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343 results on '"Orozco-terWengel, Pablo"'

2. ForestQB: An Adaptive Query Builder to Support Wildlife Research

Author

Mussa, Omar, Rana, Omer, Goossens, Benoît, Orozco-terWengel, Pablo, and Perera, Charith

Subjects
Computer Science - Information Retrieval
Abstract

This paper presents ForestQB, a SPARQL query builder, to assist Bioscience and Wildlife Researchers in accessing Linked-Data. As they are unfamiliar with the Semantic Web and the data ontologies, ForestQB aims to empower them to benefit from using Linked-Data to extract valuable information without having to grasp the nature of the data and its underlying technologies. ForestQB is integrating Form-Based Query builders with Natural Language to simplify query construction to match the user requirements. Demo available at https://iotgarage.net/demo/forestQB, Comment: In Proceedings of the 12th International Semantic Web Conference (Posters & Demonstrations Track), 2022

Published
2022

4. FOO: An Upper-Level Ontology for the Forest Observatory

Author

Hamed, Naeima, Rana, Omer, Goossens, Benoît, Orozco-terWengel, Pablo, Perera, Charith, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Pesquita, Catia, editor, Skaf-Molli, Hala, editor, Efthymiou, Vasilis, editor, Kirrane, Sabrina, editor, Ngonga, Axel, editor, Collarana, Diego, editor, Cerqueira, Renato, editor, Alam, Mehwish, editor, Trojahn, Cassia, editor, and Hertling, Sven, editor

Published
2023
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7. A population genetic analysis of the Critically Endangered Madagascar big-headed turtle, Erymnochelys madagascariensis across captive and wild populations

Author

White, Nina F. D., Mennell, Holly, Power, Georgia, Edwards, Dominic, Chrimes, Luke, Woolaver, Lance, Velosoa, Juliette, Randriamahita, Mozavelo, Richard, Rafeliarisoa, Tsilavo Hasina, Kuchling, Gerald, Lopez, Javier, Bekarany, Ernest, Charles, Namotoa, Young, Richard, Lewis, Richard, Bruford, Michael W., and Orozco-terWengel, Pablo

Published
2022
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8. Comparative phylogeography reveals dissimilar genetic differentiation patterns in two sympatric amphibian species.

Author

PAN, Tao, ZHANG, Caiwen, OROZCO TERWENGEL, Pablo, WANG, Hui, DING, Ling, YANG, Liuyang, HU, Chaochao, LI, Wengang, ZHOU, Wenliang, WU, Xiaobing, and ZHANG, Baowei

Abstract

Global climate change is expected to have a profound effect on species distribution. Due to the temperature constraints, some narrow niche species could shift their narrow range to higher altitudes or latitudes. In this study, we explored the correlation between species traits, genetic structure, and geographical range size. More specifically, we analyzed how these variables are affected by differences in fundamental niche breadth or dispersal ability in the members of two sympatrically distributed stream‐dwelling amphibian species (frog, Quasipaa yei; salamander, Pachyhynobius shangchengensis), in Dabie Mountains, East China. Both species showed relatively high genetic diversity in most geographical populations and similar genetic diversity patterns (JTX, low; BYM, high) correlation with habitat changes and population demography. Multiple clustering analyses were used to disclose differentiation among the geographical populations of these two amphibian species. Q. yei disclosed the relatively shallow genetic differentiation, while P. shangchengensis showed an opposite pattern. Under different historical climatic conditions, all ecological niche modeling disclosed a larger suitable habitat area for Q. yei than for P. shangchengensis; these results indicated a wider environment tolerance or wider niche width of Q. yei than P. shangchengensis. Our findings suggest that the synergistic effects of environmental niche variation and dispersal ability may help shape genetic structure across geographical topology, particularly for species with extremely narrow distribution. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

Author

Laikre, Linda, Hohenlohe, Paul A., Allendorf, Fred W., Bertola, Laura D., Breed, Martin F., Bruford, Michael W., Funk, W. Chris, Gajardo, Gonzalo, González-Rodríguez, Antonio, Grueber, Catherine E., Hedrick, Philip W., Heuertz, Myriam, Hunter, Margaret E., Johannesson, Kerstin, Liggins, Libby, MacDonald, Anna J., Mergeay, Joachim, Moharrek, Farideh, O’Brien, David, Ogden, Rob, Orozco-terWengel, Pablo, Palma-Silva, Clarisse, Pierson, Jennifer, Paz-Vinas, Ivan, Russo, Isa-Rita M., Ryman, Nils, Segelbacher, Gernot, Sjögren-Gulve, Per, Waits, Lisette P., Vernesi, Cristiano, and Hoban, Sean

Published
2021
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12. Correction to: Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

Author

Laikre, Linda, Hohenlohe, Paul A., Allendorf, Fred W., Bertola, Laura D., Breed, Martin F., Bruford, Michael W., Funk, W. Chris, Gajardo, Gonzalo, González-Rodríguez, Antonio, Grueber, Catherine E., Hedrick, Philip W., Heuertz, Myriam, Hunter, Margaret E., Johannesson, Kerstin, Liggins, Libby, MacDonald, Anna J., Mergeay, Joachim, Moharrek, Farideh, O’Brien, David, Ogden, Rob, Orozco-terWengel, Pablo, Palma-Silva, Clarisse, Pierson, Jennifer, Paz-Vinas, Ivan, Russo, Isa-Rita M., Ryman, Nils, Segelbacher, Gernot, Sjögren-Gulve, Per, Waits, Lisette P., Vernesi, Cristiano, and Hoban, Sean

Published
2021
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13. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints

Author

Benjelloun, Badr, primary, Leempoel, Kevin, additional, Boyer, Frédéric, additional, Stucki, Sylvie, additional, Streeter, Ian, additional, Orozco‐terWengel, Pablo, additional, Alberto, Florian J., additional, Servin, Bertrand, additional, Biscarini, Filippo, additional, Alberti, Adriana, additional, Engelen, Stefan, additional, Stella, Alessandra, additional, Colli, Licia, additional, Coissac, Eric, additional, Bruford, Michael W., additional, Ajmone‐Marsan, Paolo, additional, Negrini, Riccardo, additional, Clarke, Laura, additional, Flicek, Paul, additional, Chikhi, Abdelkader, additional, Joost, Stéphane, additional, Taberlet, Pierre, additional, and Pompanon, François, additional

Published
2023
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14. A pragmatic approach for integrating molecular tools into biodiversity conservation

Author

Bertola, Laura D., primary, Brüniche‐Olsen, Anna, additional, Kershaw, Francine, additional, Russo, Isa‐Rita M., additional, MacDonald, Anna J., additional, Sunnucks, Paul, additional, Bruford, Michael W., additional, Cadena, Carlos Daniel, additional, Ewart, Kyle M., additional, de Bruyn, Mark, additional, Eldridge, Mark D. B., additional, Frankham, Richard, additional, Guayasamin, Juan M., additional, Grueber, Catherine E., additional, Hoareau, Thierry B., additional, Hoban, Sean, additional, Hohenlohe, Paul A., additional, Hunter, Margaret E., additional, Kotze, Antoinette, additional, Kuja, Josiah, additional, Lacy, Robert C., additional, Laikre, Linda, additional, Lo, Nathan, additional, Meek, Mariah H., additional, Mergeay, Joachim, additional, Mittan‐Moreau, Cinnamon, additional, Neaves, Linda E., additional, O'Brien, David, additional, Ochieng, Joel W., additional, Ogden, Rob, additional, Orozco‐terWengel, Pablo, additional, Páez‐Vacas, Mónica, additional, Pierson, Jennifer, additional, Ralls, Katherine, additional, Shaw, Robyn E., additional, Sogbohossou, Etotépé A., additional, Stow, Adam, additional, Steeves, Tammy, additional, Vernesi, Cristiano, additional, Watsa, Mrinalini, additional, and Segelbacher, Gernot, additional

Published
2023
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17. High performance computation of landscape genomic models integrating local indices of spatial association

Author

Stucki, Sylvie, Orozco-terWengel, Pablo, Bruford, Michael W., Colli, Licia, Masembe, Charles, Negrini, Riccardo, Taberlet, Pierre, Joost, Stéphane, and Consortium, the NEXTGEN

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. The current challenges of the field mainly involve processing large numbers of models and disentangling selection from demography. Several methods address the latter, either by estimating a neutral model from population structure or by inferring simultaneously environmental and demographic effects. Here we present Sam$\beta$ada, an integrated approach to study signatures of local adaptation, providing rapid processing of whole genome data and enabling assessment of spatial association using molecular markers. Specifically, candidate loci to adaptation are identified by automatically assessing genome-environment associations. In complement, measuring the Local Indicators of Spatial Association (LISA) for these candidate loci allows to detect whether similar genotypes tend to gather in space, which constitutes a useful indication of the possible kinship relationship between individuals. In this paper, we also analyze SNP data from Ugandan cattle to detect signatures of local adaptation with Sam$\beta$ada, BayEnv, LFMM and an outlier method (FDIST approach in Arlequin) and compare their results. Sam$\beta$ada is an open source software for Windows, Linux and MacOS X available at \url{http://lasig.epfl.ch/sambada}, Comment: 1 figure in text, 1 figure in supplementary material The structure of the article was modified and some explanations were updated. The methods and results presented are the same as in the previous version

Published
2014
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19. Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data.

Author

Vlaic, Bogdan Alin, Vlaic, Augustin, Russo, Isa-Rita, Colli, Licia, Bruford, Michael William, Odagiu, Antonia, and Orozco-terWengel, Pablo

Subjects
GOAT breeds, GENETIC variation, GOATS, SINGLE nucleotide polymorphisms, DOMESTICATION of animals, ANIMAL culture, BREEDING, MITOCHONDRIAL DNA
Abstract

Simple Summary: The Carpatina goat breed from Romania is very well adapted to a range of contrasting and very different environments compared to highly specialized breeds. This adaptability makes them an important source of genetic variability for future breeding programs. To improve breeding strategies, it is necessary to evaluate the genetic diversity of the Carpatina breed. The aim of this study was therefore to investigate genetic diversity and inbreeding of old native Carpatina goat populations from different geographical areas in Romania using single nucleotide polymorphism (SNP) data for 67 individuals. Diversity, measured by average expected heterozygosity (HE), was 0.418, and average observed heterozygosity (Ho) was 0.420. Linkage disequilibrium (LD) estimation showed that the average r2 value was 0.32. The effective population size (Ne) estimate 13 generations ago ranged between 98 and 185. These results based on SNP data are very useful for the application of proper management and for designing goat breeding programs. Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Mike Bruford (1963–2023)

Author

Orozco‐terWengel, Pablo, primary, Coissac, Eric, additional, Hanotte, Olivier, additional, Pompanon, Francois, additional, Sunnucks, Paul, additional, and Taberlet, Pierre, additional

Published
2023
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23. Demographic history of the Punjab urial and implications for its management

Author

Bajwa, Amna Arshad, primary, Shehzad, Wasim, additional, Islam, Saher, additional, Imran, Muhammad, additional, Ashraf, Kamran, additional, Khan, Arman, additional, Zahoor, Muhammad Yasir, additional, Rashid, Muhammad Imran, additional, Khan, Waseem Ahmad, additional, Rehman, Habib Ur, additional, and Orozco‐Terwengel, Pablo, additional

Published
2023
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32. Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Author

Almathen, Faisal, Charruau, Pauline, Mohandesan, Elmira, Mwacharo, Joram M., Orozco-terWengel, Pablo, Pitt, Daniel, Abdussamad, Abdussamad M., Uerpmann, Margarethe, Uerpmann, Hans-Peter, De Cupere, Bea, Magee, Peter, Alnaqeeb, Majed A., Salim, Bashir, Raziq, Abdul, Dessie, Tadelle, Abdelhadi, Omer M., Banabazi, Mohammad H., Al-Eknah, Marzook, Walzer, Chris, Faye, Bernard, Hofreiter, Michael, Peters, Joris, Hanotte, Olivier, and Burger, Pamela A.

Published
2016

40. Figure 7 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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41. Figure 6 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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42. Figure 4 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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43. Supplementary material 4 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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45. Figure 2 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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46. Supplementary material 3 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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47. Figure 1 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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48. Supplementary material 1 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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49. Figure 5 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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50. Figure 9 from: Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD (2022) An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. ZooKeys 1104: 1-28. https://doi.org/10.3897/zookeys.1104.82396

Author

Mullin, Katherine E., primary, Rakotomanga, Manoa G., additional, Dawson, Jeff, additional, Glaw, Frank, additional, Rakotoarison, Andolalao, additional, Orozco-terWengel, Pablo, additional, and Scherz, Mark D., additional

Published
2022
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