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Patterns of genetic diversity of Prunus africana in Ethiopia: hot spot but not point of origin for range-wide diversity

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Abstract

We studied the genetic pattern of 21 Ethiopian populations of Prunus africana by using six nuclear and five plastid microsatellites. In total, 89 alleles were found in the nuclear and 16 haplotypes in the plastid genome. High levels of diversity both in cpSSRs (h T  = 0.703) and nSSR (H T  = 0.725) were detected. Genetic differentiation among populations at the nuclear and plastid level was moderate (F ST = 0.122 vs. G ST = 0.478). While Ethiopian populations harbored the highest plastid haplotype diversity throughout Africa, the level of nuclear diversity was lower than in the remaining part of the species’ range. Ten of the observed 16 plastid haplotypes were unique to Ethiopia, suggesting an isolated plastid evolution. Remarkably, all plastid haplotypes found in Ethiopia belonged to one single lineage, while other populations from East Africa and Madagascar contain haplotypes from up to four more divergent lineages. This suggests that in contrast to previous expectations, the Horn of Africa is a hot spot of plastid diversity but not the ancestral origin for present populations of P. africana. The ratio between pollen to seed flow was estimated to be 7.1, indicating predominant gene flow by pollen. The exhaustive pollen flow also facilitated gene exchange with West African nuclear lineages probably in the early Holocene. The Ethiopian rift formed a genetic barrier resulting in population differentiation east and west of the rift; however, it was less effective in disrupting gene flow than the Eastern Rift in more southern parts of the East African range.

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References

  • Aalbæk A (1993) Tree seed zones for Ethiopia. Forestry Research Center/National Tree Seed Project, Addis Ababa

    Google Scholar 

  • Atnafu H (2007) Genetic variation in some natural population of Prunus africana from Ethiopia as revealed by randomly amplified polymorphic DNA (RAPD). MSc Thesis, Addis Ababa University

  • Aubréville A (1976) Centres tertiaires d’origine, radiations et migrations des flores angiospermiques tropicales. Andansonia 16:297–354

    Google Scholar 

  • Bänfer G, Moog U, Fiala B, Mohamed M, Weising K, Blattner FR (2006) A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridization, vicariance and long-distance dispersals. Mol Ecol 15:4409–4424

    Article  PubMed  Google Scholar 

  • Barker N, Cunningham AB, Morrow C, Harley EH (1994) A preliminary investigation into the use of RAPD to assess the genetic diversity of a threatened African tree species: Prunus africana. Strelitzia 1:221–230

    Google Scholar 

  • Berens DG, Griebeler EM, Braun C, Chituy BB, Nathan R, Böhning-Gaese K (2013) Changes of effective gene dispersal distances by pollen and seeds across successive life stages in a tropical tree. Oikos 122:1616–1625

    Article  Google Scholar 

  • Birky CW, Maruyama T, Fuerst P (1983) An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics 103:513–527

    PubMed Central  PubMed  Google Scholar 

  • Bonnefille R, Umer M (1994) Pollen-inferred climate fluctuations in Ethiopia during the last 3000 years. Palaeogeogr Palaeoclimatol Palaeoecol 109:331–343

    Article  Google Scholar 

  • Borsch T, Hilu KW, Quandt D, Wilde V, Neinhuis C, Barthlott W (2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J Evol Biol 16:558–576

    Article  CAS  PubMed  Google Scholar 

  • Cavers S, Munro RC, Kadu CAC, Konrad H (2009) Transfer of microsatellite loci for the tropical tree Prunus africana (Hook.f.) Kalkman. Silvae Genet 58:276–279

    Google Scholar 

  • Chester M, Cowan RS, Fay MF, Rich TCG (2007) Parentage of endemic Sorbus L. (Rosaceae) species in the British Isles: evidence from plastid DNA. Bot J Linn Soc 154:291–304

    Article  Google Scholar 

  • Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterization and cross-species amplification in Prunus. Theor Appl Genet 99:65–72

    Article  CAS  Google Scholar 

  • Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1660

    Article  CAS  PubMed  Google Scholar 

  • Coetzee JA (1967) Pollen analytical studies in East and southern Africa. Palaeoecol Afr 3:1–146

    Google Scholar 

  • Cunningham AB, Mbenkum FT (1993) Sustainability of harvesting prunus Africana bark in Cameroon: a medicinal plant in international trade. UNESCO, People and Plants Working Paper 2, Paris

    Google Scholar 

  • Cunningham M, Cunningham AB, Schippmann U (1997) Trade in Prunus africana and the implementation of CITES. German Federal Agency for Nature Conservation, Bonn

    Google Scholar 

  • Dawson I, Powell W (1999) Genetic variation in the Afromontane tree Prunus africana, an endangered medicinal species. Mol Ecol 8:151–156

    Article  Google Scholar 

  • Dawson I, Were J, Lengkeek A (2000) Conservation of Prunus africana, an over-exploited African medicinal tree. In: Palmberg-Lerche C, Hald S, Sigaud P (eds) Forest genetic resources, no. 28. FAO, Rome, pp 27–33

    Google Scholar 

  • Dieringer D, Schlotterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3:167–169

    Article  CAS  Google Scholar 

  • Earl DA, von Holdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • Ennos RA (1994) Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72:250–259

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

    Article  PubMed  Google Scholar 

  • Farwig N, Braun C, Bohning-Gaese K (2008) Human disturbance reduces genetic diversity of an endangered tropical tree, Prunus africana (Rosaceae). Conserv Genet 9:317–326

    Article  Google Scholar 

  • Felsenstein J (1989) PHYLIP—Phylogeny Inference Package (version 3.2). Cladistics 5:164–166

    Google Scholar 

  • George JP, Konrad H, Collin E, Thevenet J, Ballian D, Idzojtic M, Kamm U, Zhelev P, Geburek T (2015) High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurence. Ann Bot 115:1105-1115

  • Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486

    Google Scholar 

  • Hamilton AC (1982) Environmental history of East Africa—a study of the Quaternary. Academic Press, London

    Google Scholar 

  • Hamilton AC, Taylor D (1991) History of climate and forests in tropical Africa during the last 8 million years. In: Myers N (ed) Tropical Forests and Climate. Springer, Dordrecht, pp 65–78

    Chapter  Google Scholar 

  • Hardy O, Vekemans X (2002) SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620

    Article  Google Scholar 

  • Hewitt GM (1999) Post-glacial re-colonization of European biota. Biol J Linn Soc 68:87–112

    Article  Google Scholar 

  • Hurni H (1988) Degradation and conservation of the resources in the Ethiopian highlands. Mt Res Dev 8:123–130

    Article  Google Scholar 

  • Jimu LN (2011) Threats and conservation strategies for the African cherry (Prunus africana) in its natural range—a review. J Ecol Nat Environ 3:118–130

    Google Scholar 

  • Jolly D, Taylor D, Marchant R, Hamilton A, Bonnefille R, Buchet G, Riollet G (1997) Vegetation dynamics in central Africa since 18,000 yr BP: pollen records from the interlacustrine highlands of Burundi, Rwanda and western Uganda. J Biogeogr 24:495–512

    Google Scholar 

  • Kadu CAC, Schueler S, Konrad H, Muluvi GM, Eyog-Matig O, Muchugi A, Williams VL, Ramamonjisoa L, Kapinga C, Foahom B, Katsvanga C, Hafashimana D, Obama C, Geburek T (2011) Phylogeography of the Afromontane Prunus africana reveals a former migration corridor between East and West African highlands. Mol Ecol 20:165–178

    Article  CAS  PubMed  Google Scholar 

  • Kadu CAC, Parich A, Schueler S, Konrad H, Muluvi GM, Eyog-Matig O, Muchugi A, Williams VL, Ramamonjisoa L, Kapinga C, Foahom B, Katsvanga C, Hafashimana D, Obama C, Vinceti B, Schumacher R, Geburek T (2012) Bioactive constituents in Prunus africana: geographical variation throughout Africa and associations with environmental and genetic parameters. Phytochemistry 83:70–78

    Article  CAS  PubMed  Google Scholar 

  • Kadu CAC, Konrad H, Schueler S, Muluvi GM, Eyog-Matig O, Muchugi A, Williams VL, Ramamonjisoa L, Kapinga C, Foahom B, Katsvanga C, Hafashimana D, Obama C, Geburek T (2013) Divergent pattern of nuclear genetic diversity across the range of the Afromontane Prunus africana mirrors variable Pleistocene climate of African highlands. Ann Bot 111:47–60

    Article  PubMed Central  PubMed  Google Scholar 

  • Kalkman C (1965) The old world species of Prunus sub-genus Laurocerasus. Blumea 13:33–35

    Google Scholar 

  • Koch MA, Kiefer C, Ehrich D, Vogel J, Brochmann C, Mummenhoff K (2006) Three times out of Asia Minor: the phylogeography of Arabis alpina L. (Brassicaceae). Mol Ecol 15:825–839

    Article  CAS  PubMed  Google Scholar 

  • Livingstone DA (1975) Late Quaternary climatic change in Africa. Ann Rev Ecol Syst 6:249–280

    Article  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  • Muchugi A, Lengkeek G, Agufa C, Muluvi G, Njagi E, Dawson I (2006) Genetic variation in the threatened medicinal tree Prunus africana in Cameroon and Kenya: implications for current management and evolutionary history. S Afr J Bot 72:498–506

    Article  CAS  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–292

    Article  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ohta S, Nishitani C, Yamamoto T (2005) Chloroplast microsatellites in Prunus, Rosaceae. Mol Ecol Notes 5:837–840

    Article  CAS  Google Scholar 

  • Owen RP, Barthelme JW, Renault RW, Vincens A (1982) Palaeolimnology and archaeology of Holocene deposits north-east of Lake Turkana, Kenya. Nature 298:523–529

    Article  Google Scholar 

  • Palma-Silva C, Lexer C, Paggi GM, Barbara T, Bered F, Bodanese-Zanettini MH (2009) Range-wide patterns of nuclear and chloroplast DNA diversity in Vriesea gigantea (Bromeliaceae), a neotropical forest species. Heredity 103:600–612

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Poelchau MF, Hamrick JL (2012) Differential effects of landscape-level environmental features on genetic strcutre in three co-distributed tree species in Central America. Mol Ecol 21:4970–4982

    Article  PubMed  Google Scholar 

  • Pons O, Petit RJ (1995) Estimation, variance and optimal sampling of gene diversity. I. Haploid locus. Theor Appl Genet 90:462–470

    Article  CAS  PubMed  Google Scholar 

  • Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237–1245

    PubMed Central  CAS  PubMed  Google Scholar 

  • Pritchard JK, Stephens P, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed Central  CAS  PubMed  Google Scholar 

  • Reusing M (2000) Change detection of natural high forests in Ethiopia using remote sensing and GIS techniques. International Archives of Photogrammetry Remote Sensing XXXIII (Part B7):1253–1257

  • Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG (2000) Characterization of microsatellite markers in peach Prunus persica (L.) Batsch. Theor Appl Genet 101:421–428

    Article  CAS  Google Scholar 

  • Street-Perrott FA, Perrott RA (1993) Holocene vegetation, lake levels and climate of Africa. In: Wright HE, Kutzbach JE, Webb T, Ruddiman WF, Street-Perrott FA, Bartlein PJ (eds) Global climate since the Last Glacial Maximum. University of Minnesota Press, Minneapolis, pp 318–356

    Google Scholar 

  • Teketay D, Granström A (1995) Soil seed banks in dry Afromontane forests of Ethiopia. J Veg Sci 6:777–786

    Article  Google Scholar 

  • van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  Google Scholar 

  • Vaughan SP, Russell K (2004) Characterization of novel microsatellites and development of multiplex PCR for large-scale population studies in wild cherry, Prunus avium. Mol Ecol Notes 4:429–431

    Article  CAS  Google Scholar 

  • Vincens A (1986) Diagramme pollinique d’un sondage Pleistocene superieur—Holocene du Lac Bogoria (Kenya). Rev Palaeobot Palynol 47:169–192

    Article  Google Scholar 

  • Vincens A, Buchet G, Servant M, Barton C, Ngos S, Nguetsop F, Servant-Vildary S, Tchotsoua M (2010) Vegetation response to the “African Humid Period” termination in Central Cameroon (7°N)—new pollen insight from Lake Mbalang. Clim Past 6:281–294

    Article  Google Scholar 

  • Vinceti B, Loo J, Gaisberger H, van Zonneveld MJ, Schueler S, Konrad H, Kadu CAC, Geburek T (2013) Conservation priorities for Prunus africana defined with the aid of spatial analysis of genetic data and climatic variables. PLoS One 8:e59987

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • White F (1993) Refuge theory, ice-age aridity and the history of tropical biotas: an essay in plant geography. Fragm Florist Geobot Suppl 2:385–409

    Google Scholar 

  • Yineger H, Schmidt DJ, Hughes JM (2014) Genetic structuring of remnant forest patches in an endangered medicinal tree in north-western Ethiopia. BMC Genet 15:31

    Article  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

We thank all persons involved in carrying out the sample collections and Thomas Thalmayr for his technical assistance during the laboratory analysis and with creating figures. This research was done with financial contribution of the following institutions: Addis Ababa University and Bahir Dar University, Ethiopia; BFW: Federal Research and Training Centre for Forests, Natural Hazards and Landscape, Department of Forest Genetics, Austria; and Bioversity International, Italy.

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Authors and Affiliations

  1. Department of Biology, Bahir Dar University, P.O. Box 79, Bahir Dar, Ethiopia

    Z. Mihretie

  2. Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent-Weg 8, A-1131, Vienna, Austria

    S. Schueler, H. Konrad & T. Geburek

  3. Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia

    E. Bekele

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  1. Z. Mihretie
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  2. S. Schueler
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  3. H. Konrad
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Correspondence to T. Geburek.

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Mihretie, Z., Schueler, S., Konrad, H. et al. Patterns of genetic diversity of Prunus africana in Ethiopia: hot spot but not point of origin for range-wide diversity. Tree Genetics & Genomes 11, 118 (2015). https://doi.org/10.1007/s11295-015-0945-z

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