with environmental factors along with their geographical gradient. From the four morphotypes previous cited for the complex, the analyses delimited three morphological groups. Their morphological characteristics differed in response to environmental drivers. We identified morphological characters that differentiated the groups within the complex. The development of conservation strategies and actions to fully protect a species complex requires the understanding of the morphological variation within the complex. In the Abarema cochliacarpos complex different threats and challenges are associated with the conservation of each morphotype. We highlight the importance of conserving the various morphotypes of a species complex which has a large distribution range as evolutionary significant units, something that is frequently neglected in the published literature.

opennotspecifiedMar 2007View details →

FIG. 1 in Bats of the Sangkulirang limestone karst formations, East Kalimantan - a priority region for Bornean bat conservation

FIG. 1. Map of the Sangkulirang peninsula, East Kalimantan, Indonesia, showing settlements and major rivers as well as the major karst formations (dark grey shading) and forest cover (light grey shading). Base camps used at the formations are marked by circles. Map produced by Paul Banks using a forest coverage (including plantations and burnt areas) from the Berau Forest Management Project, and karst and geographic information from Regional Development Agency (BAPPEDA) in Berau, and Anon (1973)

Data from: A century of conservation: the ongoing recovery of Svalbard reindeer

Several caribou and reindeer (Rangifer tarandus) populations have experienced recent population declines, often attributed to anthropogenic stressors such as harvesting, landscape fragmentation, and climate change. Svalbard reindeer (R. t. platyrhynchus), the wild reindeer subspecies endemic to the high-Arctic Svalbard archipelago, was protected in 1925, after most subpopulations had been eradicated by harvest. Although direct pressure from harvest has ceased, indirect anthropogenic stressors from environmental changes have increased in this climate change hot spot. An assessment of the current distribution and abundance is therefore urgently needed. We combined distance sampling (300 km transects, n = 489 reindeer groups) and total counts (1,350 km2, n = 1,349 groups) to estimate the Svalbard reindeer distribution and abundance across its entire range, which we compared with historical data from the literature and radiocarbon-dated bones. Reindeer have now recolonized nearly all non-glaciated land (i.e., areas occupied prior to human presence), and their spatial variation in abundance reflects vegetation productivity. Independent of vegetation productivity, however, recently recolonized areas have lower reindeer densities than areas not subject to past extirpation. This suggests that recovery from past overharvesting is still in progress. These incompletely recovered areas are potential targets for increased monitoring frequency and maintaining strict conservation to follow the Svalbard management goal (i.e., virtually untouched wilderness areas). Because of such ongoing recolonization, possibly combined with vegetation greening effects of recent warming, our status estimate of Svalbard reindeer abundance (22,435 [95% CI = 21,452–23,425]) is more than twice a previous estimate based on opportunistic counts. Thus, although our study demonstrates the successful outcome of strict harvesting control implemented a century ago, current and future population trajectories are likely shaped by climate change.

Data from: A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress

Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the ER. Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control in the ER.

Supplementary material 1 from: Huang J, Guo Z, Tang S, Ren W, Chu G, Wang L, Zhao L, Yu R, Xu Y, Ding Y, Zang R (2020) Floristic composition and plant diversity in distribution areas of native species congeneric with Betula halophila in Xinjiang, northwest China. Nature Conservation 42: 1-17. https://doi.org/10.3897/natureconservation.42.54735

Figure S1. The correlation between environmental variables in distribution areas of five congeneric species with Betula halophila

Data from: Influence of climate change and post-delisting management on long-term population viability of the conservation-reliant Kirtland's warbler

Rapid global climate change is resulting in novel abiotic and biotic conditions and interactions. Identifying management strategies that maximize probability of long-term persistence requires an understanding of the vulnerability of species to environmental changes. We sought to quantify the vulnerability of Kirtland's Warbler (Setophaga kirtlandii), a rare Neotropical migratory songbird that breeds almost exclusively in the Lower Peninsula of Michigan and winters in the Bahamian Archipelago, to projected environmental changes on the breeding and wintering grounds. We developed a population-level simulation model that incorporates the influence of annual environmental conditions on the breeding and wintering grounds, and parameterized the model using empirical relationships. We simulated independent and additive effects of reduced breeding grounds habitat quantity and quality, and wintering grounds habitat quality, on population viability. Our results indicated the Kirtland's Warbler population is stable under current environmental and management conditions. Reduced breeding grounds habitat quantity resulted in reductions of the stable population size, but did not cause extinction under the scenarios we examined. In contrast, projected large reductions in wintering grounds precipitation caused the population to decline, with risk of extinction magnified when breeding habitat quantity or quality also decreased. Our study indicates that probability of long-term persistence for Kirtland's Warbler will depend on climate change impacts to wintering grounds habitat quality, and contributes to the growing literature documenting the importance of considering the full annual cycle for understanding population dynamics of migratory species.

Data from: Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling

In mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and its link to fitness-related behaviors are not well understood. From vomeronasal transcriptomes, we discovered the first evidence of intact vomeronasal type-1 receptor (V1r) genes in bats, and we tested whether putatively functional bat receptors were orthologous to those of related taxa, or whether bats have evolved novel receptors. Instead of lineage-specific duplications, we found that bat V1rs in bats show high levels of orthology to those of their relatives, and receptors are under comparative levels of purifying selection compared to non-bats. Despite widespread vomeronasal organ loss in bats, V1r copies have been retained for >65 million years. The highly conserved nature of bat V1rs challenges our current understanding of mammalian V1r function and suggest roles other than conspecific recognition or mating initiation in social behavior.

Data from: Assessing the effectiveness of protected areas for conserving range-restricted rainforest butterflies in Sabah, Borneo

Rainforests on Borneo support exceptional concentrations of endemic insect biodiversity, but many of these forest-dependent species are threatened by land-use change. Totally protected areas (TPAs) of forest are key for conserving biodiversity, and we examined the effectiveness of the current TPA network for conserving range-restricted butterflies in Sabah (Malaysian Borneo). We found that mean diurnal temperature range and precipitation of the wettest quarter of the year were the most important predictors of butterfly distributions (N = 77 range-restricted species), and that species richness increased with elevation and aboveground forest carbon. On average across all species, TPAs were effective at conserving ~43% of species' ranges, but encompassed only ~40% of areas with high species richness (i.e. containing at least 50% of our study species). The TPA network also included only 33-40% of areas identified as high priority for conserving range-restricted species, as determined by a systematic conservation prioritization analysis. Hence, the current TPA network is reasonably effective at conserving range-restricted butterflies, although considerable areas of high species richness (6565 km2) and high conservation priority (11,152-12,531 km2) are not currently protected. Sabah's remaining forests, and the range-restricted species they support, are under continued threat from agricultural expansion and urban development, and our study highlights important areas of rainforest that require enhanced protection.