Skip to main content

Advertisement

SpringerLink
Log in

Influence of putative forest refugia and biogeographic barriers on the level and distribution of genetic variation in an African savannah tree, Khaya senegalensis (Desr.) A. Juss

  • Original Article
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Phylogeographic studies of tropical and subtropical tree species provide an ideal method to study the role of forest refugia in the structuring of genetic diversity in contemporary populations. To date, most studies have examined rainforest-dependent trees, yet the influence of forest refugia on savannah forest and woodland trees remains poorly understood despite their potentially important role in forest assemblages during the last glacial maximum. Here, we examine the level and structuring of genetic diversity across the geographic range of the savannah woodland tree, Khaya senegalensis—African mahogany, from Senegal to Uganda (>5000 km) and from the steppes of the Sahara desert to the fringes of Africa’s equatorial rainforests (700 km). Three chloroplast (cpDNA) loci and 13 nuclear microsatellite (nSSR) loci were genotyped in 503 individuals. Individual-based clustering of nSSR genotypes identified that all samples formed two populations that showed no pattern of geographic structuring. Population level analysis of nSSR data revealed only very weak genetic structure (F ST = 0.013) with most of the genetic diversity contained within populations. Geographical differentiation (G ST = 0.096) was low for the 14 haplotypes identified. However, whereas all haplotypes occurred in the western populations (including Cameroon), only two cosmopolitan haplotypes were found in central-eastern populations. Geographically restricted low-frequency haplotypes were found in eight western populations. Higher genetic diversity in western populations was confirmed by patterns of allelic richness, which were lower in central-eastern populations. Taken together, these results indicate that K. senegalensis displays very little genetic differentiation across its geographic range and that previously identified barriers to dispersal across the northern savannah belt of tropical Africa (e.g. the Dahomey Gap, Mega Lake Chad and the Adamawa Highlands) have not impeded contemporary gene dispersal in this species. Nevertheless, clustering of rare haplotypes indicates that the Dahomey Gap has likely been an important historical barrier to genetic connectivity between western and eastern regions of the species and that it is likely that this savannah tree also experienced range contraction around major forest refugial fringes or riparian incursions during the last glacial maximum (LGM).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Ahmed S, Compton SG, Butlin RK, Gilmartin PM (2009) Wind-borne insects mediate directional pollen transfer between desert fig trees 160 kilometers apart. PNAS 106(48):20342–20347

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Allal F, Sanou H, Millet L, Vaillant A, Camus-Kulandaivelu L, Logossa ZA, Lefèvre F, Bouvet J-M (2011) Past climate changes explain the phylogeography of Vitellaria paradox over Africa. Heredity 107:174–186

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Als TD, Hansen MM, Maes GE, Castonguay M, Riemann L, Aarestrup K, Munk P, Sparholt H, Hanel R, Bernatchez L (2011) All roads lead to home: panmixia of European eel in the Sargasso Sea. Mol Ecol 20:1333–1346

    Article  PubMed  Google Scholar 

  • Alvarez N, Thiel-Egenter C, Tribsch A, Holderegger R et al (2009) History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants. Ecol Lett 12:632–640. doi:10.1111/j.14610248.2009.01312.x

    Article  PubMed  Google Scholar 

  • Anhuf D, Ledru MP, Behling H, Da Cruz FW, Cordeiro RC, Van der Hammen T, Karmann I, Marengo JA, De Oliveira PE, Pessenda L, Siffedine A, Albuquerque AL, Da Silva Dias PL (2006) Paleo-environmental change in the Amazonian and African rainforest during the LGM. Palaeogeogr Palaeoclimatol Palaeoecol 239:510–515

    Article  Google Scholar 

  • Ashley MV (2010) Plant parentage, pollination, and dispersal: how DNA microsatellites have altered the landscape. Crit Rev Plant Sci 29(3):148–161

    Article  CAS  Google Scholar 

  • Avise JC (1994) Molecular markers, natural history and evolution. Chapman and Hill, New York

    Book  Google Scholar 

  • Bacles CFE, Lowe AJ, Ennos RA (2006) Effective seed dispersal across a fragmented landscape. Science 311:268

    Article  Google Scholar 

  • Bandelt HJ, Forester P, Rohl A (1999) Median-joining networks for inferring phylogenies. Mol Biol Evol 16:37–48

    Article  CAS  PubMed  Google Scholar 

  • Bekessy SA, Allnutt TR, Premoli AC, Lara A, Ennos RA, Burgman MA, Cortes M, Newton AC (2002) Genetic variation in the vulnerable and endemic Monkey Puzzle tree, detected using RAPDs. Heredity 88:243–249

    Article  CAS  PubMed  Google Scholar 

  • Born C, Hardy OJ, Chevallier MH, Ossari S, Atteke C, Wickings EJ, Hossaert-Mckey M (2008) Small-scale spatial genetic structure in the central African rainforest tree species Aucoumea klaineana: a stepwise approach to infer the impact of limited gene dispersal, population history and habitat fragmentation. Mol Ecol 17:2041–2050

    Article  PubMed  Google Scholar 

  • Born C, Alvarez N, McKey D, Ossari S, Wickings EJ, Hossaert-Mckey M, Chevallier MH (2011) Insights into the biogeographical history of the Lower Guinea Forest Domain: evidence for the role of refugia in the intraspecific differentiation of Aucoumea klaineana. Mol Ecol 20:131–142

    Article  PubMed  Google Scholar 

  • Bryja J, Granjon L, Dobigny G, Patzenhauerova H, Konececy A, Duplantier JM, Gauthier P, Colyn M, Durnez L, Lalis A, Nicolas V (2010) Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment geography genetic interplay. Mol Ecol 19:4783–4799

    Article  CAS  PubMed  Google Scholar 

  • Cavers S, Telford A, Arenal F, Valencia R, Navarro C, Buonamici A, Lowe AJ, Vendramin GG (2013) Cryptic species and phylogeography in Spanish Cedar, Cedrela odorata L., throughout the neotropics. J Biogeogr 40:732–746

    Article  Google Scholar 

  • Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, Mitrovica JX, Hostetler SW, McCabe AM (2009) The last glacial maximum. Science 325:710. doi:10.1126/science.1172873

    Article  CAS  PubMed  Google Scholar 

  • Daïnou K, Bizoux J-P, Doucet J-L, Mahy G, Hardy OJ, Heuertz M (2010) Forest refugia revisited: SSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Mol Ecol 19:4462–4477

    Article  PubMed  Google Scholar 

  • Dayanandan S, Dole J, Bawa K, Kesseli R (1999) Population structure delineated with microsatellite markers in fragmented populations of a tropical tree, Carapa guianensis (Meliaceae). Mol Ecol 8:1585–1592

    Article  PubMed  Google Scholar 

  • Dearden P, Chettomart S, Emphandu D, Tanakanjana N (1996) National parks and hill tribes in northern Thailand: a case study of Doi Inthanon. Soc Nat Resour 9:125–141

    Article  Google Scholar 

  • Debout GDG, Doucet J-L, Hardy OJ (2010) Population history and gene dispersal inferred from spatial genetic structure of a Central Africa timber tree, Distemonanthus benthamianus (Caesalpinioideae). Heredity 106(1):88–99

    Article  PubMed Central  PubMed  Google Scholar 

  • Dick CW (2010) Phylogeography and population structure of tropical trees. Trop Plant Biol 3:1–3

    Article  Google Scholar 

  • Diekmann OE, Serrão EA (2012) Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina. Mol Ecol 21:1647–1657

    Article  PubMed  Google Scholar 

  • Drees LR, Manu A, Wilding LP (1993) Characteristics of aeolian dusts in Niger, West Africa. Geoderma 59:213–233

    Article  Google Scholar 

  • Duminil J, Heuertz M, Doucet J-L, Bourland N, Cruaud C, Gavory F, Doumenge C, Navascués M, Hardy OJ (2010) cpDNA-based species identification and phylogeography: application to African tropical tree species. Mol Ecol 19:5469–5483

    Article  CAS  PubMed  Google Scholar 

  • Dumolin-Lapegue S, Demesure B, Fineschi S, Le Corre V, Petit RJ (1997) Phylogeographic structure of white oaks throughout the European continent. Genetics 146:1475–1487

    PubMed Central  CAS  PubMed  Google Scholar 

  • Dupont LM, Jahns S, Marret F, Ning S (2000) Vegetation change in equatorial West Africa: time-slices for the last 150 Ka. Palaeogeogr Palaeoclimatol Palaeoecol 155:95–122

    Article  Google Scholar 

  • Dupont LM, Donner B, Schneider R, Wefer G (2001) Mid-Pleistocene environmental change in tropical Africa began as early as 1.05 Ma. Geology 29:195–198

    Article  CAS  Google Scholar 

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. doi:10.1007/s12686-011-9548-7

    Article  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(3):564–567

    Article  PubMed  Google Scholar 

  • FAO (1986) Data book on endangered tree and shrub species and provenances. Forestry Paper 77. Rome

  • Fontaine C, Lovett PN, Sanou H, Maley J, Bouvet JM (2004) Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers. Heredity 93:639–648

    Article  CAS  PubMed  Google Scholar 

  • Gaoue OG, Ticktin T (2008) Impacts of bark and foliage harvest on Khaya senegalensis (Meliaceae) reproductive performance in Benin. J Appl Ecol 45:35–40

    Google Scholar 

  • Gillies ACM, Cornelius JP, Newton AC, Navarro C, Hernandez M, Wilson J (1997) Genetic variation in Costa Rican populations of the tropical timber species Cedrela odorata L, assessed using RAPDs. Mol Ecol 6:1133–1145

    Article  CAS  Google Scholar 

  • Hamilton MB (1999) Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol Ecol 8:521–522

    CAS  PubMed  Google Scholar 

  • Hampe A, Petit RJ (2005) Conserving biodiversity under climate change: the rear edge matters. Ecol Lett 8:461–467. doi:10.1111/j.1461-0248.2005.00739.x

    Article  PubMed  Google Scholar 

  • Hamrick JL (2004) Response of forest trees to global environmental changes. For Ecol Manag 197:323–335

    Article  Google Scholar 

  • Hardy OJ, Bourobou DN, Budde K, Daïnou K, Dauby G, Duminil J, Ewédjé E-E, Heuertz M, Koffi GK, Lowe AJ, Micheneau C, Poncet V (2013) Comparative phylogeography of African rain forest trees: a review of genetic signatures of vegetation history in the Guineo-Congolian domain. Compt Rendus Geosci 345:284–296

    Article  Google Scholar 

  • He C, Breuning-Madsen H, Awadzi TW (2007) Mineralogy of dust deposited during the Harmattan season in Ghana. Dan J Geogr 107(1):9–15

    Article  Google Scholar 

  • Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Review article. Nature 405:907–913

    Article  CAS  PubMed  Google Scholar 

  • Hewitt GM (2004) The structure of biodiversity-insights from molecular phylogeography. Front Zool 1:4

    Article  PubMed Central  PubMed  Google Scholar 

  • Hooghiemstra H, Lézine A-M, Leroy SAG, Dupont L, Marret F (2006) Late quaternary palynology in marine sediments: a synthesis of the understanding of pollen distribution patterns in the NW African setting. Quat Int 148:29–44

    Article  Google Scholar 

  • IUCN (2015) The IUCN red list of threatened species. Version 2015.1. www.iucnredlist.org. Downloaded on 17 June 2015

  • Jenik J (1994) The Dahomey-Gap, an important issue in African phytogeography. Mem Soc Biogeogr 3:125–133

    Google Scholar 

  • Jøker D (2000) Vitellaria paradoxa Gaertn. f. Seed leaflet No. 50, Danida Forest Seed Centre, Humlebaek, Denmark

  • Jøker D, Gaméné S (2003) Khaya senegalensis Seed leaflet No. 66, Danida Forest Seed Centre, Humlebaek Denmark

  • Jones FA, Chen J, Weng G-J, Hubbell SP (2005) A genetic evaluation of seed dispersal in the neotropical tree Jacaranda copaia (Bignoniaceae). Am Nat 166(5):543–555

    Article  CAS  PubMed  Google Scholar 

  • Kadu CAC, Schueler S, Konrad H et al (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 

  • Kalinowski ST (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189

    Article  CAS  Google Scholar 

  • Kalu AE (1977) The Africa dust plume: its characteristic and propagation across West Africa in winter. In: Morales (ed) Sahara dust. Wiley, New York, pp 95–118

    Google Scholar 

  • Karan M, Evans DS, Reilly D, Schulte K, Wright C, Innes D, Holton TA, Nikles DG, Dickinson GR (2011) Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity. Mol Ecol Resour. doi:10.1111/j.1755-0998.2011.03080.x

    PubMed  Google Scholar 

  • Kebede M, Ehrich D, Taberlet P, Nemomissa S, Brochmann C (2007) Phylogeography and conservation genetics of a giant lobelia (Lobelia giberroa) in Ethiopian and Tropical East African mountains. Mol Ecol 16:1233–1243

    Article  CAS  PubMed  Google Scholar 

  • Kennedy JD (1936) Forest flora of Southern Nigeria. Government Printer, Lago

    Google Scholar 

  • Koren I, Kaufman YJ (2004) Direct wind measurements of Saharan dust events from Terra and Aqua satellites. Geophys Res Lett 31:L06122. doi:10.1029/ 2003GL019338

    Google Scholar 

  • Lézine A-M, Vergnaud-Grazzini C (1993) Evidence of forest extension in West Africa since 22,000 BP: a pollen record from the Eastern Tropical Atlantic. Quat Sci Rev 12:203–210

    Article  Google Scholar 

  • Lowe AJ, Gillies ACM, Wilson J, Dawson IK (2000) Conservation genetics of bush mango from central/west Africa: implications from random amplified polymorphic DNA analysis. Mol Ecol 9:831–841

    Article  CAS  PubMed  Google Scholar 

  • Lowe AJ, Jourde B, Breyne P, Colpaert N, Navarro C, Cavers S (2003) Fine scale genetic structure and gene flow within Costa Rican populations of Mahogany (Swietenia macrophylla). Heredity 90:268–275

    Article  CAS  PubMed  Google Scholar 

  • Lowe AJ, Harris D, Dormontt EE, Dawson IK (2010) Testing putative African tropical forest refugia using chloroplast and nuclear DNA phylogeography. Trop Plant Biol 3:50–58

    Article  Google Scholar 

  • Maley J (1987) Fragmentation de la forêt dense humide africaine et extension des biotopes montagnards au Quaternaire récent: nouvelles données polliniques etchronologiques. Implications paléoclimatiques et biogéographiques. Palaeoecol Afr 18:307–334

    Google Scholar 

  • Maley J (1991) The African rain forest vegetation and palaeoenvironments during late quaternary. Climate Change 19:79–98

    Article  Google Scholar 

  • Maley J (1996) The African rain forest: main characteristics of changes in vegetation and climate from the upper Cretaceous to the quaternary. Proc Roy Soc Edinb 104:31–73

    Google Scholar 

  • Martin C (1991) The rainforests of West Africa. Birkhauser, Basel

    Book  Google Scholar 

  • Morris-Pocock JA, Taylor SA, Birt TP, Damus M, Piatt JF, Warheit KI, Friesen VL (2008) Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): natural replicate tests of post-Pleistocene evolution. Mol Ecol 17:4859–4873

    Article  CAS  PubMed  Google Scholar 

  • Muellner AN, Pennington TD, Koecke AV, Renner SS (2010) Biogeography of Cedrela (Meliaceae, Sapindales) in Central and South America. Am J Bot 97(3):511–518

    Article  PubMed  Google Scholar 

  • Muller F, Voccia M, Ba A, Bouvet JM (2009) Genetic diversity and gene flow in a Caribbean tree Pterocarpus officinalis Jacq.: a study based on chloroplast and nuclear microsatellites. Genetica 135:185–198

    Article  CAS  PubMed  Google Scholar 

  • Nathan R (2006) Perspective long-distance dispersal of plants. Science 313(5788):786–788

    Article  CAS  PubMed  Google Scholar 

  • Neethling M, Matthee CA, Bowie RCK, von der Heyden S (2008) Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae). BMC Evol Biol 8:325. doi:10.1186/1471-2148-8-325

    Article  PubMed Central  PubMed  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nichol JE (1999) Geomorphological evidence and Pleistocene refugia in Africa. Geogr J 165(1):79–89

    Article  Google Scholar 

  • Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D (2009) Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol 18(15):3128–3150

    Article  PubMed  Google Scholar 

  • Nikiema A, Pasternak D (2008) Khaya senegalensis (Desr.) A. Juss. Record from protabase. In: Louppe D, Oteng-Amoako AA, Brink M (eds) PROTA (Plant Resources of Tropical Africa / Ressources végétales de l’Afrique tropicale), Wageningen, Netherlands. http://database.prota.org/search.htm

  • Nikles DG (2006) The domestication of African mahogany (Khaya senegalensis) in northern Australia. Aust For 69(1):68–69

    Article  Google Scholar 

  • Novick RR, Dick CW, Lemes MR, Navarro C, Caccone A, Bermingham (2003) Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis. Mol Ecol 12:2885–2893

    Article  PubMed  Google Scholar 

  • Odee DW, Telford A, Wilson J, Gaye A, Cavers S (2012) Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion. Heredity 109(6):372–382

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Opgenoorth L, Vendramin GG, Mao K, Miehe G, Miehe S, Liepelt S, Liu J, Ziegenhagen B (2010) Tree endurance on the Tibetan Plateau marks the world’s highest known tree line of the Last Glacial Maximum. New Phytol 185:332–342

    Article  PubMed  Google Scholar 

  • Orwa C, Mutua A, Kindt R, Jamnadass R, Anthony S (2009) Agroforestree database: a tree reference and selection guide version 4.0. http://www.worldagroforestry.org/sites/treedbs/treedatabases.asp

  • Ottewell K, Grey E, Castillo F, Karubian J (2012) The pollen dispersal kernel and mating system of an insect-pollinated tropical palm, Oenocarpus bataua. Heredity 109(6):332–339

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Parmentier I, Malhi Y, Senterre B, Whittaker RJ, Alonso A, Balinga MPB, Bakayoko A, Bongers F, Chatelain C, Comiskey JA, Cortay R, Djuikouo Kamdem M-N, Doucet J-L, Gautier L, Hawthorne WD et al (2007) The odd man out? Might climate explain the lower tree α-diversity of African rain forests relative to Amazonian rain forests? J Ecol 95:1058–1071

    Article  Google Scholar 

  • Pavlacky DC, Goldizen AW, Prentis PJ, Nicholls JA, Lowe AJ (2009) A landscape genetics approach for quantifying the relative influence of historic and contemporary habitat heterogeneity on the genetic connectivity of a rainforest bird. Mol Ecol 18(14):2945–2960

    Article  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 18(14):2945–2960

    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 

  • Peakall R, Ruibal M, Lindenmayer D (2003) Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rat, Rattus fuscipes. Evolution 57(5):1182–1195

    Article  PubMed  Google Scholar 

  • Petit RJ, Brewer S, Bordacs S, Burg K, Cheddadi R, Coart E, Cottrell J, Csaikl U, Fineschi S, Goicoechea P, Jensen JS, König A, Lowe AJ, Madsen SF, Matyas G, Oledska I, Popescu F, Slade D, Van Dam B, de Beaulieu J-L, Kremer A (2002) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For Ecol Manag 156:49–74

    Article  Google Scholar 

  • Petit RJ, Aguinagalde I, de Beaulieu J-L, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Müller-Starck G, Demesure-Musch B, Palmé A, Martín JP, Rendell S, Vendramin GG (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300(5625):1563–1565

    Article  CAS  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 

  • Prentis PJ, Vesey A, Meyers NM, Mather PB (2004) Genetic structuring of the stream lily Helmholtzia glaberrima (Philydraceae) within Toolona Creek, south-eastern Queensland. Aust J Bot 52(2):201–207

    Article  Google Scholar 

  • Prentis PJ, Sigg D, Raghu S, Dhileephan K, Pavasovic A, Lowe AJ (2009) Understanding invasion history: genetic structure and diversity of two globally invasive plants and implications for their management. Divers Distrib 15:822–830

    Article  Google Scholar 

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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Richards PW (1973) Africa, the ‘odd man out’. In: Meggers BJ, Ayensu ES, Duckworth WD (eds) Tropical forest ecosystems of Africa and South America: a comparative review. Smithsonian Institution Press, Washington, DC, pp 21–26

    Google Scholar 

  • Rodríguez-Banderas A, Vargas-Mendoza CF, Buonamici A, Vendramin GG (2009) Genetic diversity and phylogeographic analysis of Pinus leiophylla: a post-glacial range expanansion. J Biogeogr 36:1807–1820

    Article  Google Scholar 

  • Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • Ruiz GJC, Schnabel A, Ennos R, Preuss S, Otero-Arnaiz A, Stone G (2010) Landscape genetics of the key African acacia species Senegalia mellifera (Vahl)–the importance of the Kenyan Rift Valley. Mol Ecol 19:5126–5139

    Article  Google Scholar 

  • Sacande M, Rønne C, Sanon M, Jøker D (2006) Adansonia digitata L. Seed leaflet No. 109, Danida Forest Seed Centre, Humlebaek, Denmark

  • Savill PS, Fox JED (1967) Trees of Sierra Leone. Forest Department, Freetown, 316 pp

  • Schneider S, Roesseli D, Excoffier L (2000) Arlequin ver. 2.000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland

    Google Scholar 

  • Sexton GJ, Frere CH, Dieters M, Godwin ID, Prentis PJ (2010) Development and characterization of microsatellite loci for Khaya senegalensis (Meliaceae). Am J Bot 97:111–113

    Article  Google Scholar 

  • Shaw J, Lickey EB, Shilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94:275–288

    Article  CAS  PubMed  Google Scholar 

  • Shimono A, Ueno S, Gu S, Zhao X, Tsumura Y, Tang Y (2010) Range shifts of Potentilla fruticosa on the Qinghai-Tibetan Plateau during glacial and interglacial periods revealed by chloroplast DNA sequence variation. Heredity 104:534–542

    Article  CAS  PubMed  Google Scholar 

  • Sinsin B, Eyog-Matig O, Sinadouwirou TLA, Assogbadjo A (2002) Caraterisation ecologique des essences fourrageres Khaya senegalensis (Desr.) et Afzelia africana Sm. Suivantles gradients de latitude et de station au Benin. In: Eyog-Matigo O, Gaue OG, Obel-Lawson E (eds) Development of appropriate conservation strategies for African forest trees identified as priority species by SAFORGEN member countries. IGRI, Nairobi, pp 15–50

    Google Scholar 

  • Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47:264–279

    Article  Google Scholar 

  • Smith J (1949) Distribution of tree species in the Sudan in relation to rainfall and soil texture. Bulletin 4. Ministry of Agriculture. Khartoum, the Sudan: Republic of Sudan

  • Styles BT, Vosa CG (1971) Chromosome numbers in Meliaceae. Taxon 20(4):485–499

    Article  Google Scholar 

  • Styles BT, White F (1991) Flora of tropical East Africa. In: Polhill RM (ed) Meliaceae. Royal Botanic Gardens 1 Kew, Balkema

    Google Scholar 

  • Synott TJ (1985) A checklist of the flora of Budongo Forest Reserve, Uganda, with notes on ecology and phenology. Occasional Papers 27, Commonwealth Forestry Institute, Oxford, UK

  • Taberlet P, Cheddadi R (2002) Quaternary refugia and persistence of biodiversity. Science 297:2009–2010

    Article  CAS  PubMed  Google Scholar 

  • Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109

    Article  CAS  PubMed  Google Scholar 

  • Tomizawa Y, Takayama K, Sungkaew S, Saleh MNB, Asakawa T, Adjie B, Ardli ER, Soe MKK, Shan WK, Tung NX, Malekal NB, Onrizal, Yllano OB, Meenakshisundaram SH, Salmo III SG, Watano Y, Baba S, Tateishi Y, Kajita T (2012) Phylogeography of Xylocarpus granatum. In: Dahdouh-Guebas F, Satyanarayana B (eds) Proceedings of the International Conference: meeting on Mangrove ecology, functioning and management (MMM3). Galle, Sri Lanka

  • Tsy JL, Lumaret R, Mayne D, Mohamed VA, Abutaba YIM, Sagna M, Raoseta S, Danthu P (2009) Chloroplast DNA phylogeography suggest a West African centre of origin for the baobab, Adansonia digitata L (Bombacoideae, Malvaceae). Mol Ecol 18:1707–1715

    Article  CAS  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 

  • White G, Boshier DH, Powell W (1999) Genetic variation within a fragmented population of Swietenia humilis Zucc. Mol Ecol 8:1899–1909

    Article  CAS  PubMed  Google Scholar 

  • White GM, Boshier DH, Powell W (2002) Increased pollen flow counteracts fragmentation in a tropical dry forest: an example from Swietenia humilis Zuccarini. Proc Natl Acad Sci USA 99:2038–2042

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wickens GE, Lowe P (2008) The Baobabs: pachycauls of Africa, Madagascar and Australia. Springer, Dordrecht, 498 p

    Book  Google Scholar 

Download references

Acknowledgments

We would like to express our appreciation for the support given to this study by the following people and organizations: Behima Kone (ICRAF, Bamoko, Mali), Yaw Boakye Agyeman (Kwame Nkrumah University, Ghana), Kojo Wilson (Forest Research Institute of Ghana), Ntim Gyakari (Forestry Commission, Ghana), Gilles Chaix (CIRAD France), William Hawthorne (Plant Sciences, Oxford England), Roger Mills (Plant Sciences Library, Oxford), Tivvy Harvey (Royal Botanical Gardens Kew England) and Garth Nikles (DEEDI, Australia). We are also grateful to the forestry staff at the Queensland Department of Employment, Economic Development and Innovation (Geoff Dickinson) and the Northern Territory Department of Regional Development, Primary Industries, Fisheries and Resources (Don Reilly) for their permission and assistance in the collection of leaf samples from trial sites established in northeast Queensland and in the Northern Territory.

Conflict of interest

The authors declare that they have no competing interests.

Data Archiving Statement

Data used in this study are publically available in Supplementary File 5.

Author information

Author notes

    Authors and Affiliations

    1. School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia

      Gary J. Sexton, I. D. Godwin & M. J. Dieters

    2. GeneCology Research Centre and Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia

      C. H. Frere

    3. World Agroforestry Centre (ICRAF), ICRAF-WCA/Sahel, BPE 5118, Bamako, Mali

      A. Kalinganire

    4. Les Amis de la Nature, BPE 570, Bamako, Mali

      A. Uwamariya

    5. School of Earth and Environmental Sciences, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia

      A. J. Lowe

    6. School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia

      P. J. Prentis

    Authors
    1. Gary J. Sexton
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. C. H. Frere
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. A. Kalinganire
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. A. Uwamariya
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. A. J. Lowe
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. I. D. Godwin
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. P. J. Prentis
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. M. J. Dieters
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Gary J. Sexton.

    Additional information

    Communicated by Y. Tsumura

    This article is part of the Topical Collection on Population structure

    P. J. Prentis and M. J. Dieters contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    ESM 1

    (DOCX 23 kb)

    ESM 2

    (DOCX 22 kb)

    ESM 3

    (DOCX 34 kb)

    ESM 4

    (DOCX 23 kb)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Sexton, G.J., Frere, C.H., Kalinganire, A. et al. Influence of putative forest refugia and biogeographic barriers on the level and distribution of genetic variation in an African savannah tree, Khaya senegalensis (Desr.) A. Juss. Tree Genetics & Genomes 11, 103 (2015). https://doi.org/10.1007/s11295-015-0933-3

    Download citation

    • Received:

    • Revised:

    • Accepted:

    • Published:

    • DOI: https://doi.org/10.1007/s11295-015-0933-3

    Keywords

    Search

    Navigation