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1. Validating local knowledge on camels: Colour phenotypes and genetic variation of dromedaries in the Nigeria-Niger corridor

Author

Pamela A. Burger, A. M. Abdussamad, P. Charruau, and D.J.U. Kalla

Subjects
Coat, Genetic diversity, General Veterinary, Ecology, Pastoralism, Bayesian clustering, Zoology, Biology, Traditional camel husbandry, veterinary(all), Phenotype, Mitochondrial DNA, Camelus dromedarius, Gene flow, parasitic diseases, Genetic variation, Microsatellite, Animal Science and Zoology, Gene pool, Microsatellites
Abstract

The traditional camel breeding concept of pastoralists in the Nigeria-Niger corridor favours certain dromedary colour phenotypes, which are associated with distinct economic and behavioural traits. With the increasing requirement of sustainable food sources in desert environments the economic interest in Nigerian dromedaries has also been growing. In this study we used mitochondrial and microsatellite data to understand if the observed colour phenotypes correspond to genetically distinct groups and whether these groups reflect the breeding concept of camel pastoralists in the Nigeria-Niger corridor. Our results showed that Nigerian dromedaries are composed of a homogenous gene pool with no specific clustering according to coat colour. Significant but low nuclear and mitochondrial differentiation was detected only between dark-brown and black-brown camels. In addition to little evidence for population structure, Nigerian dromedaries exhibited a high genetic diversity, which could be explained by continuous gene flow with other populations during the annual transhumant voyage embarked upon by pastoralists on both sides of the Nigeria-Niger corridor. In comparison to local pastoralists' knowledge, the molecular genetic data do not support a clear distinction into breeds (Ja, Kurri, and Kala) based on coat colour differences.

Published
2015
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2. Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

Author

Antoinette Kotze, H. Ziaie, Pablo Orozco-terWengel, Christian Schlötterer, Luke T. B. Hunter, H. Jowkar, Thierry Grange, Jochen Peters, Eva-Maria Geigl, Pamela A. Burger, Stéphane Ostrowski, Paul Vercammen, P. Charruau, George B. Schaller, A. Jourabchian, Chris Walzer, and Carlos Fernandes

Subjects
0106 biological sciences, Conservation genetics, 0303 health sciences, Genetic diversity, education.field_of_study, biology, Population, Population genetics, Zoology, 15. Life on land, Subspecies, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, biology.animal, Genetic structure, Acinonyx, Genetics, Acinonyx jubatus, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.

Published
2011
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3. High mitochondrial differentiation levels between wild and domestic Bactrian camels: a basis for rapid detection of maternal hybridization

Author

Pablo Orozco-terWengel, C. Vogl, Chris Walzer, Petra Kaczensky, Pamela A. Burger, Franz Schwarzenberger, K. Silbermayr, P. Charruau, and D. Enkhbileg

Subjects
Genetics, Mitochondrial DNA, biology, Haplotype, Camelus bactrianus, Introgression, General Medicine, biology.organism_classification, law.invention, law, Animal Science and Zoology, Bactrian camel, Gene pool, Restriction fragment length polymorphism, Polymerase chain reaction
Abstract

Hybridization between wild species and their domestic congeners often threatens the gene pool of the wild species. The last wild Bactrian camel (Camelus ferus) populations in Mongolia and China are examples of populations facing such a hybridization threat. To address this key issue in the conservation of wild camels, we analysed wild, hybrid and domestic Bactrian camels (Camelus bactrianus) originating from Mongolia, China and Austria. Through screening of an 804-base-pair mitochondrial fragment, we identified eight mitochondrial haplotypes and found high sequence divergence (1.9%) between C. ferus and C. bactrianus. On the basis of a mitochondrial DNA sequence fixed difference, we developed a diagnostic PCR restriction fragment length polymorphism (PCR-RFLP) assay to differentiate between wild and domestic camel samples. We applied the assay to 81 individuals and confirmed the origin of all samples including five hybrids with known maternal ancestry. The PCR-RFLP system was effective for both traditional (blood, skin) and non-invasive samples (faeces, hair), as well as for museum specimens. Our results demonstrate high levels of mitochondrial differentiation between wild and domestic Bactrian camels and that maternal hybridization can be detected by a rapid and reliable PCR-RFLP system.

Published
2010
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4. Genetic diversity and population structure of Mongolian domestic Bactrian camels (Camelus bactrianus)

Author

B, Chuluunbat, P, Charruau, K, Silbermayr, T, Khorloojav, and P A, Burger

Subjects
Cell Nucleus, endocrine system, Camelus, animal diseases, Molecular Sequence Data, Bayesian clustering, Genetic Variation, Mongolia, Sequence Analysis, DNA, Articles, mitochondrial DNA, phylogeny, DNA, Mitochondrial, Polymerase Chain Reaction, microsatellites, parasitic diseases, otorhinolaryngologic diseases, Animals, sense organs
Abstract

The tradition of animal husbandry in the context of a nomadic lifestyle has been of great significance in the Mongolian society. Both Bactrian camels and horses have been invaluable for the survival and development of human activities in the harsh arid environment of the Mongolian steppe. As camels offer unique and sustainable opportunities for livestock production in marginal agro-ecological zones, we investigated the current genetic diversity of three local Mongolian camel breeds and compared their levels of variation with common native Mongolian camels distributed throughout the country. Based on mitochondrial and nuclear markers, we found levels of genetic diversity in Mongolian populations similar to that reported for Chinese Bactrian camels and for dromedaries. Little differentiation was detected between single breeds, except for a small group originating from the northwestern Mongolian Altai. We found neither high inbreeding levels in the different breeds nor evidence for a population decline. Although the Mongolian camel census size has severely declined over the past 20 years, our analyses suggest that there still exists a stable population with adequate genetic variation for continued sustainable utilization.

Published
2014

5. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2010 - 31 July 2010

Author

Cynthia Riginos, Rasanthi M. Gunasekera, James P. Hereward, Adam E. Vorsino, C. C. Vinson, Philippe Jarne, H. A. Rose, Joël Bried, Kittipath Prapayotin-Riveros, A. M. Risterucci, Angélique Quilichini, Mark G. Wright, Asta Audzijonyte, Hélène Delatte, Rebecca N. Johnson, Ryan A. Thum, Charles R. Vossbrinck, Yan Hong, Chunhong Li, Byeong-Wha Min, Akihiro Kijima, Pierre-Jean G. Malé, P. Charruau, Andrew J. Lowe, Karen-Ann Gray, Gregory J. Bugbee, A. Y. Ciampi, Woo-Jin Kim, Gudbjorg I. Aradottir, Steven J. Hanley, Minghui Liao, Jean-François Martin, Benjamin Fartek, Jae K. Noh, Manami Kanno, Bernard Reynaud, Hyun Chul Kim, K. Silbermayr, Paul J. DeBarro, Thibaut Malausa, D. Petro, Michelle D. Marko, Michael G. Gardner, Ania M. Wieczorek, Qi Jianfei, Chris Walzer, N. Tero, Samuel Nibouche, Kwan S. Kim, Emilie C. Bess, Ann E. Noack, Jeong-Ho Lee, Shotaro Hirase, G. Bourdel, Malvina Andris, Iracilda Sampaio, Mark D. B. Eldridge, Choul-Ji Park, Pamela A. Burger, Jang W. Lee, Nathan Havil, Jason C. White, D. Enkhbileg, Russell H. Messing, Jérôme Orivel, Laurent Costet, Jeong-In Myeong, Karen Miller, G. Arnau, Phillip R. England, Nathan Lo, Francesco Bonadonna, Elizabeth A. LaRue, Marivana Borges Silva, Marie-Pierre Dubois, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Department of Biomedical Sciences, Institute of Population Genetics, University of Veterinary Medicine, University of Veterinary Medicine, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Department of Epidemiology, Biostatistics and Occupational Health [Montréal], McGill University, Institut de Chimie de Clermont-Ferrand (ICCF), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), School of Physics and Astronomy, University of Birmingham [Birmingham], Division of Cardiovascular Medicine, University of Cambridge [UK] (CAM), Birkbeck College [University of London], Department of Mathematical Sciences, TJ Watson, IBM, Southeast University [Jiangsu], State Key Lab. of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University [China], Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), School of Mechanical and Chemical Engineering, The University of Western Australia (UWA), Institut de recherche agricole pour le développement (IRAD), Ministère de la Recherche et de l'innovation, Department of Physics and Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology (KAIST), Paris-Jourdan Sciences Economiques (PSE), Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École des hautes études en sciences sociales (EHESS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Technologie Servier, Institute of Arctic and Alpine Research (INSTAAR), University of Colorado [Boulder], Centre de recherche sur l'espace sonore et l'environnement urbain [1998-2014] (CRESSON [1998-2014]), Ambiances architecturales et urbaines (AAU), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), McGill University = Université McGill [Montréal, Canada], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-École des hautes études en sciences sociales (EHESS)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS), Institute of Arctic Alpine Research [University of Colorado Boulder] (INSTAAR), Centre de recherche sur l'espace sonore et l'environnement urbain (CRESSON), École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École normale supérieure - Paris (ENS Paris), and Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-École Centrale de Nantes (ECN)

Subjects
0106 biological sciences, Identification, [SDV]Life Sciences [q-bio], Banque de gènes, computer.software_genre, 01 natural sciences, F30 - Génétique et amélioration des plantes, GENBANK, Marqueur génétique, biology, Database, CATALOGUE, Dioscorea rotundata, Dioscorea trifida, Dioscorea, GENETIQUE DES POPULATIONS, Banque de données, ECOLOGIE, Biotechnology, Écologie, PHYLOGENY, Zoology, MOLECULAR MARKERS, Licania, ECOLOGY, 010603 evolutionary biology, Dioscorea transversa, Ressource génétique végétale, REFERENCEMENT, POPULATION GENETICS, Genetics, Ressource génétique animale, Dioscorea pentaphylla, Ecology, Evolution, Behavior and Systematics, Ressource génétique, Biologie moléculaire, TAXONOMY, biology.organism_classification, L10 - Génétique et amélioration des animaux, Tuberolachnus salignus, Hirtella, computer, 010606 plant biology & botany
Abstract

Correspondance: Molecular Ecology Resources Primer Development Consortium, E-mail: editorial.office@molecol.com; International audience; This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Published
2011
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6. High mitochondrial differentiation levels between wild and domestic Bactrian camels: a basis for rapid detection of maternal hybridization

Author

K, Silbermayr, P, Orozco-terWengel, P, Charruau, D, Enkhbileg, C, Walzer, C, Vogl, F, Schwarzenberger, P, Kaczensky, and P A, Burger

Subjects
Male, Camelus, Animals, Hybridization, Genetic, Female, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Mitochondria
Abstract

Hybridization between wild species and their domestic congeners often threatens the gene pool of the wild species. The last wild Bactrian camel (Camelus ferus) populations in Mongolia and China are examples of populations facing such a hybridization threat. To address this key issue in the conservation of wild camels, we analysed wild, hybrid and domestic Bactrian camels (Camelus bactrianus) originating from Mongolia, China and Austria. Through screening of an 804-base-pair mitochondrial fragment, we identified eight mitochondrial haplotypes and found high sequence divergence (1.9%) between C. ferus and C. bactrianus. On the basis of a mitochondrial DNA sequence fixed difference, we developed a diagnostic PCR restriction fragment length polymorphism (PCR-RFLP) assay to differentiate between wild and domestic camel samples. We applied the assay to 81 individuals and confirmed the origin of all samples including five hybrids with known maternal ancestry. The PCR-RFLP system was effective for both traditional (blood, skin) and non-invasive samples (faeces, hair), as well as for museum specimens. Our results demonstrate high levels of mitochondrial differentiation between wild and domestic Bactrian camels and that maternal hybridization can be detected by a rapid and reliable PCR-RFLP system.

Published
2009

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