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37 results for “Resource conservation”
Fig. 5 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation
Fig. 5. Decision tree used for specimens euthanized to obtain tissue. Blue indicates steps in the decision tree. Green indicates procedures that will lead to preservation of tissues for genetic study. Purple indicates procedures that lead to achieving multiple goals, including cell culture and obtaining gametes for current or future ARTs. NOTE: Breeding and IVF can result in offspring that can be used for genetic purposes, thereby achieving multiple goals.
Fig. 6 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation
Fig. 6. Decision tree used to obtain tissue from live animals. Blue indicates steps in the decision tree. Green indicates procedures that will lead to preservation of tissues for genetic study. Purple indicates procedures that lead to achieving multiple goals, including obtaining gametes for current or future ARTs. NOTE: Breeding and IVF can result in offspring that can be used for genetic purposes, thereby achieving multiple goals.
Fig. 4 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation
Fig. 4. Length of time from cell culture initiation to freezing for amphibian cell lines in San Diego Zoo's Frozen Zoo®. Low = 19 days; high = 596 days; average = 154 days.
Fig. 3 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation
Fig. 3. The "tissue piecing" protocol used to preserve viable cells for establishment of cell lines in the future. A) Tissue is cut into long, thin strips. B) Tissue is diced into 1 mm3 fragments before adding medium containing 10% DMSO as a cryoprotectant. C) Prepared tissue is stored in LN2 until future cell culture is possible; those without cell culture capability can transport samples using a dry shipper to maintain cold-chain.
Fig. 2 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation
Fig. 2. Procedures used to obtain amphibian eggs or sperm for use in ARTs. A) Gravid female Leopard Frog (Lithobates sp.) after gonadotropic hormone injection. B) Expressing eggs into container by pressing on abdomen and pushing thumb toward cloaca; eggs can be fertilized (i.e., IVF) by fresh or cryopreserved sperm. Sperm can similarly be released from males by pushing towards the cloaca and releasing sperm naturally (in season) or after injection of gonadotropic hormones (e.g., HIS).
Fig. 1 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation
Fig. 1. Role of genetic resource collections in the research and conservation of amphibians. Green indicates the storage of tissues in biobanks. Purple indicates procedures associated with ARTs that lead to achieving multiple goals in amphibian research and conservation. Asterisk (*) denotes tissue or methodologies that are not currently used in ARTs but may be possible in the future. NOTE: For a more complete list of ARTs reference Clulow et al. (2014).
Supporting Data for: Resource requirements for ecosystem conservation: A combined industrial and natural ecology approach to quantifying natural capital use in nature
<p>Data used to derive allometric equations for land area use by mammals, birds, reptiles, and insects, and data for the analysis of natural resource use at the Natural Capital Laboratory site.</p>
Raw data for: Novel food resources and conservation of ecological interactions between the Andean Araucaria and the Austral parakeet
<p><span>In fragile ecosystems, the introduction of exotic species could alter some ecological processes. The Austral parakeet (<em>Enicognathus</em> <em>ferrugineous</em>) shows close ecological and evolutionary relationships with the Andean Araucaria (<em>Araucaria</em> <em>araucana</em>), so any alteration in these interactions may have negative consequences for both partners and for ecosystem functioning and structure. We conducted extensive roadside surveys to estimate the abundance of parakeets in the northern Patagonian Andes over four years and recorded the food plants consumed by foraging flocks. The use of native habitats and humanized areas like villages and farms was influenced by Araucaria seed crop. In masting years, the large seed crop allowed a massive use of this resource during the non-breeding season, and even during the breeding season. The exploitation of exotic plants was minor in the masting year, but became predominant in non-masting years, especially during the non-breeding season. This feeding switch towards exotic plants primarily arose because the low Araucaria seed crop in non-masting years is entirely consumed just after production by domestic and wild exotic mammals living in Araucaria forests year-round, thus forcing the displacement of parakeets towards anthropic habitats to exploit exotic plants. Given the degradation of the remaining Andean Araucaria forests due to the impact of exotic mammals on the ecological interaction between Araucaria and Austral parakeets, ambitious programs to exclude or reduce the density of these alien mammals, including livestock, are warranted. </span></p>
Resources for "BMF CP 99: Parents as motivations for children's energy conservation behaviors"
<p>The current study is conducted to examine the following research questions:</p> <ul> <li>How are the father’s interactions with children regarding energy saving associated with the children’s energy conservation behaviors?</li> <li>How are the mother’s interactions with children regarding energy saving associated with the children’s energy conservation behaviors?</li> </ul>
Male diversity matters: Genetic structuring of insular male date palm (Phoenix dactylifera L.) revealed valuable breeding and conservation resources
Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favorable fruit production is related to quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterization of the male pollen as a superior one for each female cultivar should be the first step to establish an intensive program to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. A total number of 125 alleles was detected with an average of 8.33 alleles per locus. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of Phoenix dactylifera L. breeding programs as well as for the protection and conservation of valuable resources.
Data and code from: Loss of resource-conservative species affects plant phylogenetic and functional structure under long-term snow addition
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Raw data for: Novel food resources and conservation of ecological interactions between the Andean Araucaria and the Austral parakeet
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Datasets of the study: "Describing variability in pig genes involved in coronavirus infections: towards a One Health perspective in conservation of animal genetic resources"
<p><strong>Dataset description</strong></p> <p>Sequencing data (*.bam files) of four pig genes (<em>ACE2</em>, <em>ANPEP</em>, <em>DPP4</em> and <em>TMPRSS2</em>)<em> </em>that can serve as receptors or protease for priming the infection of coronaviruses.</p> <p>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; Krškopolje, 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.</p> <p>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.</p> <p><strong>Sequencing data</strong></p> <p>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.</p> <p><strong>Data processing</strong></p> <p>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 <em>Sus scrofa</em> 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. </p> <p>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)].</p>
Data from: Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability
Germplasm collections play a significant role among strategies for conservation of diversity. It is common to select a core collection to represent the genetic diversity of a germplasm collection, in order to minimize the cost of conservation, while ensuring the maximization of genetic variation. We aimed to solve two main problems: (1) to select a set of individuals, from an in situ data set, that is genetically complementary to an existing germplasm collection, and (2) to define a core collection for a germplasm collection. We proposed a new multi-objective optimization (MOO) approach based on principles of systematic conservation planning (SCP) incorporating heterozygosity information; therefore, optimization takes genotypic diversity and variability patterns into account as well. As a case study, we used Dipteryx alata microsatellite loci information from two sources, an ex situ germplasm collection located at the Agronomy School of the Federal University of Goiás (UFG-AS), and an in situ data set composed of 642 sampled individual trees. We were able to identify within a population of several individuals, the exact accessions/samples that should be chosen in order to preserve the species diversity. We found that material from nine in situ individual trees are enough to complement the UFG-AS germplasm collection as it is, and that it is possible to define a core collection of 20 individual trees representing all studied genetic diversity. Moreover, we defined a method (a protocol) to deal with large amounts of accessions in the context of MOO. The proposed approach can be used to help constructing collections with maximal allelic richness and can also be extended to the in situ conservation. As far as we know, this is the first time that principles of SCP and the MOO approach are applied to the problem of complementing a germplasm collection and of finding a core collection for a germplasm collection.
Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic
California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction enzyme that does not cleave the chloroplast genome in Lasthenia. A total of 316,106 catalog loci were obtained across all twelve individuals in the library. Of these, 713 loci were polymorphic, yielding 3918 candidate SNPs. Next, we genotyped an additional 285 additional plants to validate and characterize 71 of the candidate SNPs. Of these, 44 were polymorphic among VP complexes. A preliminary analysis of the distribution of genetic variation using these loci revealed significant isolation-by-distance across the species' geographic range. Weaker, but in some cases significant, genetic differentiation was detected among subpopulations from different pools within a single VP complex. Thus, in this study, RADseq allowed the discovery of SNP markers that can characterize patterns of genetic variation at multiple spatial scales in L. fremontii, which can be used to inform the conservation and mitigation of VP populations.
Data from: A Mesoamerican origin of cherimoya (Annona cherimola Mill.). Implications for the conservation of plant genetic resources
Knowledge on the structure and distribution of genetic diversity is a key aspect in order to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the neotropics and used as a food source by pre-Columbian cultures, was collected from 6 different countries across the American continent and amplified with 9 highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops.
Data from: Does wildlife resource selection accurately inform corridor conservation?
Evaluating landscape connectivity and identifying and protecting corridors for animal movement have become central challenges in applied ecology and conservation. Currently, resource selection analyses are widely used to focus corridor planning where animal movement is predicted to occur. An animal's behavioural state (e.g. foraging, dispersing) is a significant determinant of resource selection patterns, yet has largely been ignored in connectivity assessments. We review 16 years of connectivity studies employing resource selection analysis to evaluate how researchers have incorporated animal behaviour into corridor planning, and highlight promising new approaches for identifying wildlife corridors. To illustrate the importance of behavioural information in such analyses, we present an empirical case study to test behaviour-specific predictions of connectivity with long-distance dispersal movements of African wild dogs Lycaon pictus. We conclude by recommending strategies for developing more realistic connectivity models for future conservation efforts. Our review indicates that most connectivity studies conflate resource selection with connectivity requirements, which may result in misleading estimates of landscape resistance, and lack validation of proposed connectivity models with movement data. Our case study shows that including only directed movement behaviour when measuring resource selection reveals markedly different, and more accurate, connectivity estimates than a model measuring resource selection independent of behavioural state. Synthesis and applications. Our results, using African wild dogs as a case study, suggest that resource selection analyses that fail to consider an animal's behavioural state may be insufficient in targeting movement pathways and corridors for protection. This failure may result in misidentification of wildlife corridors and misallocation of limited conservation resources. Our findings underscore the need for considering patterns of animal movement in appropriate behavioural contexts to ensure the effective application of resource selection analyses for corridor planning.
Data from: Resource tracking and its conservation implications for an obligate frugivore (Procnias tricarunculatus, the three-wattled bellbird)
In Monteverde, Costa Rica, the vulnerable Three-wattled Bellbird (Procnias tricarunculatus) feeds primarily upon the fruit of Lauraceae species during its reproductive and post-reproductive seasons. To understand and advance appropriate conservation measures, this study identified the bellbird's foraging challenges in its search for a temporally and spatially fluctuating resource. Although there are at least 96 species of Lauraceae found in the five life zones of Monteverde, the distinct distributions of tree species both among and within life zones require the bellbirds to track seasonal fruiting across the various zones. In this six-year study, we monitored the fruiting of tree species and bellbird abundance in 24 study plots within its post-reproductive life zone, the Premontane Wet forest, in order to identify preferred bellbird food resources and how the fruiting of these species drives the spatial distribution of the bellbird. Our research revealed phenological patterns of annual, biennial, and triennial fruiting with high levels of fruiting synchrony within several identified key fruit species. Of critical conservation importance is that no single species of Lauraceae produced a consistent food supply for bellbirds each year. Therefore, even within life zones, the bellbird's survival depends on its mobility to search for and obtain fruit, as well as the availability of fruits of multiple tree species. The conservation implications include focused attention on multiple core areas within given life zones, protection of existing forest and remnant trees, and forest restoration with plantings of multiple tree species. We suspect that other tropical frugivorous species face similar conservation challenges.
Aphid conservation biological control in arable crops via flower strips: the predominant role of plant resources over diversity effects
<p>Dataset and R code</p>
Data from: A Mesoamerican origin of cherimoya (Annona cherimola Mill.). Implications for the conservation of plant genetic resources
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Allen Brain Atlas
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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