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Pečnerová P, Lord E, Garcia-Erill G, Hanghøj K, Rasmussen MS, Meisner J, Liu X, van der Valk T, Santander CG, Quinn L, Lin L, Liu S, Carøe C, Dalerum F, Götherström A, Måsviken J, Vartanyan S, Raundrup K, Al-Chaer A, Rasmussen L, Hvilsom C, Heide-Jørgensen MP, Sinding MHS, Aastrup P, Van Coeverden de Groot PJ, Schmidt NM, Albrechtsen A, Dalén L, Heller R, Moltke I, Siegismund HR. Population genomics of the muskox' resilience in the near absence of genetic variation. Mol Ecol 2024; 33:e17205. [PMID: 37971141 DOI: 10.1111/mec.17205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/07/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
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Affiliation(s)
- Patrícia Pečnerová
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Zoo, Frederiksberg, Denmark
| | - Edana Lord
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Genís Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Malthe Sebro Rasmussen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Cindy G Santander
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Long Lin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Biodiversity Research Institute (CSIC-UO-PA), Mieres, Spain
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johannes Måsviken
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Russian Academy of Sciences, Magadan, Russia
| | | | - Amal Al-Chaer
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linett Rasmussen
- Copenhagen Zoo, Frederiksberg, Denmark
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mads Peter Heide-Jørgensen
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Greenland Institute of Natural Resources, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Peter Aastrup
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | | | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Redlef Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Garcia-Erill G, Kjaer MM, Albrechtsen A, Siegismund HR, Heller R. Vicariance followed by secondary gene flow in a young gazelle species complex. Mol Ecol 2020; 30:528-544. [PMID: 33226701 PMCID: PMC7898927 DOI: 10.1111/mec.15738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/03/2023]
Abstract
Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (Nanger granti, N. notata and N. petersii). The three lineages have nonoverlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early‐stage evolutionary dynamics of allopatric speciation in detail. Here, we use genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within N. granti, which coincides with the previously suggested two subspecies, N. g. granti and N. g. robertsii. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, N. granti and N. petersii also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Michael Munkholm Kjaer
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark.,Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Hans Redlef Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
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3
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Frandsen P, Fontsere C, Nielsen SV, Hanghøj K, Castejon-Fernandez N, Lizano E, Hughes D, Hernandez-Rodriguez J, Korneliussen TS, Carlsen F, Siegismund HR, Mailund T, Marques-Bonet T, Hvilsom C. Targeted conservation genetics of the endangered chimpanzee. Heredity (Edinb) 2020; 125:15-27. [PMID: 32346130 DOI: 10.1038/s41437-020-0313-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 11/09/2022] Open
Abstract
Populations of the common chimpanzee (Pan troglodytes) are in an impending risk of going extinct in the wild as a consequence of damaging anthropogenic impact on their natural habitat and illegal pet and bushmeat trade. Conservation management programmes for the chimpanzee have been established outside their natural range (ex situ), and chimpanzees from these programmes could potentially be used to supplement future conservation initiatives in the wild (in situ). However, these programmes have often suffered from inadequate information about the geographical origin and subspecies ancestry of the founders. Here, we present a newly designed capture array with ~60,000 ancestry informative markers used to infer ancestry of individual chimpanzees in ex situ populations and determine geographical origin of confiscated sanctuary individuals. From a test panel of 167 chimpanzees with unknown origins or subspecies labels, we identify 90 suitable non-admixed individuals in the European Association of Zoos and Aquaria (EAZA) Ex situ Programme (EEP). Equally important, another 46 individuals have been identified with admixed subspecies ancestries, which therefore over time, should be naturally phased out of the breeding populations. With potential for future re-introduction to the wild, we determine the geographical origin of 31 individuals that were confiscated from the illegal trade and demonstrate the promises of using non-invasive sampling in future conservation action plans. Collectively, our genomic approach provides an exemplar for ex situ management of endangered species and offers an efficient tool in future in situ efforts to combat the illegal wildlife trade.
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Affiliation(s)
- Peter Frandsen
- Research and Conservation, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark. .,Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
| | - Claudia Fontsere
- Institute of Evolutionary Biology, (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Svend Vendelbo Nielsen
- Bioinformatics Research Center, Department of Mathematics, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Natalia Castejon-Fernandez
- Bioinformatics Research Center, Department of Mathematics, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Esther Lizano
- Institute of Evolutionary Biology, (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafant, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyala del Vallès, 08193, Barcelona, Spain
| | - David Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | | | - Thorfinn Sand Korneliussen
- GLOBE, Section for Geogenetics, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,National Research University, Higher School of Economics, 20 Myasnitskaya Ulitsa, 101000, Moscow, Russia
| | - Frands Carlsen
- Research and Conservation, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark
| | - Hans Redlef Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Thomas Mailund
- Bioinformatics Research Center, Department of Mathematics, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafant, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyala del Vallès, 08193, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac, 408028, Barcelona, Spain
| | - Christina Hvilsom
- Research and Conservation, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark
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Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 2019; 364:364/6446/eaav6202. [DOI: 10.1126/science.aav6202] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/16/2019] [Indexed: 12/17/2022]
Abstract
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
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Hansen CCR, Hvilsom C, Schmidt NM, Aastrup P, Van Coeverden de Groot PJ, Siegismund HR, Heller R. The Muskox Lost a Substantial Part of Its Genetic Diversity on Its Long Road to Greenland. Curr Biol 2018; 28:4022-4028.e5. [DOI: 10.1016/j.cub.2018.10.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/06/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023]
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Dhikusooka MT, Ayebazibwe C, Namatovu A, Belsham GJ, Siegismund HR, Wekesa SN, Balinda SN, Muwanika VB, Tjørnehøj K. Unrecognized circulation of SAT 1 foot-and-mouth disease virus in cattle herds around Queen Elizabeth National Park in Uganda. BMC Vet Res 2016; 12:5. [PMID: 26739166 PMCID: PMC4704403 DOI: 10.1186/s12917-015-0616-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 12/08/2015] [Indexed: 11/12/2022] Open
Abstract
Background Foot-and-mouth disease (FMD) is endemic in Uganda in spite of the control measures used. Various aspects of the maintenance and circulation of FMD viruses (FMDV) in Uganda are not well understood; these include the role of the African buffalo (Syncerus caffer) as a reservoir for FMDV. To better understand the epidemiology of FMD at the livestock-wildlife-interface, samples were collected from young, unvaccinated cattle from 24 pastoral herds that closely interact with wildlife around Queen Elizabeth National Park in Uganda, and analysed for evidence of FMDV infection. Results In total, 37 (15 %) of 247 serum samples had detectable antibodies against FMDV non-structural proteins (NSPs) using a pan-serotypic assay. Within these 37 sera, antibody titres ≥ 80 against the structural proteins of serotypes O, SAT 1, SAT 2 and SAT 3 were detected by ELISA in 5, 7, 4 and 3 samples, respectively, while neutralizing antibodies were only detected against serotype O in 3 samples. Two FMDV isolates, with identical VP1 coding sequences, were obtained from probang samples from clinically healthy calves from the same herd and are serotype SAT 1 (topotype IV (EA-I)). Based on the VP1 coding sequences, these viruses are distinct from previous cattle and buffalo SAT 1 FMDV isolates obtained from the same area (19–30 % nucleotide difference) and from the vaccine strain (TAN/155/71) used within Uganda (26 % nucleotide difference). Eight herds had only one or a few animals with antibodies against FMDV NSPs while six herds had more substantial evidence of prior infection with FMDV. There was no evidence for exposure to FMDV in the other ten herds. Conclusions The two identical SAT 1 FMDV VP1 sequences are distinct from former buffalo and cattle isolates from the same area, thus, transmission between buffalo and cattle was not demonstrated. These new SAT 1 FMDV isolates differed significantly from the vaccine strain used to control Ugandan FMD outbreaks, indicating a need for vaccine matching studies. Only six herds had clear serological evidence for exposure to O and SAT 1 FMDV. Scattered presence of antibodies against FMDV in other herds may be due to the occasional introduction of animals to the area or maternal antibodies from past infection and/or vaccination. The evidence for asymptomatic FMDV infection has implications for disease control strategies in the area since this obstructs early disease detection that is based on clinical signs in FMDV infected animals. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0616-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moses Tefula Dhikusooka
- National Animal Disease Diagnostics and Epidemiology Centre, Ministry of Agriculture Animal Industry and Fisheries, P. O. Box 513, Entebbe, Uganda.
| | - Chrisostom Ayebazibwe
- National Animal Disease Diagnostics and Epidemiology Centre, Ministry of Agriculture Animal Industry and Fisheries, P. O. Box 513, Entebbe, Uganda.
| | - Alice Namatovu
- National Animal Disease Diagnostics and Epidemiology Centre, Ministry of Agriculture Animal Industry and Fisheries, P. O. Box 513, Entebbe, Uganda. .,Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, DK 4771, Denmark.
| | - Hans Redlef Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK 2200, Copenhagen N, Denmark.
| | - Sabenzia Nabalayo Wekesa
- Foot-and-Mouth Disease Laboratory, Ministry of Livestock Development, P. O. Box 18021, Embakasi, Nairobi, Kenya. .,Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Sheila Nina Balinda
- Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Vincent B Muwanika
- Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Kirsten Tjørnehøj
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, DK 4771, Denmark.
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Dhikusooka MT, Tjørnehøj K, Ayebazibwe C, Namatovu A, Ruhweza S, Siegismund HR, Wekesa SN, Normann P, Belsham GJ. Foot-and-mouth disease virus serotype SAT 3 in long-horned Ankole calf, Uganda. Emerg Infect Dis 2015; 21:111-4. [PMID: 25531186 PMCID: PMC4285273 DOI: 10.3201/eid2101.140995] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
After a 16-year interval, foot-and-mouth disease virus serotype SAT 3 was isolated in 2013 from an apparently healthy long-horned Ankole calf that grazed close to buffalo in Uganda. The emergent virus strain is ≈20% different in nucleotide sequence (encoding VP1 [viral protein 1]) from its closest relatives isolated previously from buffalo in Uganda.
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Wekesa SN, Sangula AK, Belsham GJ, Tjornehoj K, Muwanika VB, Gakuya F, Mijele D, Siegismund HR. Characterisation of recent foot-and-mouth disease viruses from African buffalo (Syncerus caffer) and cattle in Kenya is consistent with independent virus populations. BMC Vet Res 2015; 11:17. [PMID: 25644407 PMCID: PMC4334418 DOI: 10.1186/s12917-015-0333-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 01/22/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Understanding the epidemiology of foot-and-mouth disease (FMD), including roles played by different hosts, is essential for improving disease control. The African buffalo (Syncerus caffer) is a reservoir for the SAT serotypes of FMD virus (FMDV). Large buffalo populations commonly intermingle with livestock in Kenya, yet earlier studies have focused on FMD in the domestic livestock, hence the contribution of buffalo to disease in livestock is largely unknown. This study analysed 47 epithelia collected from FMD outbreaks in Kenyan cattle between 2008 and 2012, and 102 probang and serum samples collected from buffalo in three different Kenyan ecosystems; Maasai-Mara (MME) (n = 40), Tsavo (TSE) (n = 33), and Meru (ME) (n = 29). RESULTS Antibodies against FMDV non-structural proteins were found in 65 of 102 (64%) sera from buffalo with 44/102 and 53/102 also having neutralising antibodies directed against FMDV SAT 1 and SAT 2, respectively. FMDV RNA was detected in 42% of the buffalo probang samples by RT-qPCR (Cycle Threshold (Ct) ≤32). Two buffalo probang samples were positive by VI and were identified as FMDV SAT 1 and SAT 2 by Ag-ELISA, while the latter assay detected serotypes O (1), A (20), SAT 1 (7) and SAT 2 (19) in the 47 cattle epithelia. VP1 coding sequences were generated for two buffalo and 21 cattle samples. Phylogenetic analyses revealed SAT 1 and SAT 2 virus lineages within buffalo that were distinct from those detected in cattle. CONCLUSIONS We found that FMDV serotypes O, A, SAT 1 and SAT 2 were circulating among cattle in Kenya and cause disease, but only SAT 1 and SAT 2 viruses were successfully isolated from clinically normal buffalo. The buffalo isolates were genetically distinct from isolates obtained from cattle. Control efforts should focus primarily on reducing FMDV circulation among livestock and limiting interaction with buffalo. Comprehensive studies incorporating additional buffalo viruses are recommended.
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Affiliation(s)
- Sabenzia Nabalayo Wekesa
- Foot-and-Mouth Disease Laboratory, Embakasi, P. O. Box 18021, 00500, Nairobi, Kenya.
- Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062/7298, Kampala, Uganda.
| | | | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771, Kalvehave, Denmark.
| | - Kirsten Tjornehoj
- National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771, Kalvehave, Denmark.
| | - Vincent B Muwanika
- Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062/7298, Kampala, Uganda.
| | - Francis Gakuya
- Kenya Wildlife Service, Veterinary Services Department, P.O Box 40241 (00100), Nairobi, Kenya.
| | - Dominic Mijele
- Kenya Wildlife Service, Veterinary Services Department, P.O Box 40241 (00100), Nairobi, Kenya.
| | - Hans Redlef Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen, Denmark.
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Dhikusooka MT, Tjørnehøj K, Ayebazibwe C, Namatovu A, Ruhweza S, Siegismund HR, Wekesa SN, Normann P, Belsham GJ. Foot-and-Mouth Disease Virus Serotype SAT 3 in Long-Horned Ankole Calf, Uganda. Emerg Infect Dis 2015. [DOI: 10.3201/2101.140995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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10
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Namatovu A, Belsham GJ, Ayebazibwe C, Dhikusooka MT, Wekesa SN, Siegismund HR, Muwanika VB, Tjørnehøj K. Challenges for Serology-Based Characterization of Foot-and-Mouth Disease Outbreaks in Endemic Areas; Identification of Two Separate Lineages of Serotype O FMDV in Uganda in 2011. Transbound Emerg Dis 2013; 62:522-34. [PMID: 24118785 DOI: 10.1111/tbed.12170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Indexed: 11/27/2022]
Abstract
Control of foot-and-mouth disease (FMD) in Uganda by ring vaccination largely depends on costly trivalent vaccines, and use of monovalent vaccines could improve the cost effectiveness. This, however, requires application of highly specific diagnostic tests. This study investigated outbreaks of FMD in seven Ugandan districts, during 2011, using the PrioCHECK® FMDV NS ELISA, solid-phase blocking ELISAs (SPBEs) and virus neutralization tests (VNTs), together with virological analyses for characterization of the responsible viruses. Two hundred and eighteen (218) cattle and 23 goat sera as well as 82 oropharyngeal fluid/epithelial tissue samples were collected. Some 50% of the cattle and 17% of the goat sera were positive by the PrioCHECK® FMDV NS ELISA, while SPBEs identified titres ≥80 for antibodies against serotype O FMD virus (FMDV) in 51% of the anti-NSP positive cattle sera. However, 35% of the anti-NSP positive cattle sera had SPBE titres ≥80 against multiple serotypes, primarily against serotypes O, SAT 1 and SAT 3. Comparison of SPBEs and VNTs for the detection of antibodies against serotypes O, SAT 1 and SAT 3 in 72 NSP positive cattle sera showed comparable results against serotype O (P = 0.181), while VNTs detected significantly fewer samples positive for antibodies against SAT 1 and SAT 3 than the SPBEs (P < 0.001). Detection of antibodies against serotype O was consistent with the isolation of serotype O FMDVs from 13 samples. Four of these viruses were sequenced and belonged to two distinct lineages within the East Africa-2 (EA-2) topotype, each differing from the currently used vaccine strain (EA-1 topotype). The relationships of these lineages to other serotype O viruses in the Eastern Africa region are discussed. To enhance the control of FMD in Uganda, there is need to improve the specificity of the SAT-SPBEs, perform vaccine matching and implement improved regional FMD control.
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Affiliation(s)
- A Namatovu
- National Animal Disease Diagnostics and Epidemiology Centre, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda.,Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - G J Belsham
- National Veterinary Institute, Technical University of Denmark, Kalvehave, Denmark
| | - C Ayebazibwe
- National Animal Disease Diagnostics and Epidemiology Centre, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda
| | - M T Dhikusooka
- National Animal Disease Diagnostics and Epidemiology Centre, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda
| | - S N Wekesa
- Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda.,Foot-and-Mouth Disease Laboratory, Ministry of Livestock Development, Nairobi, Kenya
| | - H R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - V B Muwanika
- Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - K Tjørnehøj
- National Veterinary Institute, Technical University of Denmark, Kalvehave, Denmark
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11
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Heller R, Chikhi L, Siegismund HR. The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. PLoS One 2013; 8:e62992. [PMID: 23667558 PMCID: PMC3646956 DOI: 10.1371/journal.pone.0062992] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 04/01/2013] [Indexed: 11/19/2022] Open
Abstract
Many coalescent-based methods aiming to infer the demographic history of populations assume a single, isolated and panmictic population (i.e. a Wright-Fisher model). While this assumption may be reasonable under many conditions, several recent studies have shown that the results can be misleading when it is violated. Among the most widely applied demographic inference methods are Bayesian skyline plots (BSPs), which are used across a range of biological fields. Violations of the panmixia assumption are to be expected in many biological systems, but the consequences for skyline plot inferences have so far not been addressed and quantified. We simulated DNA sequence data under a variety of scenarios involving structured populations with variable levels of gene flow and analysed them using BSPs as implemented in the software package BEAST. Results revealed that BSPs can show false signals of population decline under biologically plausible combinations of population structure and sampling strategy, suggesting that the interpretation of several previous studies may need to be re-evaluated. We found that a balanced sampling strategy whereby samples are distributed on several populations provides the best scheme for inferring demographic change over a typical time scale. Analyses of data from a structured African buffalo population demonstrate how BSP results can be strengthened by simulations. We recommend that sample selection should be carefully considered in relation to population structure previous to BSP analyses, and that alternative scenarios should be evaluated when interpreting signals of population size change.
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12
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Abstract
The savannah biome of sub-Saharan Africa harbours the highest diversity of ungulates (hoofed mammals) on Earth. In this review, we compile population genetic data from 19 codistributed ungulate taxa of the savannah biome and find striking concordance in the phylogeographic structuring of species. Data from across taxa reveal distinct regional lineages, which reflect the survival and divergence of populations in isolated savannah refugia during the climatic oscillations of the Pleistocene. Data from taxa across trophic levels suggest distinct savannah refugia were present in West, East, Southern and South-West Africa. Furthermore, differing Pleistocene evolutionary biogeographic scenarios are proposed for East and Southern Africa, supported by palaeoclimatic data and the fossil record. Environmental instability in East Africa facilitated several spatial and temporal refugia and is reflected in the high inter- and intraspecific diversity of the region. In contrast, phylogeographic data suggest a stable, long-standing savannah refuge in the south.
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Affiliation(s)
- E D Lorenzen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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13
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Heller R, Siegismund HR. Relationship between three measures of genetic differentiation G(ST), D(EST) and G'(ST): how wrong have we been? Mol Ecol 2009; 18:2080-3; discussion 2088-91. [PMID: 19645078 DOI: 10.1111/j.1365-294x.2009.04185.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R Heller
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark.
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14
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Okello JBA, Wittemyer G, Rasmussen HB, Arctander P, Nyakaana S, Douglas-Hamilton I, Siegismund HR. Effective population size dynamics reveal impacts of historic climatic events and recent anthropogenic pressure in African elephants. Mol Ecol 2008; 17:3788-99. [PMID: 18643879 DOI: 10.1111/j.1365-294x.2008.03871.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two hundred years of elephant hunting for ivory, peaking in 1970-1980s, caused local extirpations and massive population declines across Africa. The resulting genetic impacts on surviving populations have not been studied, despite the importance of understanding the evolutionary repercussions of such human-mediated events on this keystone species. Using Bayesian coalescent-based genetic methods to evaluate time-specific changes in effective population size, we analysed genetic variation in 20 highly polymorphic microsatellite loci from 400 elephants inhabiting the greater Samburu-Laikipia region of northern Kenya. This area experienced a decline of between 80% and 90% in the last few decades when ivory harvesting was rampant. The most significant change in effective population size, however, occurred approximately 2500 years ago during a mid-Holocene period of climatic drying in tropical Africa. Contrary to expectations, detailed analyses of four contemporary age-based cohorts showed that the peak poaching epidemic in the 1970s caused detectable temporary genetic impacts, with genetic diversity rebounding as juveniles surviving the poaching era became reproductively mature. This study demonstrates the importance of climatic history in shaping the distribution and genetic history of a keystone species and highlights the utility of coalescent-based demographic approaches in unravelling ancestral demographic events despite a lack of ancient samples. Unique insights into the genetic signature of mid-Holocene climatic change in Africa and effects of recent poaching pressure on elephants are discussed.
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Affiliation(s)
- J B A Okello
- Biotechnology and Molecular Genetics, FB2-UFT, University of Bremen, Leobenerstrasse UFT, 28359 Bremen, Germany.
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15
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16
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Okello JBA, Nyakaana S, Masembe C, Siegismund HR, Arctander P. Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion. Heredity (Edinb) 2006; 95:206-15. [PMID: 16030528 DOI: 10.1038/sj.hdy.6800711] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Mitochondrial DNA control region sequence variation was obtained and the population history of the common hippopotamus was inferred from 109 individuals from 13 localities covering six populations in sub-Saharan Africa. In all, 100 haplotypes were defined, of which 98 were locality specific. A relatively low overall nucleotide diversity was observed (pi = 1.9%), as compared to other large mammals so far studied from the same region. Within populations, nucleotide diversity varied from 1.52% in Zambia to 1.92% in Queen Elizabeth and Masai Mara. Overall, low but significant genetic differentiation was observed in the total data set (F(ST) = 0.138; P = 0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (F(CT) = 0.103; P = 0.015). Evidence that the common hippopotamus recently expanded were revealed by: (i) lack of clear geographical structure among haplotypes, (ii) mismatch distributions of pairwise differences (r = 0.0053; P = 0.012) and site-frequency spectra, (iii) Fu's neutrality statistics (F(S) = -155.409; P < 0.00001) and (iv) Fu and Li's statistical tests (D* = -3.191; P < 0.01, F* = -2.668; P = 0.01). Mismatch distributions, site-frequency spectra and neutrality statistics performed at subspecies level also supported expansion of Hippopotamus amphibius across Africa. We interpret observed common hippopotamus population history in terms of Pleistocene drainage overflow and suggest recognising the three subspecies that were sampled in this study as separate management units in future conservation planning.
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Affiliation(s)
- J B A Okello
- Molecular Biology Laboratory, Makerere University Institute of Environment & Natural Resources, PO Box 7298, Kampala, Uganda.
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17
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Okello JBA, Wittemyer G, Rasmussen HB, Douglas-Hamilton I, Nyakaana S, Arctander P, Siegismund HR. Noninvasive genotyping and Mendelian analysis of microsatellites in African savannah elephants. ACTA ACUST UNITED AC 2005; 96:679-87. [PMID: 16251516 DOI: 10.1093/jhered/esi117] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We obtained fresh dung samples from 202 (133 mother-offspring pairs) savannah elephants (Loxodonta africana) in Samburu, Kenya, and genotyped them at 20 microsatellite loci to assess genotyping success and errors. A total of 98.6% consensus genotypes was successfully obtained, with allelic dropout and false allele rates at 1.6% (n = 46) and 0.9% (n = 37) of heterozygous and total consensus genotypes, respectively, and an overall genotyping error rate of 2.5% based on repeat typing. Mendelian analysis revealed consistent inheritance in all but 38 allelic pairs from mother-offspring, giving an average mismatch error rate of 2.06%, a possible result of null alleles, mutations, genotyping errors, or inaccuracy in maternity assignment. We detected no evidence for large allele dropout, stuttering, or scoring error in the dataset and significant Hardy-Weinberg deviations at only two loci due to heterozygosity deficiency. Across loci, null allele frequencies were low (range: 0.000-0.042) and below the 0.20 threshold that would significantly bias individual-based studies. The high genotyping success and low errors observed in this study demonstrate reliability of the method employed and underscore the application of simple pedigrees in noninvasive studies. Since none of the sires were included in this study, the error rates presented are just estimates.
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Affiliation(s)
- J B A Okello
- Molecular Biology Laboratory, Makerere University Institute of Environment and Natural Resources, P. O. Box 7298, Kampala, Uganda.
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18
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Andersen NS, Siegismund HR, Meyer V, Jørgensen RB. Low level of gene flow from cultivated beets (Beta vulgaris L. ssp. vulgaris) into Danish populations of sea beet (Beta vulgaris L. ssp. maritima (L.) Arcangeli). Mol Ecol 2005; 14:1391-405. [PMID: 15813779 DOI: 10.1111/j.1365-294x.2005.02490.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Gene flow from sugar beets to sea beets occurs in the seed propagation areas in southern Europe. Some seed propagation also takes place in Denmark, but here the crop-wild gene flow has not been investigated. Hence, we studied gene flow to sea beet populations from sugar beet lines used in Danish seed propagation areas. A set of 12 Danish, two Swedish, one French, one Italian, one Dutch, and one Irish populations of sea beets, and four lines of sugar beet were analysed. To evaluate the genetic variation and gene flow, eight microsatellite loci were screened. This analysis revealed hybridization with cultivated beet in one of the sea beet populations from the centre of the Danish seed propagation area. Triploid hybrids found in this population were verified with flow cytometry. Possible hybrids or introgressed plants were also found in the French and Italian populations. However, individual assignment test using a Bayesian method provided 100% assignment success of diploid individuals into their correct subspecies of origin, and a Bayesian Markov chain Monte Carlo (MC MC) approach revealed clear distinction of individuals into groups according to their subspecies of origin, with a zero level of genetic admixture among subspecies. This underlines that introgression beyond the first hybridization is not extensive. The overall pattern of genetic distance and structure showed that Danish and Swedish sea beet populations were closely related to each other, and they are both more closely related to the population from Ireland than to the populations from France, the Netherlands, and Italy.
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Affiliation(s)
- N S Andersen
- Plant Research Department, Risø National Laboratory, Postbox 49, Roskilde, DK-4000, Denmark (Center for Bioethics and Risk Assessment)
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19
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Muwanika VB, Nyakaana S, Siegismund HR, Arctander P. Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci. Heredity (Edinb) 2004; 91:361-72. [PMID: 14512951 DOI: 10.1038/sj.hdy.6800341] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Global climate fluctuated considerably throughout the Pliocene and Pleistocene, influencing the evolutionary history of a wide range of species. Using both mitochondrial sequences and microsatellites, we have investigated the evolutionary consequences of such environmental fluctuation for the patterns of genetic variation in the common warthog, sampled from 24 localities in Africa. In the sample of 181 individuals, 70 mitochondrial DNA haplotypes were identified and an overall nucleotide diversity of 4.0% was observed. The haplotypes cluster in three well-differentiated clades (estimated net sequence divergence of 3.1-6.6%) corresponding to the geographical origins of individuals (i.e. eastern, western and southern African clades). At the microsatellite loci, high polymorphism was observed both in the number of alleles per locus (6-21), and in the gene diversity (in each population 0.59-0.80). Analysis of population differentiation indicates greater subdivision at the mitochondrial loci (FST=0.85) than at nuclear loci (FST=0.20), but both mitochondrial and nuclear loci support the existence of the three warthog lineages. We interpret our results in terms of the large-scale climatic fluctuations of the Pleistocene.
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Affiliation(s)
- V B Muwanika
- Institute of Environment and Natural Resources, Makerere University, PO Box 7298, Kampala, Uganda.
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20
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Weidema IR, Siegismund HR, Philipp M. Distribution of genetic variation within and among Danish populations of Armeria maritima, with special reference to the effects of population size. Hereditas 2004. [DOI: 10.1111/j.1601-5223.1996.00121.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Abstract
We have earlier shown extensive introgression between oilseed rape (Brassica napus) and B. rapa in a weedy population using AFLP markers specific for the nuclear genomes. In order to describe the progress of this introgression, we examined 117 offspring from 12 maternal plants from the introgressed population with the same AFLP-markers; AFLP data were supported by chromosome counting. We also analysed the offspring with a species-specific chloroplast marker and finally evaluated the reproductive system in selected maternal plants. Our results indicated a high outcrossing rate of the introgressed maternal plants. It seemed that B. rapa most often functioned as the maternal plant in the introgression process and that the amount of oilseed rape DNA was highly diminished in the offspring compared to their introgressed maternal plants. However, our analysis of plants from the weedy population indicated that introgression can lead to both (1) exchange of chloroplast DNA between species producing B. rapa-like plants with B. napus chloroplasts and (2) incorporation of B. napus C-genome DNA into the B. rapa genome. Therefore, we question whether it can be regarded as containment to position transgenes in the chloroplast or in specific parts of the nuclear genome of B. napus.
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Affiliation(s)
- L B Hansen
- Botanical Institute, Øster Farimagsgade 2D, DK-1353 Copenhagen K, Denmark
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22
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Abstract
An earlier study of the morphological variation in the circumpolar genus Dryas in Greenland revealed that populations in east Greenland are highly variable and this variation was interpreted as a hybrid zone between D. octopetala and D. integrifolia. It was proposed that populations of Dryas in east Greenland immigrated postglacially from Svalbard. The purpose of our study was to investigate the population structure of the Dryas integrifolia-octopetala complex using a combination of morphological and genetic characters. Populations of Dryas were sampled in Greenland, Svalbard, Iceland and north Scandinavia (Sweden). The morphological traits clearly separated west Greenland from Svalbard, Iceland and north Scandinavia. A large number of individuals from east Greenland and some from north Greenland could be interpreted as hybrids between the morphs. The genetic pattern was, however, partly different as the greatest amount of differentiation among regions was found between west and north Greenland (FRT = 0.65). The highest degree of genetic variation appeared within east Greenland. This was in accordance with the putative hybrid origin of the populations, as concluded based on the morphological results. The total amount of genetic differentiation found among the six regions (FRT = 0.61) was larger than between the two species (FRT = 0.44). The genetic pattern matched the proposed postglacial migration routes.
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Affiliation(s)
- M Philipp
- Botanical Institute, University of Copenhagen, Øster Farimagsgade 2D, DK-1353 Copenhagen K, Denmark.
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23
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Siegismund HR. Disparity in population differentiation of sex-linked and autosomal variation in sibling species of the Jaera albifrons (Isopoda) complex. J Hered 2002; 93:432-9. [PMID: 12642644 DOI: 10.1093/jhered/93.6.432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The genetic variation at four enzyme loci is described for 22 populations of three Jaera species--J. albifrons, J. ischiosetosa, and J. praehirsuta--in the J. albifrons complex (Crustacea, Isopoda) in Denmark. The variation at three of the loci is similar, with the allele frequency spectra close to each other in all three species. An evolutionary tree based on the variation at these three loci revealed that the populations from the different species are completely intermixed in the tree. This was supported by hierarchical F-statistics where the between-species component was zero. At a fourth locus, Gpi (glucose phosphate isomerase), the species differ substantially. This locus is sex linked in J. ischiosetosa, but in the two other species, J. albifrons and J. praehirsuta, it is either found on autosomes or is sex linked with a high recombination rate between the locus and the centromere. An evolutionary tree for this locus partitions the populations into separate groups and a hierarchical F-statistic has a between-species component of about 50%. The results are attributed to introgression with a higher rate for autosomes than for sex chromosomes.
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Affiliation(s)
- H R Siegismund
- Department of Evolutionary Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
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24
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Nyakaana S, Arctander P, Siegismund HR. Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci. Heredity (Edinb) 2002; 89:90-8. [PMID: 12136410 DOI: 10.1038/sj.hdy.6800110] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2001] [Accepted: 04/22/2002] [Indexed: 11/08/2022] Open
Abstract
Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern, western and southern Africa. In the total sample, 43 haplotypes were identified and an overall nucleotide diversity of 2.0% was observed. High levels of polymorphism were also observed at the microsatellite loci both at the level of number of alleles and gene diversity. Nine to 14 alleles per locus across populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72 in the localities studied. An analysis of molecular variance showed significant genetic differentiation between populations within regions and also between regions. The extent of subdivision between populations at the mtDNA control region was approximately twice as high as shown by the microsatellite loci (mtDNA F(ST) = 0.59; microsatellite R(ST) = 0.31). We discuss our results in the light of Pleistocene refugia and attribute the observed pattern to population divergence in allopatry accompanied by a recent population admixture following a recent population expansion.
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Affiliation(s)
- S Nyakaana
- Institute of Environment and Natural Resources, Makerere University, P.O. Box 7298, Kampala, Uganda.
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25
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Simonsen BT, Siegismund HR, Arctander P. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation. Mol Ecol 1998; 7:225-37. [PMID: 9532761 DOI: 10.1046/j.1365-294x.1998.00343.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed to be strongly philopatric and to form large aggregations that remain within separate home ranges with little interchange between units, but the level of differentiation within the species is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequence data and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability within the species. The high level of genetic variation within the species was found to be evenly distributed among populations and only at the continental level were we able to consistently detect significant differentiation, contrasting with the assumed philopatric behaviour of the buffalo. Results of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male-biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic population due to human activity, and at the continental level, reflects an effect of geographical distance between populations.
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Affiliation(s)
- B T Simonsen
- Department of Population Biology, University of Copenhagen, Denmark.
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26
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Andersen LW, Holm LE, Siegismund HR, Clausen B, Kinze CC, Loeschcke V. A combined DNA-microsatellite and isozyme analysis of the population structure of the harbour porpoise in Danish waters and west Greenland. Heredity (Edinb) 1997; 78 ( Pt 3):270-6. [PMID: 9119703 DOI: 10.1038/hdy.1997.41] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
One hundred and twenty-four specimens of the harbour porpoise, Phocoena phocoena, occurring in inner Danish waters (IDW), the North Sea and West Greenland were analysed to study subdivision into genetically differentiated subpopulations using PCR-amplified DNA-microsatellites and isozyme markers. Three polymorphic microsatellites, 415/416, 417/418 and Igf-I (insulin-like growth factor I) were detected with nine, eight and 15 alleles, respectively, and from a former study two polymorphic isozymes, Mpi-1 and Pgm, with three and two alleles, respectively, were used in the analysis. Overall deviations from the expected Hardy-Weinberg distribution were only observed in the total sample and at a single locus in the North Sea-summer sample and at two loci in the West Greenland sample. Whenever this occurred a surplus of homozygotes was observed, suggesting a Wahlund effect, a null allele or nonrandom mating. The analysis of the genetical population structure showed that harbour porpoises from West Greenland, the North Sea and IDW were three geographically, genetically differentiated populations even though connected through some degree of gene flow. A tendency for females to be more stationary than males was suggested. Furthermore, the population structure suggested a closer relationship between IDW and the North Sea.
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Affiliation(s)
- L W Andersen
- Department of Genetics and Ecology, University of Aarhus, Denmark.
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27
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Arctander P, Kat PW, Aman RA, Siegismund HR. Extreme genetic differences among populations of Gazella granti, Grant's gazelle in Kenya. Heredity (Edinb) 1996; 76 ( Pt 5):465-75. [PMID: 8666544 DOI: 10.1038/hdy.1996.69] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mitochondrial DNA (mtDNA) control region sequences from six Kenyan Grant's gazelle (Gazella granti) populations were highly divergent among locations. Neighbouring populations not separated by geographical or vegetational barriers exhibited and nucleotide sequence divergence about 14 per cent. A similar level of divergence separates Grant's gazelles from a closely related species, the Soemmering's gazelle (G. soemmeringii). Nuclear microsatellite repeat number variation at two loci also indicated substantial population genetic differentiation. Despite high levels of sequence divergence populations of Grant's gazelles were more closely related to each other than to Soemmering's and Thompson's gazelles (G. thomsoni) as measured by nucleotide sequence divergence at the mtDNA protein coding cytochrome b gene and the nuclear alpha-lactalbumin gene. This pattern of extensive differentiation is hypothesized to have resulted from recently established contacts between formerly allopatric populations.
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Affiliation(s)
- P Arctander
- Department of Population Biology, University of Copenhagen, Denmark
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28
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Mukaratirwa S, Siegismund HR, Kristensen TK, Chandiwana SK. Genetic structure and parasite compatibility of Bulinus globosus (Gastropoda: Planorbidae) from two areas of different endemicity of Schistosoma haematobium in Zimbabwe. Int J Parasitol 1996; 26:269-80. [PMID: 8786216 DOI: 10.1016/0020-7519(95)00130-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A comparative study of the genetic structure of 8 populations of B.globosus from 2 areas of different endemicity of Schistosoma haematobium was done. Five populations were from Chiweshe (high endemicity) and three were from Plumtree (low endemicity). Genetic structure, as determined by allozyme genetics, revealed high levels of genetic variability in Chiweshe populations (Ho = 0.12-0.26) and low levels in Plumtree (Ho = 0.06-0.12). Populations from Chiweshe were genetically heterogeneous whereas in Plumtree the populations were uniform. There were significant deviations from Hardy-Weinberg proportions at different loci in Chiweshe populations. The observed excess of homozygotes was probably caused by partial selfing. The compatibility studies showed variation between allopatric and sympatric combinations of snails and parasites, and the Plumtree parasite had a significant influence on the compatibility parameters. This strain had a positive correlation (P < 0.01) of its infection rate with allele frequency of Est-2(100) and a negative correlation (P < 0.05) with allele Idh100.
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Abstract
The structure of elephant populations from east and south Africa has been analyzed by Georgiadis et al. (1994) on the basis of restriction site variation of mitochondrial DNA. They used F statistics based on identity by descent in tests for subdivision and reached the conclusion that there was a significant differentiation at the continental level, but that "populations were not significantly subdivided at the regional levels." The data were reanalyzed by Monte-Carlo permutation tests where population subdivision was tested by using F statistics based on partitioning the total haplotype diversity among populations. This resulted in identical conclusions at the continental level, but revealed in addition a significant subdivision at the regional level indicating haplotype frequency differences among the populations.
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Affiliation(s)
- H R Siegismund
- Arboretum, Royal Veterinary and Agricultural University, Hørsholm, Denmark
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30
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Siegismund HR, Christiansen FB. Selection component analysis of natural polymorphisms using population samples including mother-offspring combinations, III. Theor Popul Biol 1985. [DOI: 10.1016/0040-5809(85)90002-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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