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Talenti A, Wilkinson T, Cook EA, Hemmink JD, Paxton E, Mutinda M, Ngulu SD, Jayaraman S, Bishop RP, Obara I, Hourlier T, Garcia Giron C, Martin FJ, Labuschagne M, Atimnedi P, Nanteza A, Keyyu JD, Mramba F, Caron A, Cornelis D, Chardonnet P, Fyumagwa R, Lembo T, Auty HK, Michaux J, Smitz N, Toye P, Robert C, Prendergast JGD, Morrison LJ. Continent-wide genomic analysis of the African buffalo (Syncerus caffer). Commun Biol 2024; 7:792. [PMID: 38951693 PMCID: PMC11217449 DOI: 10.1038/s42003-024-06481-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/21/2024] [Indexed: 07/03/2024] Open
Abstract
The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights into the evolutionary history of the species, and the key selective pressures shaping populations, including assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, scaffold N50 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from across the species distribution. Principal component and admixture analyses provided little support for the currently described four subspecies. Estimating Effective Migration Surfaces analysis suggested that geographical barriers have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes indicated a substantial drop occurring in all populations 5-10,000 years ago, coinciding with the increase in human populations. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure upon the African buffalo. These findings have important implications for understanding bovid evolution, buffalo conservation and population management.
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Affiliation(s)
- Andrea Talenti
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
| | - Toby Wilkinson
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
| | - Elizabeth A Cook
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Johanneke D Hemmink
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Edith Paxton
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
| | - Matthew Mutinda
- Kenya Wildlife Service, P.O. Box 40241, Nairobi, 00100, Kenya
| | | | - Siddharth Jayaraman
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
| | - Richard P Bishop
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Isaiah Obara
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | | | | | - Anne Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute, Box 661, Arusha, Tanzania
| | - Furaha Mramba
- Vector and Vector-Borne Diseases Institute, Tanga, Tanzania
| | - Alexandre Caron
- ASTRE, University of Montpellier (UMR), CIRAD, 34090, Montpellier, France
- CIRAD, UMR ASTRE, RP-PCP, Maputo, 01009, Mozambique
- Faculdade Veterinaria, Universidade Eduardo Mondlan, Maputo, Mozambique
| | - Daniel Cornelis
- CIRAD, Forêts et Sociétés, 34398, Montpellier, France
- Forêts et Sociétés, University of Montpellier, CIRAD, 34090, Montpellier, France
| | | | - Robert Fyumagwa
- Tanzania Wildlife Research Institute, Box 661, Arusha, Tanzania
| | - Tiziana Lembo
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Harriet K Auty
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Johan Michaux
- Laboratoire de Génétique de la Conservation, Institut de Botanique (Bat. 22), Université de Liège (Sart Tilman), Chemin de la Vallée 4, B4000, Liège, Belgium
| | - Nathalie Smitz
- Royal Museum for Central Africa (BopCo), Leuvensesteenweg 13, 3080, Tervuren, Belgium
| | - Philip Toye
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Christelle Robert
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, United Kingdom
| | - James G D Prendergast
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
| | - Liam J Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom.
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom.
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Kumar SL, Singh R, Gurao A, Mishra SK, Kumar P, Vohra V, Niranjan SK, Sodhi M, Dash SK, Sarangdhar S, Mukesh M, Kataria RS. Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers. Mol Biol Rep 2022; 49:6029-6040. [DOI: 10.1007/s11033-022-07389-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
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3
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A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium. PLoS One 2021; 16:e0259685. [PMID: 34882683 PMCID: PMC8659316 DOI: 10.1371/journal.pone.0259685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
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Ünal EÖ, Işık R, Şen A, Geyik Kuş E, Soysal Mİ. Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers. Animals (Basel) 2021; 11:ani11041067. [PMID: 33918824 PMCID: PMC8070036 DOI: 10.3390/ani11041067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy-Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy-Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.
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Affiliation(s)
- Emel Özkan Ünal
- Department of Animal Science, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey;
- Correspondence: (E.Ö.Ü.); (M.İ.S.)
| | - Raziye Işık
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey;
| | - Ayşe Şen
- Department of Animal Science, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey;
| | - Elif Geyik Kuş
- GenoMetri Biotechnology Research and Development Consultancy Services Limited Company, 35430 İzmir, Turkey;
| | - Mehmet İhsan Soysal
- Department of Animal Science, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey;
- Correspondence: (E.Ö.Ü.); (M.İ.S.)
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de Jager D, Glanzmann B, Möller M, Hoal E, van Helden P, Harper C, Bloomer P. High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes. Sci Rep 2021; 11:4540. [PMID: 33633171 PMCID: PMC7907399 DOI: 10.1038/s41598-021-83823-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
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Affiliation(s)
- Deon de Jager
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Cindy Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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de Jager D, Harper CK, Bloomer P. Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa. PLoS One 2020; 15:e0236717. [PMID: 32797056 PMCID: PMC7428177 DOI: 10.1371/journal.pone.0236717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/13/2020] [Indexed: 12/03/2022] Open
Abstract
Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.
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Affiliation(s)
- Deon de Jager
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Cindy Kim Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
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Miller SM, Clarke AB, Bloomer P, Guthrie AJ, Harper CK. Evaluation of microsatellites for common ungulates in the South African wildlife industry. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0554-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Spencer PBS, Yurchenko AA, David VA, Scott R, Koepfli KP, Driscoll C, O'Brien SJ, Menotti-Raymond M. The Population Origins and Expansion of Feral Cats in Australia. J Hered 2015; 107:104-14. [PMID: 26647063 DOI: 10.1093/jhered/esv095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris).
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Affiliation(s)
- Peter B S Spencer
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond).
| | - Andrey A Yurchenko
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Victor A David
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Rachael Scott
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Klaus-Peter Koepfli
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Carlos Driscoll
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Stephen J O'Brien
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Marilyn Menotti-Raymond
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
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10
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Mager KH, Colson KE, Groves P, Hundertmark KJ. Population structure over a broad spatial scale driven by nonanthropogenic factors in a wide-ranging migratory mammal, Alaskan caribou. Mol Ecol 2014; 23:6045-57. [DOI: 10.1111/mec.12999] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 11/05/2014] [Accepted: 11/13/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Karen H. Mager
- Department of Biology and Wildlife; University of Alaska Fairbanks; P. O. Box 756100 Fairbanks AK 99775 USA
| | - Kevin E. Colson
- Institute of Arctic Biology; University of Alaska Fairbanks; P. O. Box 757000 Fairbanks AK 99775 USA
| | - Pam Groves
- Institute of Arctic Biology; University of Alaska Fairbanks; P. O. Box 757000 Fairbanks AK 99775 USA
| | - Kris J. Hundertmark
- Department of Biology and Wildlife; University of Alaska Fairbanks; P. O. Box 756100 Fairbanks AK 99775 USA
- Institute of Arctic Biology; University of Alaska Fairbanks; P. O. Box 757000 Fairbanks AK 99775 USA
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11
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van Hooft P, Greyling BJ, Getz WM, van Helden PD, Zwaan BJ, Bastos ADS. Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly. PLoS One 2014; 9:e111778. [PMID: 25372610 PMCID: PMC4221135 DOI: 10.1371/journal.pone.0111778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/23/2014] [Indexed: 11/18/2022] Open
Abstract
Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important implications for our understanding not only of the evolutionary and ecological dynamics of sex-ratio distorters and suppressors, but also of the functioning of deleterious and sexually-antagonistic alleles, and their impact on population viability.
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Affiliation(s)
- Pim van Hooft
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Hatfield, South Africa
- * E-mail:
| | - Ben J. Greyling
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Hatfield, South Africa
- Agricultural Research Council, Irene, South Africa
| | - Wayne M. Getz
- Department of Environmental Science Policy & Management, University of California, Berkeley, California, United States of America
- School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical TB Research, US/MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Bas J. Zwaan
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Armanda D. S. Bastos
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Hatfield, South Africa
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12
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Smitz N, Cornélis D, Chardonnet P, Caron A, de Garine-Wichatitsky M, Jori F, Mouton A, Latinne A, Pigneur LM, Melletti M, Kanapeckas KL, Marescaux J, Pereira CL, Michaux J. Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer). BMC Evol Biol 2014; 14:203. [PMID: 25367154 PMCID: PMC4232705 DOI: 10.1186/s12862-014-0203-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/16/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the "genetic health" of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites. RESULTS The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (A r ) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (P a ) of 11), low differentiation, and an absence of an inbreeding depression signal (mean F IS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (F IS = 0.062, mean A r = 6.160, P a = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century. CONCLUSIONS We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.
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Affiliation(s)
- Nathalie Smitz
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
| | - Daniel Cornélis
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | | | - Alexandre Caron
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-RP-PCP, University of Zimbabwe, Harare, Zimbabwe
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Michel de Garine-Wichatitsky
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-RP-PCP, University of Zimbabwe, Harare, Zimbabwe
- />Department of Biological Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Ferran Jori
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- />Department of Animal Science and Production, Botswana College of Agriculture, Gaborone, Botswana
| | - Alice Mouton
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
| | - Alice Latinne
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
- />Institut des Sciences de l’Evolution-CNRS-IRD, Université de Montpellier 2, Montpellier, France
- />Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Lise-Marie Pigneur
- />Research Unit in Environmental and Evolutionary Biology, University of Namur, Namur, Belgium
| | - Mario Melletti
- />Independent researcher, Via Di Villa Chigi, Rome, Italy
| | - Kimberly L Kanapeckas
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- />Department of Genetics and Biochemistry, Clemson University, Clemson, USA
| | - Jonathan Marescaux
- />Research Unit in Environmental and Evolutionary Biology, University of Namur, Namur, Belgium
| | | | - Johan Michaux
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
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Jacquet F, Nicolas V, Colyn M, Kadjo B, Hutterer R, Decher J, Akpatou B, Cruaud C, Denys C. Forest refugia and riverine barriers promote diversification in the West African pygmy shrew (Crocidura obscuriorcomplex, Soricomorpha). ZOOL SCR 2013. [DOI: 10.1111/zsc.12039] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- François Jacquet
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
| | - Violaine Nicolas
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
| | - Marc Colyn
- Université de Rennes 1, CNRS, Ecobio UMR 6553, Station Biologique; 35380 Paimpont France
| | - Blaise Kadjo
- Université de Cocody-Abidjan-UFR Biosciences, Systématique, Biologie et Ecologie des Mammifères; 22 BP 582 Abidjan 22 Côte d'Ivoire
| | - Rainer Hutterer
- Zoologisches Forschungsmuseum A. Koenig, Section of Mammals; Adenauerallee 160 D-53113 Bonn Germany
| | - Jan Decher
- Zoologisches Forschungsmuseum A. Koenig, Section of Mammals; Adenauerallee 160 D-53113 Bonn Germany
| | - Bertin Akpatou
- Université de Cocody-Abidjan-UFR Biosciences, Systématique, Biologie et Ecologie des Mammifères; 22 BP 582 Abidjan 22 Côte d'Ivoire
| | - Corinne Cruaud
- Génoscope, Centre National de Séquençage; 2 rue Gaston Crémieux CP5706 91057 Evry Cedex France
| | - Christiane Denys
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
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14
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Pan-African genetic structure in the African buffalo (Syncerus caffer): investigating intraspecific divergence. PLoS One 2013; 8:e56235. [PMID: 23437100 PMCID: PMC3578844 DOI: 10.1371/journal.pone.0056235] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.
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15
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Epps CW, Castillo JA, Schmidt-Küntzel A, du Preez P, Stuart-Hill G, Jago M, Naidoo R. Contrasting historical and recent gene flow among African buffalo herds in the Caprivi Strip of Namibia. ACTA ACUST UNITED AC 2013; 104:172-81. [PMID: 23341534 DOI: 10.1093/jhered/ess142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Population genetic structure is often used to infer population connectivity, but genetic structure may largely reflect historical rather than recent processes. We contrasted genetic structure with recent gene-flow estimates among 6 herds of African buffalo (Syncerus caffer) in the Caprivi Strip, Namibia, using 134 individuals genotyped at 10 microsatellite loci. We tested whether historical and recent gene flows were influenced by distance, potential barriers (rivers), or landscape resistance (distance from water). We also tested at what scales individuals were more related than expected by chance. Genetic structure across the Caprivi Strip was weak, indicating that historically, gene flow was strong and was not affected by distance, barriers, or landscape resistance. Our analysis of simulated data suggested that genetic structure would be unlikely to reflect human disturbances in the last 10-20 generations (75-150 years) because of slow predicted rates of genetic drift, but recent gene-flow estimates would be affected. Recent gene-flow estimates were not consistently affected by rivers or distance to water but showed that isolation by distance appears to be developing. Average relatedness estimates among individuals exceeded random expectations only within herds. We conclude that historically, African buffalo moved freely throughout the Caprivi Strip, whereas recent gene flow has been more restricted. Our findings support efforts to maintain the connectivity of buffalo herds across this region and demonstrate the utility of contrasting genetic inferences from different time scales.
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Affiliation(s)
- Clinton W Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.
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16
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van der Hoek Y, Lustenhouwer I, Jeffery KJ, van Hooft P. Potential effects of prescribed savannah burning on the diet selection of forest buffalo (Syncerus caffer nanus) in Lopé National Park, Gabon. Afr J Ecol 2012. [DOI: 10.1111/aje.12010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | - Ivo Lustenhouwer
- Resource Ecology Group; Wageningen University; Droevendaalsesteeg 3a, 6708 PB; Wageningen; The Netherlands
| | | | - Pim van Hooft
- Resource Ecology Group; Wageningen University; Droevendaalsesteeg 3a, 6708 PB; Wageningen; The Netherlands
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17
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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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18
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Influence of habitat fragmentation on the genetic structure of large mammals: evidence for increased structuring of African buffalo (Syncerus caffer) within the Serengeti ecosystem. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0291-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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van Hooft P, Prins HHT, Getz WM, Jolles AE, van Wieren SE, Greyling BJ, van Helden PD, Bastos ADS. Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio. BMC Evol Biol 2010; 10:106. [PMID: 20416038 PMCID: PMC2875233 DOI: 10.1186/1471-2148-10-106] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 04/23/2010] [Indexed: 11/22/2022] Open
Abstract
Background The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. Stable Y-chromosomal polymorphism due one of these factors only seems possible when there are Y-chromosomal distorters of an equal sex ratio, which act by negatively affecting X-gametes, or Y-chromosomal suppressors of a female-biased sex ratio. These sex-ratio (SR) genes modify (suppress) gamete transmission in their own favour at a fitness cost, allowing for stable polymorphism. Results Here we show temporal correlations between Y-chromosomal haplotype frequencies and foetal sex ratios in the KNP buffalo population, suggesting SR genes. Frequencies varied by a factor of five; too high to be alternatively explained by Y-chromosomal effects on pregnancy loss. Sex ratios were male-biased during wet and female-biased during dry periods (male proportion: 0.47-0.53), seasonally and annually. Both wet and dry periods were associated with a specific haplotype indicating a SR distorter and SR suppressor, respectively. Conclusions The distinctive properties suggested for explaining Y-chromosomal polymorphism in African buffalo may not be restricted to this species alone. SR genes may play a broader and largely overlooked role in mammalian sex-ratio variation.
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Affiliation(s)
- Pim van Hooft
- Resource Ecology Group, Wageningen University, 6708 PB Wageningen, The Netherlands.
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20
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HELLER R, OKELLO JBA, SIEGISMUND H. Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa. Mol Ecol 2010; 19:1324-34. [DOI: 10.1111/j.1365-294x.2010.04589.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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21
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Gargani M, Pariset L, Soysal MI, Ozkan E, Valentini A. Genetic variation and relationships among Turkish water buffalo populations. Anim Genet 2009; 41:93-6. [PMID: 19799598 DOI: 10.1111/j.1365-2052.2009.01954.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genetic variation and relationships among six Turkish water buffalo populations, typical of different regions, were assessed using a set of 26 heterologous (bovine) microsatellite markers. Between seven and 17 different alleles were identified per microsatellite in a total of 254 alleles. The average number of alleles across all loci in all the analysed populations was found to be 12.57. The expected mean heterozygosity (H(e)) per population ranged between 0.5 and 0.58. Significant departures from Hardy-Weinberg equilibrium were observed for 44 locus-population combinations. Population differentiation was analysed by estimation of the F(st) index (values ranging from 0.053 to 0.123) among populations. A principal component analysis of variation revealed the Merzifon population to show the highest differentiation compared with the others. In addition, some individuals of the Danamandira population appeared clearly separated, while the Afyon, Coskun, Pazar and Thural populations represented a single cluster. The assignment of individuals to their source populations, performed using the Bayesian clustering approach implemented in the structure 2.2 software, supports a high differentiation of Merzifon and Danamandira populations. The results of this study are useful for the development of conservation strategies for the Turkish buffalo.
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Affiliation(s)
- M Gargani
- Department of Animal Production, University of Tuscia, Viterbo, Italy
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22
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Sibeko KP, Geysen D, Oosthuizen MC, Matthee CA, Troskie M, Potgieter FT, Coetzer JAW, Collins NE. Four p67 alleles identified in South African Theileria parva field samples. Vet Parasitol 2009; 167:244-54. [PMID: 19836893 DOI: 10.1016/j.vetpar.2009.09.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Previous studies characterizing the Theileria parva p67 gene in East Africa revealed two alleles. Cattle-derived isolates associated with East Coast fever (ECF) have a 129bp deletion in the central region of the p67 gene (allele 1), compared to buffalo-derived isolates with no deletion (allele 2). In South Africa, Corridor disease outbreaks occur if there is contact between infected buffalo and susceptible cattle in the presence of vector ticks. Although ECF was introduced into South Africa in the early 20th century, it has been eradicated and it is thought that there has been no cattle to cattle transmission of T. parva since. The variable region of the p67 gene was amplified and the gene sequences analyzed to characterize South African T. parva parasites that occur in buffalo, in cattle from farms where Corridor disease outbreaks were diagnosed and in experimentally infected cattle. Four p67 alleles were identified, including alleles 1 and 2 previously detected in East African cattle and buffalo, respectively, as well as two novel alleles, one with a different 174bp deletion (allele 3), the other with a similar sequence to allele 3 but with no deletion (allele 4). Sequence variants of allele 1 were obtained from field samples originating from both cattle and buffalo. Allele 1 was also obtained from a bovine that tested T. parva positive from a farm near Ladysmith in the KwaZulu-Natal Province. East Coast fever was not diagnosed on this farm, but the p67 sequence was identical to that of T. parva Muguga, an isolate that causes ECF in Kenya. Variants of allele 2 were obtained from all T. parva samples from both buffalo and cattle, except Lad 10 and Zam 5. Phylogenetic analysis revealed that alleles 3 and 4 are monophyletic and diverged early from the other alleles. These novel alleles were not identified from South African field samples collected from cattle; however allele 3, with a p67 sequence identical to those obtained in South African field samples from buffalo, was obtained from a Zambian field isolate of a naturally infected bovine diagnosed with ECF. The p67 genetic profiles appear to be more complex than previously thought and cannot be used to distinguish between cattle- and buffalo-derived T. parva isolates in South Africa. The significance of the different p67 alleles, particularly the novel variants, in the epidemiology of theileriosis in South Africa still needs to be determined.
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Affiliation(s)
- Kgomotso P Sibeko
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort 0110, South Africa.
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23
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Is Homo sapiens polytypic? Human taxonomic diversity and its implications. Med Hypotheses 2009; 74:195-201. [PMID: 19695787 DOI: 10.1016/j.mehy.2009.07.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 07/22/2009] [Indexed: 11/23/2022]
Abstract
The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.
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Mullen LM, Vignieri SN, Gore JA, Hoekstra HE. Adaptive basis of geographic variation: genetic, phenotypic and environmental differences among beach mouse populations. Proc Biol Sci 2009; 276:3809-18. [PMID: 19656790 DOI: 10.1098/rspb.2009.1146] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A major goal in evolutionary biology is to understand how and why populations differentiate, both genetically and phenotypically, as they invade a novel habitat. A classical example of adaptation is the pale colour of beach mice, relative to their dark mainland ancestors, which colonized the isolated sandy dunes and barrier islands on Florida's Gulf Coast. However, much less is known about differentiation among the Gulf Coast beach mice, which comprise five subspecies linearly arrayed on Florida's shoreline. Here, we test the role of selection in maintaining variation among these beach mouse subspecies at multiple levels-phenotype, genotype and the environments they inhabit. While all beach subspecies have light pelage, they differ significantly in colour pattern. These subspecies are also genetically distinct: pair-wise F(st)-values range from 0.23 to 0.63 and levels of gene flow are low. However, we did not find a correlation between phenotypic and genetic distance. Instead, we find a significant association between the average 'lightness' of each subspecies and the brightness of the substrate it inhabits: the two most genetically divergent subspecies occupy the most similar habitats and have converged on phenotype, whereas the most genetically similar subspecies occupy the most different environments and have divergent phenotypes. Moreover, allelic variation at the pigmentation gene, Mc1r, is statistically correlated with these colour differences but not with variation at other genetic loci. Together, these results suggest that natural selection for camouflage-via changes in Mc1r allele frequency-contributes to pigment differentiation among beach mouse subspecies.
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Affiliation(s)
- Lynne M Mullen
- Department of Organismic and Evolutionary Biology and The Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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25
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Nicolas V, Bryja J, Akpatou B, Konecny A, Lecompte E, Colyn M, Lalis A, Couloux A, Denys C, Granjon L. Comparative phylogeography of two sibling species of forest-dwelling rodent (Praomys rostratus and P. tullbergi) in West Africa: different reactions to past forest fragmentation. Mol Ecol 2009; 17:5118-34. [PMID: 19120992 DOI: 10.1111/j.1365-294x.2008.03974.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two sibling species of the rodent genus Praomys occur in West African forests: P. tullbergi and P. rostratus. By sampling across their geographical ranges (459 individuals from 77 localities), we test the hypothesis that climatic oscillations during the Quaternary made an impact on the observed pattern of cytochrome b sequence variation. We show that, although these two species have parapatric geographical distributions, their phylogeographical histories are dissimilar, which could be related to their distinct ecological requirements. Since the arid phases of the Pleistocene were characterized by isolated forest patches, and intervening wetter periods by forest expansion, these changes in forest cover may be the common mechanism responsible for the observed phylogeographical patterns in both of these species. For example, in both species, most clades had either allopatric or parapatric geographical distributions; however, genetic diversity was much lower in P. tullbergi than in P. rostratus. The genetic pattern of P. tullbergi fits the refuge hypothesis, indicating that a very small number of populations survived in distinct forest blocks during the arid phases, then expanded again with forest recovery. In contrast, a number of populations of P. rostratus appear to have survived during the dry periods in more fragmented forest habitats, with varying levels of gene flow between these patches depending on climatic conditions and forest extent. In addition, historical variations of the West African hydrographic network could also have contributed to the pattern of genetic differentiation observed in both species.
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Affiliation(s)
- V Nicolas
- Muséum National d'Histoire Naturelle, Département de Systématique et Evolution, UMR 5202, Laboratoire Mammifères et Oiseaux, 57 rue Cuvier, CP 51, 75005 Paris, France.
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Bekhuis PDBM, De Jong CB, Prins HHT. Diet selection and density estimates of forest buffalo in Campo-Ma’an National Park, Cameroon. Afr J Ecol 2008. [DOI: 10.1111/j.1365-2028.2008.00956.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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HELLER R, LORENZEN ED, OKELLO JBA, MASEMBE C, SIEGISMUND HR. Mid-Holocene decline in African buffalos inferred from Bayesian coalescent-based analyses of microsatellites and mitochondrial DNA. Mol Ecol 2008; 17:4845-58. [DOI: 10.1111/j.1365-294x.2008.03961.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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LORENZEN ELINED, ARCTANDER PETER, SIEGISMUND HANSR. High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites. Mol Ecol 2008; 17:2812-24. [DOI: 10.1111/j.1365-294x.2008.03781.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Brown DM, Brenneman RA, Koepfli KP, Pollinger JP, Milá B, Georgiadis NJ, Louis EE, Grether GF, Jacobs DK, Wayne RK. Extensive population genetic structure in the giraffe. BMC Biol 2007; 5:57. [PMID: 18154651 PMCID: PMC2254591 DOI: 10.1186/1741-7007-5-57] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 12/21/2007] [Indexed: 12/03/2022] Open
Abstract
Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.
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Affiliation(s)
- David M Brown
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
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Wu HL, Wan QH, Fang SG. Microsatellite analysis of genetic variation and population subdivision for the black muntjac, Muntiacus crinifrons. Biochem Genet 2007; 45:775-88. [PMID: 17939033 DOI: 10.1007/s10528-007-9117-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 07/31/2007] [Indexed: 11/29/2022]
Abstract
The black muntjac (Muntiacus crinifrons) is a rare deer found only in a restricted region in east China. Recent studies of mitochondrial DNA diversity have shown a markedly low level of nucleotide diversity for the species, and the Suichang population was genetically differentiated from the two other populations, in Huangshan and Tianmushan mountains. In this study, we extended the analysis of genetic diversity and population subdivision for the black muntjac using data from 11 highly polymorphic nuclear DNA microsatellite loci. Contrary to the results based on mtDNA data, the microsatellite loci revealed that the black muntjac retained a rather high nuclear genetic diversity (overall average H (E) = 0.78). Nevertheless, both types of markers supported the idea that the extant black muntjac population is genetically disrupted (overall phi (ST) = 0.16 for mtDNA and overall F (ST) = 0.053 for microsatellite, both P < 0.001). The correlation between genetic differentiation and geographic distance was not significant (Mantel test; P > 0.05), implying that the patterns of genetic differentiation observed in this study might result from recent habitat fragmentation or loss. Based on the results from the mtDNA and nuclear DNA data sets, two management units were defined for the species, Huangshan/Tianmushan and Suichang. We also recommend that a new captive population be established with individuals from the Suichang region as a founder source.
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Affiliation(s)
- Hai-Long Wu
- College of Life Sciences, State Conservation Center for Gene Resources of Endangered Wildlife, and Key Lab. of Conservation Genetics and Reproductive Biology for Endangered Wild Animals, Ministry of Education, Zhejiang University, Hangzhou, P.R. China
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Bradshaw CJA, Isagi Y, Kaneko S, Brook BW, Bowman DMJS, Frankham R. Low genetic diversity in the bottlenecked population of endangered non-native banteng in northern Australia. Mol Ecol 2007; 16:2998-3008. [PMID: 17614913 DOI: 10.1111/j.1365-294x.2007.03365.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Undomesticated (wild) banteng are endangered in their native habitats in Southeast Asia. A potential conservation resource for the species is a large, wild population in Garig Gunak Barlu National Park in northern Australia, descended from 20 individuals that were released from a failed British outpost in 1849. Because of the founding bottleneck, we determined the level of genetic diversity in four subpopulations in the national park using 12 microsatellite loci, and compared this to the genetic diversity of domesticated Asian Bali cattle, wild banteng and other cattle species. We also compared the loss of genetic diversity using plausible genetic data coupled to a stochastic Leslie matrix model constructed from existing demographic data. The 53 Australian banteng sampled had average microsatellite heterozygosity (HE) of 28% compared to 67% for outbred Bos taurus and domesticated Bos javanicus populations. The Australian banteng inbreeding coefficient (F) of 0.58 is high compared to other endangered artiodactyl populations. The 95% confidence bounds for measured heterozygosity overlapped with those predicted from our stochastic Leslie matrix population model. Collectively, these results show that Australian banteng have suffered a loss of genetic diversity and are highly inbred because of the initial population bottleneck and subsequent small population sizes. We conclude that the Australian population is an important hedge against the complete loss of wild banteng, and it can augment threatened populations of banteng in their native range. This study indicates the genetic value of small populations of endangered artiodactyls established ex situ.
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Affiliation(s)
- Corey J A Bradshaw
- School for Environmental Research, Institute of Advanced Studies, Charles Darwin University, Darwin, NT 0909, Australia.
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Vignieri SN, Hallerman EM, Bergstrom BJ, Hafner DJ, Martin AP, Devers P, Grobler P, Hitt N. Mistaken view of taxonomic validity undermines conservation of an evolutionarily distinct mouse: a response to Ramey et al. (2005). Anim Conserv 2006. [DOI: 10.1111/j.1469-1795.2006.00038.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Harley EH, Baumgarten I, Cunningham J, O'Ryan C. Genetic variation and population structure in remnant populations of black rhinoceros, Diceros bicornis, in Africa. Mol Ecol 2005; 14:2981-90. [PMID: 16101768 DOI: 10.1111/j.1365-294x.2005.02660.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Black rhinoceros (Diceros bicornis) are one of the most endangered mammal species in Africa, with a population decline of more than 96% by the end of the last century. Habitat destruction and encroachment has resulted in fragmentation of the remaining populations. To assist in conservation management, baseline information is provided here on relative genetic diversity and population differentiation among the four remaining recognized subspecies. Using microsatellite data from nine loci and 121 black rhinoceros individuals, and comparing the results with those of other African species affected in similar ways, Diceros bicornis michaeli retained the most genetic diversity (heterozygosity 0.675) compared with Diceros bicornis minor (0.459) and Diceros bicornis bicornis (0.505), suggesting that the duration of the known bottlenecks in these populations has only had a limited impact on diversity. Comparable and moderate degrees of population differentiation were found between D. b. minor, D. b. bicornis and D. b. michaeli. Results from the single sample available of the most endangered subspecies, Diceros bicornis longipes, showed the least diversity of all individuals examined. This information should assist conservation management decisions, especially those affecting population viability assessments and selection of individuals for translocations, and will also facilitate subspecies identification for ex situ individuals of uncertain origin.
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Affiliation(s)
- Eric H Harley
- Department of Clinical Laboratory Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
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Alpers DL, Van Vuuren BJ, Arctander P, Robinson TJ. Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation. Mol Ecol 2005; 13:1771-84. [PMID: 15189202 DOI: 10.1111/j.1365-294x.2004.02204.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The roan antelope (Hippotragus equinus) is the second largest African antelope, distributed throughout the continent in sub-Saharan savannah habitat. Mitochondrial DNA (mtDNA) control region sequencing (401 bp, n = 137) and microsatellite genotyping (eight loci, n = 137) were used to quantify the genetic variability within and among 18 populations of this species. The within-population diversity was low to moderate with an average mtDNA nucleotide diversity of 1.9% and average expected heterozygosity with the microsatellites of 46%, but significant differences were found among populations with both the mtDNA and microsatellite data. Different levels of genetic resolution were found using the two marker sets, but both lent strong support for the separation of West African populations (samples from Benin, Senegal and Ghana) from the remainder of the populations studied across the African continent. Mismatch distribution analyses revealed possible past refugia for roan in the west and east of Africa. The West African populations could be recognized together as an evolutionarily significant unit (ESU), referable to the subspecies H. e. koba. Samples from the rest of the continent constituted a geographically more diverse assemblage with genetic associations not strictly corresponding to the other recognized subspecies.
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Affiliation(s)
- D L Alpers
- Department of Zoology, University of Stellenbosch, Private Bag XI, Matieland 7602, South Africa
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Eggert LS, Rasner CA, Woodruff DS. The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers. Proc Biol Sci 2002; 269:1993-2006. [PMID: 12396498 PMCID: PMC1691127 DOI: 10.1098/rspb.2002.2070] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.
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Affiliation(s)
- Lori S Eggert
- Section of Ecology, Behavior and Evolution, Division of Biology, University of California, San Diego, La Jolla, CA 92093-0116, USA.
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Larson S, Jameson R, Etnier M, Fleming M, Bentzen P. Loss of genetic diversity in sea otters (Enhydra lutris) associated with the fur trade of the 18th and 19th centuries. Mol Ecol 2002; 11:1899-903. [PMID: 12296934 DOI: 10.1046/j.1365-294x.2002.01599.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sea otter (Enhydra lutris) populations experienced widespread reduction and extirpation due to the fur trade of the 18th and 19th centuries. We examined genetic variation within four microsatellite markers and the mitochondrial DNA (mtDNA) d-loop in one prefur trade population and compared it to five modern populations to determine potential losses in genetic variation. While mtDNA sequence variability was low within both modern and extinct populations, analysis of microsatellite allelic data revealed that the prefur trade population had significantly more variation than all the extant sea otter populations. Reduced genetic variation may lead to inbreeding depression and we believe sea otter populations should be closely monitored for potential associated negative effects.
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Affiliation(s)
- Shawn Larson
- The Seattle Aquarium, 1483 Alaskan Way, Pier 59, Seattle, WA 98101, USA.
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Larson S, Jameson R, Bodkin J, Staedler M, Bentzen P. MICROSATELLITE DNA AND MITOCHONDRIAL DNA VARIATION IN REMNANT AND TRANSLOCATED SEA OTTER (ENHYDRA LUTRIS) POPULATIONS. J Mammal 2002. [DOI: 10.1644/1545-1542(2002)083<0893:mdamdv>2.0.co;2] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Van Hooft WF, Groen AF, Prins HHT. Phylogeography of the African buffalo based on mitochondrial and Y-chromosomal loci: Pleistocene origin and population expansion of the Cape buffalo subspecies. Mol Ecol 2002; 11:267-79. [PMID: 11856427 DOI: 10.1046/j.1365-294x.2002.01429.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Population genetics and phylogeography of the African buffalo (Syncerus caffer) are inferred from genetic diversity at mitochondrial D-loop hypervariable region I sequences and a Y-chromosomal microsatellite. Three buffalo subspecies from different parts of Africa are included. Nucleotide diversity of the subspecies Cape buffalo at hypervariable region I is high, with little differentiation between populations. A mutation rate of 13-18% substitutions/million years is estimated for hypervariable region I. The nucleotide diversity indicates an estimated female effective population size of 17 000-32 000 individuals. Both mitochondrial and Y-chromosomal diversity are considerably higher in buffalo from central and southwestern Africa than in Cape buffalo, for which several explanations are hypothesized. There are several indications that there was a late middle to late Pleistocene population expansion in Cape buffalo. This also seems to be the period in which Cape buffalo evolved as a separate subspecies, according to the net sequence divergence with the other subspecies. These two observations are in agreement with the hypothesis of a rapid evolution of Cape buffalo based on fossil data. Additionally, there appears to have been a population expansion from eastern to southern Africa, which may be related to vegetation changes. However, as alternative explanations are also possible, further analyses with autosomal loci are needed.
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Affiliation(s)
- W F Van Hooft
- Wageningen University, Department of Environmental Sciences, Tropical Nature Conservation and Vertebrate Ecology Group, Bornsesteeg 69, 6708 PD Wageningen, The Netherlands.
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