• Please log in or register to access this feature.

INVITED REVIEWS AND META-ANALYSES

You have free access to this content

Comparative phylogeography of African savannah ungulates†

  1. E. D. LORENZEN1,2,
  2. R. HELLER3,
  3. H. R. SIEGISMUND3

Article first published online: 15 JUN 2012

DOI: 10.1111/j.1365-294X.2012.05650.x

Issue

Molecular Ecology

Molecular Ecology

Volume 21, Issue 15, pages 3656–3670, August 2012

Additional Information

How to Cite

LORENZEN, E. D., HELLER, R. and SIEGISMUND, H. R. (2012), Comparative phylogeography of African savannah ungulates. Molecular Ecology, 21: 3656–3670. doi: 10.1111/j.1365-294X.2012.05650.x

Author Information

  1. 1

    Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA

  2. 2

    Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen K, Denmark

  3. 3

    Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark

*Eline D. Lorenzen, Fax: +1 (510) 643 6264; E-mail: elinelorenzen@gmail.com

  1. †

    This manuscript is dedicated to our friend and colleague Peter Arctander, who retired from his position as professor at the Department of Biology, University of Copenhagen, in 2011. Peter initiated DNA laboratories in Copenhagen and at Makerere University, Uganda, which is still very active today. He pioneered phylogeographic research on African ungulates, devoting so much effort to developing the infrastructure necessary to achieve many of the studies that form the basis of this review; his major contributions to the field will be appreciated for many years.

Publication History

  1. Issue published online: 17 JUL 2012
  2. Article first published online: 15 JUN 2012
  3. Received 3 February 2012; revision received 5 April 2012; accepted 18 April 2012

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article (HTML) Get PDF (1486K)

References

  • Alpers DL, van Vuuren BJ, Arctander P, Robinson TJ (2004) Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation. Molecular Ecology, 13, 1771–1784.
    Direct Link:
  • Arctander P, Johansen C, Coutellec-Vreto MA (1999) Phylogeography of three closely related African bovids (tribe Alcelaphini). Molecular Biology and Evolution, 16, 1724–1739.
  • Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, Massachusetts.
  • Barnett R, Yamaguchi N, Barnes I, Cooper A (2006) The origin, current diversity and future conservation of the modern lion (Panthera leo). Proceedings of the Royal Society of Biological Sciences, 273, 2119–2125.
  • 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). Molecular Ecology, 9, 1997–2008.
    Direct Link:
  • Bobe R, Behrensmeyer AK (2004) The expansion of grassland ecosystems in Africa in relation to mammalian evolution and the origin of the genus Homo. Palaeogeography, Palaeoclimatology, Palaeoecology, 207, 399–420.
  • Bobe R, Behrensmeyer AK, Chapman RE (2002) Faunal change, environmental variability and late Pliocene hominin evolution. Journal of Human Evolution, 42, 475–497.
  • Brouat C, Tatard C, Bâ K et al. (2009) Phylogeography of the Guinea multimammate mouse (Mastomys erythroleucus): a case study for Sahelian species in West Africa. Journal of Biogeography, 36, 2237–2250.
    Direct Link:
  • Brown DM, Brenneman RA, Koepfli KP et al. (2007) Extensive population genetic structure in the giraffe. BMC Biology, 5, 57, doi:10.1186/1741-7007-5-57.
  • Campos PF, Willerslev E, Sher A et al. (2010) Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proceedings of the National Academy of Sciences of the United States of America, 107, 5675–5680.
  • Castiglia R, Solano E, Makundi RH, Hulselmans J, Verheyen E, Colangelo P (2012) Rapid chromosomal evolution in the mesic four-striped grass rat Rhabdomys dilectus (Rodentia, Muridae) revealed by mtDNA phylogeographic analysis. Journal of Zoological Systematics and Evolutionary Research, 50, 165–172.
    Direct Link:
  • Charruau P, Fernandes C (2011) Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates. Molecular Ecology, 20, 706–724.
    Direct Link:
  • Christy C (1924) Big game and pygmies. MacMillan, London.
  • Cordingley JE, Sundaresan SR, Fischhoff IR, Shapiro B, Ruskey J, Rubenstein DI (2009) Is the endangered Grevy’s zebra threatened by hybridization? Animal Conservation, 12, 505–513.
    Direct Link:
  • Cowling SA, Cox PM, Jones CD, Maslin MA, Peros M, Spall SA (2008) Simulated glacial and interglacial vegetation across Africa: implications for species phylogenies and trans – African migration of plants and animals. Global Change Biology, 14, 827–840.
    Direct Link:
  • Debruyne R, Chu G, King CE et al. (2008) Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Current Biology, 18, 1320–1326.
  • Dehghani R, Wanntorp L, Pagani P, Källersjö M, Werdelin L, Veron G (2008) Phylogeography of the white-tailed mongoose (Herpestidae, Carnivora, Mammalia) based on partial sequences of the mtDNA control region. Journal of Zoology, 276, 385–393.
    Direct Link:
  • Dupont LM (2011) Orbital scale vegetation change in Africa. Quaternary Science Reviews, 30, 3589–3602.
  • Edwards SV, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839–1854.
  • Edwards EJ, Osborne CP, Strömberg CAE et al. (2010) The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science, 328, 587–591.
  • Emslie R, Brooks M (2002) How many southern white rhinos were there? A response to Kees Rookmaaker. Pachyderm, 33, 100–101.
  • Estes RD (1991) The behaviour guide to African mammals; including hoofed mammals, carnivores, primates. The University of California Press, Berkeley.
  • Feakins SJ, deMenocal PB, Eglinton TI (2005) Biomarker records of late Neogene changes in northeast African vegetation. Geology, 33, 977.
  • Fernández MH, Vrba ES (2005) A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biological Reviews of the Cambridge Philosophical Society, 80, 269–302.
    Direct Link:
  • Flagstad O, Syversten PO, Stenseth NC, Jakobsen KS (2001) Environmental change and rates of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation. Proceedings of the Royal Society of Biology, 268, 667–677.
  • Fuchs J, Crowe TM, Bowie RCK (2011) Phylogeography of the fiscal shrike (Lanius collaris): a novel pattern of genetic structure across the arid zones and savannas of Africa. Journal of Biogeography, 38, 2210–2222.
    Direct Link:
  • Gentry AW (1992) The subfamilies and tribes of the family Bovidae. Mammal Review, 22, 1–32.
    Direct Link:
  • Groves C, Grubb P (2011) Ungulate taxonomy. Johns Hopkins University Press, Baltimore, Maryland.
  • Haffer J (1969) Speciation in Amazonian forest birds. Science, 165, 131–137.
  • 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. Molecular Ecology, 17, 4845–4858.
    Direct Link:
  • Ho SYW, Larson G (2006) Molecular clocks: when times are a-changin’. Trends in Genetics, 22, 79–83.
  • Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B (2008) The effect of inappropriate calibration: three case studies in molecular ecology. PLoS ONE, 3, e1615.
  • Ishida Y, Oleksyk TK, Georgiadis NJ et al. (2011) Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants. PLoS ONE, 6, e20642.
  • IUCN (2011) IUCN Red List of Threatened Species. Version 2011.2. http://www.iucnredlist.org. accessed 26 January 2012.
  • Kappelman J, Plummer T, Bishop L, Duncan A, Appleton S (1997) Bovids as indicators of Plio-Pleistocene paleoenvironments in east Africa. Journal of Human Evolution, 32, 229–256.
  • Kingdon J (1997) The Kingdon field guide to African mammals. pp. 447–454. A&C Black Publishers, London.
  • Lehmann CER, Archibald SA, Hoffmann WA, Bond WJ (2011) Deciphering the distribution of the savanna biome. New Phytologist, 191, 197–209.
    Direct Link:
  • Lorenzen E, 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. Molecular Ecology, 13, 3007–3019.
    Direct Link:
  • Lorenzen ED, Arctander P, Siegismund HR (2006a) Regional genetic structuring and evolutionary history of the impala Aepyceros melampus. Journal of Heredity, 97, 119–132.
  • Lorenzen ED, Simonsen BT, Kat PW, Arctander P, Siegismund HR (2006b) Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression. Molecular Ecology, 15, 3787–3799.
    Direct Link:
  • Lorenzen ED, De Neergaard R, Arctander P, Siegismund HR (2007a) Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob). Molecular Ecology, 16, 3241–3252.
    Direct Link:
  • Lorenzen ED, Arctander P, Siegismund HR (2007b) Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant’s gazelles. Conservation Genetics, 9, 593–601.
  • Lorenzen ED, Arctander P, Siegismund HR (2008) High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites. Molecular Ecology, 17, 2812–2824.
    Direct Link:
  • Lorenzen ED, Masembe C, Arctander P, Siegismund HR (2010) A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope. Journal of Biogeography, 37, 571–581.
    Direct Link:
  • Lorenzen ED, Nogués-Bravo D, Orlando L et al. (2011) Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479, 359–365.
  • Maggs GL, Craven P, Kolberg HH (1998) Plant species richness, endemism, and genetic resources in Namibia. Biodiversity and Conservation, 7, 435–446.
  • Marsden CD, Woodroffe R, Mills MGL et al. (2012) Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus). Molecular Ecology, 21, 1379–1393.
    Direct Link:
  • Masembe C, Muwanika VB, Nyakaana S, Arctander P, Siegismund HR (2006) Three genetically divergent lineages of the Oryx in eastern Africa: evidence for an ancient introgressive hybridization. Conservation Genetics, 7, 551–562.
  • Maslin M (2007) Tectonics, orbital forcing, global climate change, and human evolution in Africa: introduction to the African paleoclimate special volume. Journal of Human Evolution, 53, 2484–2498.
  • Maslin M, Pancost RD, Wilson KE, Lewis J, Trauth MH (2012) Three and half million year history of moisture availability of South West Africa: evidence from ODP Site 1085 biomarker records. Palaeogeography, 317–318, 41–47.
  • Mathee CA, Robinson TJ (1999) Mitochondrial DNA population structure of roan and sable antelope: implications for the translocation and conservation of the species. Molecular Ecology, 8, 227–238.
    Direct Link:
  • Mayaux P, Bartholomé E, Fritz S, Belward A (2004) A new land-cover map of Africa for the year 2000. Journal of Biogeography, 31, 861–877.
    Direct Link:
  • deMenocal PB (1995) Plio-Pleistocene African climate. Science, 270, 53–59.
  • deMenocal PB (2004) African climate change and faunal evolution during the Pliocene-Pleistocene. Earth and Planetary Science Letters, 220, 3–24.
  • Miller JM, Hallager S, Monfort SL et al. (2010) Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus). Conservation Genetics, 12, 423–431.
  • Moodley Y, Bruford MW (2007) Molecular biogeography: towards an integrated framework for conserving pan-African biodiversity. PLoS ONE, 2, e454.
  • Moodley Y, Harley EH (2005) Population structuring in mountain zebra (Equus zebra): the molecular consequences of divergent demographic histories. Conservation Genetics, 6, 953–968.
  • Moodley Y, Bruford MW, Bleidorn C, Wronski T, Apio A, Plath M (2009) Analysis of mitochondrial DNA data reveals non-monophyly in the bushbuck (Tragelaphus scriptus) complex. Mammalian Biology, 74, 418–422.
  • Moritz C (1998) Comparative phylogeography: concepts and applications. Molecular Ecology, 7, 67–69.
  • 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. Molecular Ecology, 10, 711–719.
    Direct Link:
  • Ogutu JO, Piepho HP, Dublin HT, Bhola N, Reid RS (2008) Rainfall influences on ungulate population abundance in the Mara-Serengeti ecosystem. Journal of Animal Ecology, 77, 814–829.
    Direct Link:
  • 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.
  • Okello JBA, Wittemeyer G, Rasmussen HB et al. (2008) Effective population size dynamics reveal impacts of historic climate events and recent anthropogenic pressure in African elephants. Molecular Ecology, 17, 3788–3799.
    Direct Link:
  • Osmers B, Petersen BS, Hartl GB, Grobler JP, Kotze A, van Aswegen E (2011) Genetic analysis of southern African gemsbok (Oryx gazella) reveals high variability, distinct lineages and strong divergence from the East African Oryx beisa. Mammalian Biology, 77, 60–66.
  • Ouma C, Roca A, Were T, Raballah E (2010) Genetic structure of hartebeest populations straddling a transition zone between morphotypes. Journal of Basic and Applied Scientific Research, 1, 131–149.
  • Owen-Smith N, Cumming DHM (1993) Comparative foraging strategies of grazing ungulates in African savanna grasslands. Proceedings of the XVII International Grasslands Congress, 8–21 February 1993, New Zealand Grassland Association, pp. 691–698. Palmerston North, New Zealand.
  • Pitra C, Hansen AJ, Lieckfeldt D, Arctander P (2002) An exceptional case of historical outbreeding in African sable antelope populations. Molecular Ecology, 11, 1197–1208.
    Direct Link:
  • Pitra C, Vaz Pinto P, O’Keeffe BWJ, Willows-Munro S, van Vuuren BJ, Robinson TJ (2006) DNA-led rediscovery of the giant sable antelope in Angola. European Journal of Wildlife Resources, 52, 145–152.
  • Quinn RL, Lepre CJ, Wright JD, Feibel CS (2007) Paleogeographic variations of pedogenic carbonate delta13C values from Koobi Fora, Kenya: implications for floral compositions of Plio-Pleistocene hominin environments. Journal of Human Evolution, 53, 560–573.
  • Ramakrishnan U, Hadly EA (2009) Using phylochronology to reveal cryptic population histories. Molecular Ecology, 18, 1310–1330.
    Direct Link:
  • Rambaut A (2000) Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics, 16, 395–399.
  • Remington CL (1968) Suture-zones of hybrid interaction between recently joined biotas. In: Evolutionary biology (eds Dobzhansky T, Hecht MK and Steere CW), pp. 321–428. Plenum Press, New York, New York.
  • Reynolds SC (2007) Mammalian body size changes and Plio-Pleistocene environmental shifts: implications for understanding hominin evolution in eastern and southern Africa. Journal of Human Evolution, 53, 528–548.
  • Reynolds SC (2010). Morphological evaluation of genetic evidence for a Pleistocene extirpation of eastern African impala. South African Journal of Science, 106, 11–12.
  • Riginos C, Grace JB (2008) Savanna tree density, herbivores, and the herbaceous community: bottom-up vs. top-down effects. Ecology, 89, 2228–2238.
  • Rohland N, Pollack JL, Nagel D et al. (2005) The population history of extant and extinct hyenas. Molecular Biology and Evolution, 22, 2435–2443.
  • Ruxton AE, Schwarz E (1929) On hybrid hartebeests and on the distribution of Alcelaphus buselaphus. Proceedings of the Zoological Society of London, 1929, 567–583.
  • Sezonlin M, Dupas S, le Rü B et al. (2006) Phylogeography and population genetics of the maize stalk borer Busseola fusca (Lepidoptera, Noctuidae) in sub-Saharan Africa. Molecular Ecology, 15, 407–420.
    Direct Link:
  • Shafer ABA, Cullingham CI, Côté SD, Coltman DW (2010) Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Molecular Ecology, 19, 4589–4621.
    Direct Link:
  • Simpson GG (1945) Principles of classification and a classification of mammals. Bulletin of the American Museum of Natural History, 85, 1–350.
  • Smith CI, Chamberlain AT, Riley MS, Stringer C, Collins MJ (2003) The thermal history of human fossils and the likelihood of successful DNA amplification. Journal of Human Evolution, 45, 203–217.
  • Smith N, Berthouly C, Cornelis D, Heller R, Van Hooft WF, Chardonnet P, Caron A, Prins HHT, Jansen van Vuuren B, de Long HH, Michaux JR. (in press) Pan-African genetic structure in the African buffalo (Syncerus caffer): investgating sub-species divergence. PLoS ONE.
  • Staver AC, Archibald S, Levin S (2011) Tree cover in sub-Saharan Africa: rainfall and fire constrain forest and savanna as alternative stable states. Ecology, 92, 1063–1072.
  • Szabo B, Haynes C, Maxwell TA (1995) Ages of Quaternary pluvial episodes determined by uranium-series and radiocarbon dating of lacustrine deposits of Eastern Sahara. Palaeogeography, Palaeoclimatology, Palaeoecology, 113, 227–242.
  • du Toit JT, Cumming DHM (1999) Functional significance of ungulate diversity in African savannas and the ecological implications of the spread of pastoralism. Biodiversity and Conservation, 8, 1643–1661.
  • Trauth MH, Maslin MA, Deino AL, Strecker MR, Bergner AGN, Dünforth M (2007) High- and low-latitude forcing of Plio-Pleistocene East African climate and human evolution. Journal of Human Evolution, 53, 475–486.
  • Trauth M, Larrasoaña J, Mudelsee M (2009) Trends, rhythms and events in Plio-Pleistocene African climate. Quaternary Science Reviews, 28, 399–411.
  • Van Hooft WF, Groen AF, Prins HHT (2000) Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa. Molecular Ecology, 9, 2017–2025.
    Direct Link:
  • Van Hooft WF, Groen AF, Prins HHT (2002) Phylogeography of the African buffalo based on mitochondrial and Y-chromosomal loci: pleistocene origin and population expansion of the Cape buffalo subspecies. Molecular Ecology, 11, 267–279.
    Direct Link:
  • Van Vuuren BJ, Robinson TJ (2001) Retrieval of Four Adaptive Lineages in Duiker Antelope: evidence from Mitochondrial DNA Sequences and Fluorescence Hybridization. Molecular Phylogenetics and Evolution, 20, 409–425.
  • Vasconcelos R, Froufe E, Brito JC, Carranza S, Harris DJ (2010) Phylogeography of the African common toad, Amietophrynus regularis, based on mitochondrial DNA sequences: inferences regarding the Cape Verde population and biogeographical patterns. African Zoology, 45, 291–298.
  • de Vivo M, Carmignotto AP (2004) Holocene vegetation change and the mammal faunas of South America and Africa. Journal of Biogeography, 31, 943–957.
    Direct Link:
  • Vrba ES (1995) The fossil record of African antelopes (Mammalia, Bovidae) in relation to human evolution and paleoclimate. In: Paleoclimate and evolution (eds Vrba ES, Denton GH, Partridge TC and Burckle LH), pp. 385–424. Yale University Press, New Haven, Connecticut.
  • Wichman HA, Payne CT, Ryder OA, Hamilton MJ, Maltbie M, Baker RJ (1991) Genomic distribution of heterochromatic sequences in equids: implications to rapid chromosomal evolution. The Journal of Heredity, 82, 369–377.
  • Wilson DE, Reeder DM (2005) Mammal species of the World. A taxonomic and geographic reference. (eds Wilson DE and Reeder DM), pp. 2142. Johns Hopkins University Press, Baltimore.
View Full Article (HTML) Get PDF (1486K)