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opencc-by-4.0Jan 2018View details →

Database of Pines from the Forests paper: "Intraspecific Variation in Pines from the Trans-Mexican Volcanic Belt Grown Under Two Watering Regimes: Implications for Management of Genetic Resources"

Raw data from the Forests paper: "Intraspecific Variation in Pines from the Trans-Mexican Volcanic Belt Grown under Two Watering Regimes: Implications for Management of Genetic Resources" Forests 2018 9(2), 71. doi:<a href="http://dx.doi.org/10.3390/f9020071">10.3390/f9020071. </a> The database correspond to seedlings of four Mexican pines: P. oocarpa, P. patula and P. pseudostrobus, that were submitted to two watering treatments: Field Capacity (FC) and Drought-Stress (DS), during 90 days. Growth and biomass, survival and ontogenetic score were measured.

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-by-4.0Sep 2009View details →

Fig. 2 in Microsatellite variation and population genetic structure of a neotropical endangered Bryconinae species Brycon insignis Steindachner, 1877: implications for its conservation and sustainable management

Fig. 2. UPGMA clustering of the Nei's genetic distance (1972) of the Brycon insignis sampling locations based on six microsatellite loci. Bootstrap values above 50% are shown above branches indicating percentage support in 5000 permutations. Power Company Hatchery (PCH), São João River (SJR), Paraíba do Sul River (PSR), Imbé River (IMR), Muriaé River (MUR) and Itabapoana River (ITR).

opencc-by-3.0-usJul 2022View details →

Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning: Cleaned Data

The included files and script are to allow for reconstruction of the data directory and cleaned data used in "Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning" ( https://doi.org/10.1101/2022.07.29.502051 ). Code used is available at 10.5281/zenodo.7401113 . <table> <tbody> <tr> <th>Filename</th> <th>Description</th> </tr> <tr> <td>interim.tar.gz</td> <td>Contains site grouping dictonary</td> </tr> <tr> <td>processed.tar.gz</td> <td>Processed data</td> </tr> <tr> <td>raw.tar.gz</td> <td>Input data</td> </tr> <tr> <td>SetupInstructions.sh</td> <td>Bash script to prepare folders and unzipped data expected by code in 10.5281/zenodo.7401113</td> </tr> <tr> <td>SetupInstructions.txt</td> <td>Instructions for unzipping the data</td> </tr> <tr> <td>Train_Test_Split_Reference_Phenotypes.csv</td> <td>Reference spreadsheet to allow for easily exploring training and test set groupings</td> </tr> </tbody> </table> <ul> </ul> This work was supported through funding from the USDA Agricultural Research Service, ARS project number 5070-21000-041-000-D. Raw data provided by the [Genomes to Field Initiative](https://www.genomes2fields.org/) and the [Daymet database](https://daymet.ornl.gov/).

publicMar 2025View details →

Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: Implications for conservation and management

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publicJul 2025View details →

Data from: A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish

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publicMar 2024View details →

Dataset and R code: Genetic diversity of lion populations in Kenya: evaluating past management practices and recommendations for future conservation actions by Chege M et.al

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publicApr 2023View details →

Genetic structure and historic demography of endangered unarmored threespine stickleback at southern latitudes signals a need for new management directives

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opencc-zeroApr 2024View details →

Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow

Red deer (Cervus elaphus) throughout central Europe are impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.

opencc-zeroSep 2021View details →

Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis

Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as Bothrops insularis, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (i) characterize the genetic diversity of ex-situ and in-situ populations of B. insularis using heterologous microsatellites; (ii) investigate genetic structure among and within these populations; and (iii) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the B. neuwiedi group were used to access genetic diversity indexes of ex-situ and in-situ populations. Low-to-medium genetic diversity parameters were found. Both populations showed low — albeit significant — values of system of mating inbreeding coefficient, whereas only the in-situ population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the in-situ one, which is crucial for considering a reintroduction process into the island.

opencc-zeroMar 2023View details →

Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird

Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

zenodo36/100

Additional Files for "Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank"

Additional files for the article entitled "Assessing the potential of germplasm collections for managing genetic diversity: the case of the French National Cryobank". Additional file 1: Table S1 Title: Report on the output of material since the creation of the French National Cryobank Additional file 2: Figure S1 Title: Summary of material outputs from the French National Cryobank since 1999 Additional file 3: Table S2 Title: Descriptors from the French National Cryobank data for six species Additional file 4: Figure S2 Title: Distribution of data and definition of intervals regarding breed diffusion (A), donor birth-year classes (B), and classes of donor’s age at 1st collection (C) Additional file 5: Table S3 Title: Statistics of the number of effective donors (De) according to species Additional file 6: Table S4 Title: Distribution of donors and doses across breeds Description: In green, the breeds for which the FNC collections meet FAO conditions for reconstitution of an extinct breed. In blue, the breeds for which the collections of the FNC do not yet meet FAO conditions for reconstitution of an extinct breed. In gray, FAO recommendations not available. Based on the 2012 FAO report, with 100 founder females for ruminants and horses, or 30 founder females for pigs (with a pregnancy rate of 0.6). Additional file 7: Figure S3 Title: Evolution of genetic contributions of sires and their production of direct descendants in the French National Cryobank over the period 2011–2020 for three livestock species Description: Two breeds of pigs are represented in pink (a, b), three breeds of sheep are represented in blue (c, d, e), and five breeds of cattle are represented in ochre (f, g, h, i, j). Additional file 8: Figure S4 Title: Distribution of individual IDIs of cryopreserved sires for the 17 breeds analyzed Description: Pig breeds are represented in pink, sheep breeds are represented in blue, and cattle breeds are represented in ochre. Additional file 9: Figure S5 Title: Correlation between IDI values and the year of birth of donors Additional file 10: Figure S6 Title: Prediction of IDI values based on donor’s year of birth and the motivation for entry into collection Description: Type I (for endangered breeds) is represented in purple and type III (for representative individuals of a breed over a period) is represented in orange.

opencc-by-4.0Jul 2023View details →

opencc-zeroDec 2022View details →

Data from: Past population control biases interpretations of contemporary genetic data: implications for future invasive Sitka black-tailed deer management in Haida Gwaii

Invasive species management practices often include genetic analyses to better inform decision-making and resource allocation. Yet, past management actions may artificially bias recovered patterns of genetic variation; for example, a population bottleneck caused by contemporary culling may mirror some patterns associated with historical isolation. Here, we aimed to disentangle the impacts of past management activities from natural processes for Sitka black-tailed deer (Odocoileus hemionus sitkensis), an invasive species that has been repeatedly culled on two islands, SGang Gwaay and Reef, within the Haida Gwaii archipelago (Canada). We applied a recently developed Genotyping-in-Thousands by sequencing panel to contemporary (e.g., blood, serum, tissue, muscle, feces) and archived deer samples, the latter collected prior to management activity within the system (c. 1997–1998), which allowed us to contextualize conflicting patterns of isolation and connectivity previously observed on SGang Gwaay and Reef. Successful genotyping (92.6%) and population genetic analysis of 292 individuals at 236 SNPs revealed signals of historical isolation on SGang Gwaay and Reef, provided evidence of a founder effect during initial colonization, and indicated an absence of ongoing gene flow. Furthermore, our spatiotemporal analyses consistently supported a priori predictions associated with bottlenecks within post-cull populations, such as within-island loss of genetic variation, elevated within-island kinship, and increased levels of among-island genetic differentiation. These findings are promising for future management of deer on SGang Gwaay and Reef, suggesting that eradications on these islands may be durable. More broadly, our work highlights the importance of understanding management history before interpreting contemporary population genetic data.

ClinicalTrials.gov36/100

Development of a Dietary Intervention Model Based on Genetic Data as an Implementation of a Healthy Lifestyle in the Management of Systemic Lupus Erythematosus Patients

ClinicalTrials.gov study NCT07183007. IPD Sharing: NO. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

ClinicalTrials.gov36/100

Exploring the Impact of Genetic Variations on The Clinical Efficacy of Nalbuphine in Postoperative Pain Management

ClinicalTrials.gov study NCT06996561. IPD Sharing: YES. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →