Smitz, Nathalie ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Berthouly, C.; Centre de Coopération Internationale en Recherche Agronomique pour le Developpement (CIRAD), Campus International de Baillarguet, Montferrier-le-Lez, France
Cornélis, D.; Centre de Coopération Internationale en Recherche Agronomique pour le Developpement (CIRAD), Campus International de Baillarguet, Montferrier-le-Lez, France
Heller, R.; Department of Biology- Bioinformatics, University of Copenhagen, Copenhagen, Denmark
van Hooft, P.; Resource Ecology Group, Wageningen University, Wageningen, Netherlands
Chardonnet, P.; International Foundation for the Conservation of Wildlife (IGF), Paris, France
Caron, A.; Centre de Coopération Internationale en Recherche Agronomique pour le Developpement (CIRAD), Campus International de Baillarguet, Montferrier-le-Lez, France, Department Environment and Societies, Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), University of Zimbabwe, Harare, Zimbabwe, Department of Zoology and Entomology- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
Arctander P, Johansen C, Coutellec-Vreto MA, (1999) Phylogeography of three closely related African bovids (tribe Alcelaphini). Mol Biol Evol 16: 1724-1739.
Muwanika VB, Nyakaana S, Siegismund HR, Arctander P, (2003) Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci. Heredity 91: 361-372.
Nersting LG, Arctander P, (2001) Phylogeography and conservation of impala and greater kudu. Mol Ecol 10: 711-719.
Girman DJ, Kat PW, Mills MGL, Ginsberg JR, Borner M, et al. (1993) Molecular genetic and morphological analyses of the African wild dog (Lycaon pictus). J Hered 84: 450-459.
Marsden CD, Woodroffe R, Mills MGL, McNutt JW, Creel S, et al. (2012) Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus). Mol Ecol. doi:10.1111/j.1365-294X.2012.05477.x.
Birungi J, Arctander P, (2000) Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the African antelope, kob (Kobus kob). Mol Ecol 9: 1997-2008.
Lorenzen ED, De Neergaard R, Arctander P, Siegismund HR, (2007) Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob). Mol Ecol 16: 3241-3252.
Bertola LD, van Hooft WF, Vrieling K, Uit de Weerd DR, York DS, et al. (2011) Genetic diversity, evolutionary history and implications for conservation of the lion (Panthera leo) in West and Central Africa. J Biogeogr 38(7): 1356-1367 doi:10.1111/j.1365-2699.2011.02500.x.
Alpers DL, Jansen van Vuuren B, Arctander P, Robinson TJ, (2004) Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation. Mol Ecol 13: 1771-1784.
Lorenzen ED, Simonsen BT, Kat PW, Arctander P, Siegismund HR, (2006) Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression. Mol Ecol 15: 3787-3799 doi: 10.1111/j.1365-294X.2006.03059.x.
Nyakaana S, Arctander P, Siegismund HR, (2002) Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci. Heredity 89: 90-98.
Moodley Y, Bruford MW, (2007) Molecular Biogeography: Towards an Integrated Framework for Conserving Pan-African Biodiversity. PLoS ONE (5): e454.
Lorenzen ED, Arctander P, Siegismund HR, (2006) Regional genetic structuring and evolutionary history of the Impala Aepyceros melampus. J Heredity 97: 119-132.
Pitra C, Hansen AJ, Lieckfeldt D, Arctander P, (2002) An exceptional case of historical outbreeding in African sable antelope populations. Mol Ecol 11: 1197-1208.
Pitra C, VazPinto P, O'Keeffe BWJ, Willows-Munro S, Jansen Van Vuuren B, et al. (2006) DNA-led rediscovery of the giant sable antelope in Angola. Eur J Wildlife Res 52: 145-152.
Jansen van Vuuren B, Robinson TJ, VazPinto P, Estes R, Matthee CA, (2010) Western Zambian sable: are they a geographic extension of the giant sable antelope? S Afr J Wildl Res 40: 35-42.
Flagstad O, Syvertsen P, Stenseth N, Jakobsen K, (2001) Environmental change and rates of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation. Proc R Soc Lond B 268: 667-677 doi: 10.1098/rspb.2000.1416.
Hewitt GM, (2004) The structure of biodiversity - insights from molecular phylogeography. Front Zool 1: 4.
Lorenzen ED, Siegismund HR, (2004) No suggestion of hybridization between the vulnerable black-faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia. Mol Ecol 13: 3007-3019.
Prins HHT (1996) Ecology and Behaviour of the African Buffalo: Social Inequality and Decision Making. Wildlife Ecology and Behaviour Series Vol. 1. London: Chapman & Hall.
Melletti M, Penteriani V, Mirabile M, Boitani L, (2007) Some behavioral aspects of forest buffalo (Syncerus caffer nanus): from herd to individual. J Mammal 88: 1312-1318.
Bekhuis PDBM, de Jong CB, Prins HHT, (2008) Diet selection and density estimates of forest buffalo in Campo-Ma'an National Park, Cameroon. Afr J Ecol 46: 668-675.
Corson PJ (2002) Le buffle d'Afrique: biologie, chasse et mythologie. France: Du Gerfaut. 263 p.
Wilson DE, Reeder DAM (2005) Mammal species of the world: a taxonomic and geographic reference. Baltimore: Johns Hopkins University Press. 2142 p.
Kingdon J (1997) The Kingdon Field Guide to African Mammals. London and New York: Academic Press, Natural World. 450 p.
East R (1998) African antelope database. Gland: IUCN/SSC Antelope Specialist Group.
Fritz H, (1997) Low ungulate biomass in West African savannas: primary production or missing megaherbivores or large predator species? Ecography 20: 417-421.
Stark MA, (1986) Daily movement, grazing activity and diet of savanna buffalo, Syncerus caffer brachyceros, in Benoue National Park, Cameroon. Afr J Ecol 24: 255-262.
Cribiu EP, Popescu CP, (1980) Chromosome constitution of a hybrid between East African buffalo (Syncerus caffer caffer) and dwarf forest buffalo (Syncerus caffer nanus). Ann Genet Sel Anim 12: 291-293.
Hsu TC, Benirschke K (1970) An Atlas of Mammalian Chromosomes. Vol. 4, Folio 192. New York: Springer-Verlag.
Templeton AR, Georgiadis NJ (1996) A landscape approach to conservation genetics: conserving evolutionary processes in the African bovidae. In: Avise JC, Hamrick JL, editors. Conservation Genetics: Case Histories from Nature. New York: Chapman & Hall.
O'Ryan C, Harley EH, Bruford MW, Beaumont M, Wayne RK, et al. (1998) Microsatellite analysis of genetic diversity in fragmented South African buffalo populations. Animal Conserv 1: 85-94.
Simonsen BT, Siegismund HR, Arctander P, (1998) Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation. Mol Ecol 7: 225-237.
Van Hooft WF, Groen AF, Prins HHT, (2000) Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa. Mol Ecol 9: 2017-2025.
Van Hooft WF, Groen AF, Prins HT, (2002) Phylogeography of the African buffalo based on mitochondrial and Y-chromosomal loci: Pleistocene origin and population expansion of the Cape buffalo subspecies. Mol Ecol 11: 267-279.
Van Hooft WF, Groen AF, Prins HHT, (2003) Genetic structure of African buffalo herds based on variation at the mitochondrial D-loop and autosomal microsatellite loci: evidence for male-biased gene flow. Conserv Genet 4: 467-477.
Van Hooft P, Greyling BJ, Prins HHT, Getz WM, Jolles AE, et al. (2007) Selection at the Y chromosome of the African buffalo driven by rainfall. PLoS ONE 10.
Van Hooft WF, Prins HHT, Getz WM, Jolles AE, Van Wieren SE, et al. (2010) Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio. BMC Evol Biol 10.
Greyling BJ, Kryger P, du Plessis S, Van Hooft WF, Van Helden P, et al. (2008) Development of a high-throughput microsatellite typing approach for forensic and population genetic analysis of wild and domestic African Bovini. Afr J Biotechnol 7; 655-660.
Wenink PW, Groen AF, Roelke-Parker ME, Prins HHT, (1998) African buffalo maintain high genetic diversity in the major histocompatibility complex in spite of historically known population bottlenecks. Mol Ecol 7: 1315-1322.
Heller R, Lorenzen ED, Okello JBA, Masembe C, Siegismund HR, (2008) Mid-Holocene decline in African buffalos inferred from Bayesian coalescent-based analyses of microsatellites and mitochondrial DNA. Mol Ecol 17: 4845-4858.
Heller R, Okello JBA, Siegismund HR, (2010) 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 19: 1324-1334.
Aquadro CF, Greenberg BD, (1983) Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences for seven individuals. Genetics 103: 287-312.
Groves CP, Grubb P (2011) Ungulate taxonomy. Baltimore: Johns Hopkins University Press.
Grubb P, (1972) Variation and incipient speciation in the African buffalo. Zeitschrift für Säugetierkunde 37: 121-144.
Dettman JR, Sirjusingh C, Kohn LM, Anderson JB, (2007) Incipient speciation by divergent adaptation and antagonistic epistasis in Yeast. Nature 447: 585-588.
Villagomez DAF, Pinton A, (2008) Chromosomal abnormalities, meiotic behavior and fertility in domestic animals. Cytogenet Genome Res 120: 69-80.
Fang M, Berg F, Ducos A, Andersson L, (2006) Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38. Anim Genet 37: 459-464.
Kingdon J (1982) East African Mammals, an Atlas of Evolution in Africa. Vol. III, Part C (Bovids). London: Academic Press.
Sinclair ARE (1977) The African buffalo: a study of resource limitation of populations. Chicago: University of Chicago Press.
Nyakaana S, Arctander P, (1999) Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow. Mol Ecol 8: 1105-1115.
Simonsen BT (1997) Population Structure and History of African Bovids. PhD Thesis. Department of Population Biology, Zoological Institute, University of Copenhagen.
Arctander P, Kat PW, Aman RA, Siegismund H, (1996) Extreme genetic variations between populations of Grants gazelle (Gazella granti) in Kenya. Heredity 76: 465-475.
Arctander P, Kat PW, Simonsen BT, Siegismund HR (1996) Population genetics of Kenyan impalas - consequences for conservation. In: Wayne RK, Smith TB, editors. Molecular Genetics in Conservation. Oxford: Oxford University Press.
Korte LM, (2008) Habitat selection at two spatial scales and diurnal activity patterns of adult female forest buffalo. J Mammal 89: 115-125.
Korte LM, (2008) Variation of group size among African buffalo herds in a forest-savanna mosaic landscape. J Zool 275: 229-236.
Gentry AW (1978) Bovidae. In: Maglioi VJ, Cooke HBS, editors. Evolution of African Mammals. Cambridge: Harvard University Press. 540-572.
Finlay EK, Gaillard C, Vahidi SMF, Mirhoseini SZ, Jianlin H, et al. (2007) Bayesian inference of population expansions in domestic bovines. Biol Lett 3: 449-452.
Heller R, Bruniche-Olsen A, Siegismund HR, (2012) Cape buffalo mitogenomics reveals a Holocene shift in the African human-megafauna dynamics. Mol Ecol 21: 3947-3959.
Cohen AS, Stone JR, Beuning KRM, Park LE, Reinthal PN, et al. (2007) Ecological consequences of early Late Pleistocene megadroughts in tropical Africa. PNAS 1-6. doi:10.1073/pnas.0703873104.
Vrba ES, (1992) Mammals as a key to evolutionary theory. J Mammal 73: 1-28.
Endler JA (1977) Geographic Variation, Speciation, and Clines. Princeton, New Jersey: Princeton University Press.
Klein RG, (1988) The archaeological significance of animal bones from Acheulean sites in Southern Africa. Afr Archaeol Rev 6: 3-25.
Klein RG (1995) Mammalian extinctions and Stone Age people in Africa. In: Martin PS, Klein RG, editors. Quaternary Extinctions: a Prehistoric Revolution. Tucson, London: The University of Arizona Press. 553-573.
Porat N, Chazan M, Grun R, Aubert M, Eisenmann V, et al. (2010) New radiometric ages for the Fauresmith industry from Kathu Pan, Southern Africa: implications for the Earlier to Middle Stone Age transition. J Archaeol Sci 37: 269-283 doi: 10.1016/j.jas.2009.09.038.
deMenocal PB, (2004) African climate change and faunal evolution during the Pliocene-Pleistocene. Earth Planet Sc Lett 220: 3-24.
Dupont LM, Agwu COC, (1992) Latitudinal shifts of forest and savanna in NW Africa during the Brunhes chron: further marine palynological results from site M 16145 (9oN, 19oW). Veg Hist Archaeobot 1: 163-175.
Dupont LM, Jahns S, Marret F, Ning S, (2000) Vegetation change in equatorial West Africa: time-slices for the last 150 ka. Palaeogeogr Palaeocl 155: 95-122.
Groves CP, (1992) How old are subspecies? A tiger's eye view of human evolution. Perspect Hum Biol 2: 153-160.
Moritz C, (1994) Defining 'evolutionary significant units' for conservation. Trends Ecol Evol 9: 373-375.
Nowak RM (1991) Walker's Mammals of the World (Fifth Edition). Baltimore: The Johns Hopkins University Press.
Alden PC, Estes RD, Schlitter D, McBride B (1995) National Audubon Society Field Guide to African Wildlife. New York: Chanticleer Press.
Buchholtz C, (1990) Cattle. In: Parker, SP, editor. Grzimek's Encyclopedia of Mammals. New York: McGraw-Hill. 5: 360-417.
Brown DM, Brenneman RA, Koepfli KP, Pollinger JP, Mila B, et al. (2007) Extensive population genetic structure in the giraffe. BMC Biol 5: 13.
Eriksson J, Hohmann G, Boesch C, Vigilant L, (2004) Rivers influence the population genetic structure of bonobos (Pan paniscus). Mol Ecol 13: 3425-3435.
Okello JBA, Nyakaana S, Masembe C, Siegismund HR, Arctander P, (2005) Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion. Heredity 95: 206-215.
Kraus RH, van Hooft P, Waldenström J, Latorre-Margalef N, Ydenberg RC, et al. (2009) Avian influenza surveillance: on the usability of FTA® cards to solve biosafety and transport issues. Wildfowl Special Issue 2: 215-223.
Kraus RH, van Hooft P, Waldenström J, Latorre-Margalef N, Ydenberg RC, et al. (2011) Avian influenza surveillance with FTA® cards: field methods, biosafety and transport issues solved. J Vis Exp 54: 21847074.
Douzery E, Randi E, (1997) The mitochondrial control region of Cervidae: Evolutionary patterns and phylogenetic content. Mol Biol Evol 14(11): 1154-1166.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins D, (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality tools. Nucl Acids Res 25: 4876-4882.
Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid S 41: 95-98.
Technelysium website. Chromas available: http://www.Technelysium.com.au/chromas.html. Accessed 2013 Jan 21.
Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C, (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205: 125-140 DOI:10.1016/S0378-1119(97)00404-6.
Joly S, Stevens MI, Jansen van Vuuren B, (2007) Haplotype networks can be misleading in the presence of missing data. Syst Biol 56: 857-862.
Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN: a software for population genetics data analysis, Version 2.000. Geneva: Genetics and Biometry Laboratory.
Crandall KA, Templeton AR, (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134: 959-969.
Excoffier L, Laval G, Schneider S, (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform 1: 47-50.
Nei M (1987) Molecular Evolutionary Genetics. New York: Columbia University Press.
Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Rogers AR, Harpending H, (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9: 552-569.
Rogers AR, (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49: 608-615.
Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus P, et al. (2004) Rise and fall of the Beringian steppe bison. Science 306: 1561-1565.
Fu XY, (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
Drummond AJ, Rambaut A, (2007) Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214 doi: 10.1186/1471-2148-7-214.
Lemey P, Rambaut A, Drummond AJ, Suchard MA, (2009) Bayesian phylogeography finds its roots. PloS Comput Biol 5: e1000520.
Akaike H, (1974) A new look at the statistical model identification. IEEE T Automat Contr 19: 716-723.
Hasewaga M, Kishino H, Yano T, (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
Hey J, (2005) On the number of New World founders: a population genetic portrait of the peopling of the Americas. PloS Biol 3: 965-975.
Hey J, Nielsen R, (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D-persimilis. Genetics 167: 747-760.