Tosso, F.; TERRA Research CentreCentral African Forests, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, Belgium, Evolutionary Biology and Ecology Unit CP 160/12, Faculté des SciencesUniversité Libre de Bruxelles, 50 avenue F. Roosevelt, Brussels, Belgium
Hardy, O. J.; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des SciencesUniversité Libre de Bruxelles, 50 avenue F. Roosevelt, Brussels, Belgium
Doucet, Jean-Louis ; Université de Liège - ULiège > Ingénierie des biosystèmes (Biose) > Laboratoire de Foresterie des régions trop. et subtropicales
Daïnou, Kasso ; Université de Liège - ULiège > Ingénierie des biosystèmes (Biose) > Laboratoire de Foresterie des régions trop. et subtropicales
Kaymak, E.; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des SciencesUniversité Libre de Bruxelles, 50 avenue F. Roosevelt, Brussels, Belgium
Migliore, J.; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des SciencesUniversité Libre de Bruxelles, 50 avenue F. Roosevelt, Brussels, Belgium
Language :
English
Title :
Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology
Acosta, M.C., Premoli, A.C., Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus, Nothofagaceae). Mol. Phylogenet. Evol. 54 (2010), 235–242.
Armstrong, K., Stone, G., Nicholls, J., Valderrama Escallon, E., Anderberg, A., Smedmark, J., Gautier, L., Naciri, Y., Milne, R., Richardson, J.E., Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae. Front Genet., 5, 2014.
Aubréville, A., Légumineuses. Césalpinioidées. Flore du Cameroun., 1970, Museum National d'Histoire Naturelle, Paris.
Baker, W.J., Couvreur, T.L.P., Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography. J. Biogeogr. 40 (2013), 274–285.
Barneby, R.C., Neotropical Fabales at NY: asides and oversights. Brittonia 48 (1996), 174–187.
Bruneau, A., Mercure, M., Lewis, G.P., Herendeen, P.S., Phylogenetic patterns and diversification in the caesalpinioid legumes This paper is one of a selection of papers published in the Special Issue on systematics research. Botany 86 (2008), 697–718.
Bryant, D., Moulton, V., Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21:2 (2004), 255–265.
Cattell, R., The scree test for the number of factors. MBR 1 (1966), 245–276.
Cardoso, D., De Queiroz, L.P., Pennington, R.T., De Lima, H.C., Fonty, É., Wojciechowski, M.F., Lavin, M., Revisiting the phylogeny of papilionoid legumes: new insights from comprehensively sampled early-branching lineages. Am. J. Bot. 99:12 (2012), 1991–2013.
Cavender-Bares, J., Gonzalez-Rodriguez, A., Pahlich, A., Koehler, K., Deacon, N., Phylogeography and climatic niche evolution in live oaks (Quercus series Virentes) from the tropics to the temperate zone. J. Biogeogr. 38 (2011), 962–981.
Chessel, D., Dufour, A., Dray, S., Jombart, T., Lobry, J., Ollier, S., Thioulouse, J., 2012. ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences. R Package Version 1.5-0.
Chevreux, B., Wetter, T., Suhai, S., 1999. Genome sequence assembly using trace signals and additional sequence information. In: German Conference on Bioinformatics, Heidelberg, pp. 45–56.
Christenhusz, M.J.M., Chase, M.W., Biogeographical patterns of plants in the Neotropics – dispersal rather than plate tectonics is most explanatory. Bot. J. Linn. Soc. 171 (2013), 277–286.
Conti, E., Eriksson, T., Schonenberger, J., Sytsma, K.J., Baum, D.A., Orti, G., Early Tertiary out-of-India dispersal of the Crypteroniaceae: evidence from phylogeny and molecular dating. Evolution 56 (2002), 1931–1942.
Couvreur, T.L.P., Porter-Morgan, H., Wieringa, J.J., Chatrou, L.W., Little ecological divergence associated with speciation in two African rain forest tree genera. BMC Evol. Biol., 11(1), 2011, 296.
Couvreur, T.L.P., Pirie, M.D., Chatrou, L.W., Saunders, R.M.K., Su, Y.C.F., Richardson, J.E., Erkens, R.H.J., Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal. J. Biogeogr. 38:4 (2011), 664–680.
Couvreur, T.L.P., Odd man out: why are there fewer plant species in African rain forests?. Plant Syst. Evol. 301:5 (2015), 1299–1313.
Cronn, R., Wendel, J.F., Cryptic trysts, genomic mergers, and plant speciation. New Phytol. 161 (2004), 133–142.
Daïnou, K., Mahy, G., Duminil, J., Dick, C., Doucet, J.-L., Donkpégan, A., Pluijgers, M., Sinsin, B., Lejeune, P., Hardy, O.J., Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae). Heredity, 113, 2014, 74.
Daïnou, K., Blanc-Jolivet, C., Degen, B., Kimani, P., Ndiade-Bourobou, D., Donkpegan, A.S., Tosso, F., Kaymak, E., Bourland, N., Doucet, J.-L., Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences–a case study in the tree genus Milicia. BMC Evol. Biol., 16, 2016, 259.
Darriba, D., Taboada, G.L., Doallo, R., Posada, D., jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods., 9(8), 2012 772-772.
Dauby, G., Duminil, J., Heuertz, M., Koffi, G., Stevart, T., Hardy, O.J., Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover. Mol. Ecol. 23 (2014), 2299–2312.
Doyle, J.J., A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19 (1987), 11–15.
Drummond, A.J., Rambaut, A., BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol., 7, 2007, 1.
Duminil, J., Brown, R.P., Ewédjè, E.-E.B., Mardulyn, P., Doucet, J.-L., Hardy, O.J., Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae). BMC Evol. Biol., 13, 2013, 1.
Duminil, J., Kenfack, D., Viscosi, V., Grumiau, L., Hardy, O.J., Testing species delimitation in sympatric species complexes: the case of an African tropical tree, Carapa spp. (Meliaceae). Mol. Phylogenet. Evol. 62:1 (2012), 275–285.
Duminil, J., Mona, S., Mardulyn, P., Doumenge, C., Walmacq, F., Doucet, J.L., Hardy, O.J., Late Pleistocene molecular dating of past population fragmentation and demographic changes in African rain forest tree species supports the forest refuge hypothesis. J. Biogeogr. 42 (2015), 1443–1454.
Erkens, R.H., Maas, J., Couvreur, T.L.P., From Africa via Europe to South America: migrational route of a species-rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae). J. Biogeogr. 36 (2009), 2338–2352.
Faye, A., Deblauwe, V., Mariac, C., Damien, R., Sonké, B., Vigouroux, Y., Couvreur, T.L.P., Phylogeography of the genus Podococcus (Palmae/Arecaceae) in Central African rain forests: climate stability predicts unique genetic diversity. Mol. Phylogenet. Evol. 105 (2016), 126–138.
Faye, A., Pintaud, J.C., Baker, W.J., Vigouroux, Y., Sonke, B., Couvreur, T.L.P., Phylogenetics and diversification history of African rattans (Calamoideae, Ancistrophyllinae). Bot. J. Linn. Soc. 182:2 (2016), 256–271.
Flower, B.P., Kennett, J.P., The middle Miocene climatic transition: East Antarctic ice sheet development, deep ocean circulation and global carbon cycling. Palaeogeogr. Palaeoclimatol. Palaeoecol. 108 (1994), 537–555.
Fougère-Danezan, M., Phylogénie moléculaire et morphologique des Detarieae résinifères (Leguminosae, Caesalpinioideae): contribution à l'étude de l'histoire biogéographique des légumineuses. Toulouse, 3, 2005.
Fougère-Danezan, M., Herendeen, P.S., Maumont, S., Bruneau, A., Morphological evolution in the variable resin-producing Detarieae (Fabaceae): do morphological characters retain a phylogenetic signal?. Ann. Bot. 105 (2010), 311–325.
Gower, J.C., A general coefficient of similarity and some of its properties. Biometrics, 1971, 857–871.
Hardy, O.J., Born, C., Budde, K., Daïnou, K., Dauby, G., Duminil, J., Ewédjé, E.-E.B., Gomez, C., Heuertz, M., Koffi, G.K., Comparative phylogeography of African rain forest trees: a review of genetic signatures of vegetation history in the Guineo-Congolian region. CR Geosci. 345 (2013), 284–296.
Hill, M., Smith, A., Principal component analysis of taxonomic data with multi-state discrete characters. Taxon, 1976, 249–255.
Houle, A., Floating islands: a mode of long distance dispersal for small and medium-sized terrestrial vertebrates. Divers. Distributions 4 (1998), 201–216.
Huson, D.H., Bryant, D., Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23 (2006), 254–267.
Jacobs, B.F., Palaeobotanical studies from tropical Africa: relevance to the evolution of forest, woodland and savannah biomes. Philos. Trans. Roy. Soc. B. 359 (2004), 1573–1583.
Jardim, A., Killeen, T.J., Fuentes, A., 2003. Guia de los arboles y arbustos del Bosque Seco Chiquitano, Bolívia. Santa Cruz de la Sierra, Bolivia: Editorial FAN ix, 324p.-illus., col. illus. ISBN, 1400631683.
Kaiser, H.F., The application of electronic computers to factor analysis. Educ. Psychol. Meas. 20:1 (1960), 141–151.
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., Drummond, A., Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:12 (2012), 1647–1649.
Kiers, H.A., Simple structure in component analysis techniques for mixtures of qualitative and quantitative variables. Psychometrika 56 (1991), 197–212.
Koboldt, D.C., Zhang, Q., Larson, D.E., Shen, D., Mclellan, M.D., Lin, L., Miller, C.A., Mardis, E.R., Ding, L., Wilson, R.K., VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22 (2012), 568–576.
Laliberté, E., Legendre, P., Shipley, B., Laliberté, M.E., Package ‘FD’. Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology. Ecology 91:1 (2010), 299–305.
Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (2009), 1754–1760.
Lorenzi, H., 1998. Árvores brasileiras: manual de identificação e cultivo de plantas arbóreas nativas do Brasil. Nova Odessa: Editora Plantarum 352p.-col. illus. Por Geog, 4.
Losos, J.B., Warheit, K., Schoener, T., Adaptive differentiation following experimental island colonization inAnolis lizards. Nature 387 (1997), 70–73.
Martin, M., Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17:1 (2011), 1–10.
Malé, P.J.G., Bardon, L., Besnard, G., Coissac, E., Delsuc, F., Engel, J., Lhuillier, E., Scotti-Saintagne, C., Tinaut, A., Chave, J., Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Mol. Ecol. Resour. 14 (2014), 966–975.
Maley, J., The African rain forest–main characteristics of changes in vegetation and climate from the Upper Cretaceous to the Quaternary. Proc. Royal Soc Edinburgh. Section B. Biol. Sci. 104 (1996), 31–73.
Mariac, C., Scarcelli, N., Pouzadou, J., Barnaud, A., Billot, C., Faye, A., Kougbeadjo, A., Maillol, V., Martin, G., Sabot, F., Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mol. Ecol. Resour. 14 (2014), 1103–1113.
Martín-Bravo, S., Daniel, T.F., Molecular evidence supports ancient long-distance dispersal for the amphi-Atlantic disjunction in the giant yellow shrimp plant (Barleria oenotheroides). Am. J. Bot. 103 (2016), 1103–1116.
Mcloughlin, S., The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Aust. J. Bot. 49 (2001), 271–300.
Mcpherson, H., Van Der Merwe, M., Delaney, S.K., Edwards, M.A., Henry, R.J., Mcintosh, E., Rymer, P.D., Milner, M.L., Siow, J., Rossetto, M., Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol., 13, 2013, 8.
Muellner, A.N., Savolainen, V., Samuel, R., Chase, M.W., The mahogany family “out-of-Africa”: divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity. Mol. Phylogenet. Evol. 40 (2006), 236–250.
Neophytou, C., Dounavi, A., Fink, S., Aravanopoulos, F.A., Interfertile oaks in an island environment: I. High nuclear genetic differentiation and high degree of chloroplast DNA sharing between Q. alnifolia and Q. coccifera in Cyprus. A multipopulation study. Eur. J. For. Res. 130 (2011), 543–555.
Peñalba, J.V., Smith, L.L., Tonione, M.A., Sass, C., Hykin, S.M., Skipwith, P.L., McGuire, J.A., Bowie, R.C.K., Moritz, C., Sequence capture using PCR - generated probes: a cost - effective method of targeted high - throughput sequencing for nonmodel organisms. Mol. Ecol. Resour. 14:5 (2014), 1000–1010.
Pennington, R.T., Richardson, J.E., Lavin, M., Insights into the historical construction of species-rich biomes from dated plant phylogenies, phylogenetic community structure and neutral ecological theory. New Phytol. 172 (2006), 605–616.
Piñeiro, R., Dauby, G., Kaymak, E., Hardy, O.J., 2017. Pleistocene population expansions of shade-tolerant trees indicate fragmentation of the African rainforest during the Ice Ages. In: Proc. R. Soc. B., vol. 284, 1866. doi:10.1098/rspb.2017.1800.
Plana, V., Mechanisms and tempo of evolution in the African Guineo-Congolian rainforest. Philos Trans. Roy. Soc. B-Biol. Sci. 359 (2004), 1585–1594.
Premoli, A.C., Mathiasen, P., Cristina Acosta, M., Ramos, V.A., Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus ss How deep can it be?. New Phytol. 193 (2012), 261–275.
Raven, H.P., Axelrod, D.I., Angiosperm biodiversity and past continental movements. Ann. Mo. Bot. Gard. 61 (1974), 539–673.
Renner, S.S., Clausing, G., Meyer, K., Historical biogeography of Melastomataceae: the roles of Tertiary migration and long-distance dispersal. Am. J. Bot. 88:7 (2001), 1290–1300.
Renner, S., Plant dispersal across the tropical Atlantic by wind and sea currents. Int. J. Plant Sci. 165 (2004), S23–S33.
Renner, S., Foreman, D., Murray, D., Timing transantarctic disjunctions in the Atherospermataceae (Laurales): evidence from coding and noncoding chloroplast sequences. Syst. Biol. 49 (2000), 579–591.
Revell, L.J., phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3:2 (2012), 217–223.
Reznick, D.N., Shaw, F.H., Rodd, F.H., Shaw, R.G., Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata). Science 275 (1997), 1934–1937.
Richardson, J.E., Weitz, F.M., Fay, M.F., Cronk, Q.C., Linder, H.P., Reeves, G., Chase, M.W., Rapid and recent origin of species richness in the Cape flora of South Africa. Nature 412:6843 (2001), 181–183.
Richardson, J.E., Whitlock, B.A., Meerow, A.W., Madriñán, S., The age of chocolate: a diversification history of Theobroma and Malvaceae. Front. Ecol. Evol., 3, 2015, 120.
Rohland, N., Reich, D., Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22 (2012), 939–946.
Scarcelli, N., Mariac, C., Couvreur, T.L.P., Faye, A., Richard, D., Sabot, F., Berthouly-Salazar, C., Vigouroux, Y., Intra - individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?. Mol. Ecol. Resour. 16:2 (2016), 434–445.
Schluter, D., 1998. Ecological causes of speciation. Endless forms: species and speciation, 114-129.
Slik, J.F., Arroyo-Rodríguez, V., Aiba, S.-I., Alvarez-Loayza, P., Alves, L.F., Ashton, P., Balvanera, P., Bastian, M.L., Bellingham, P.J., Van Den Berg, E., An estimate of the number of tropical tree species. Proc. Natl. Acad. Sci. 112 (2015), 7472–7477.
Smith, T.B., Wayne, R.K., Girman, D.J., Bruford, M.W., A role for ecotones in generating rainforest biodiversity. Science 276 (1997), 1855–1857.
Sytsma, K.J., Litt, A., Zjhra, M.L., Pires, J.C., Nepokroeff, M., Conti, E., Walker, J., Wilson, P.G., Clades, clocks, and continents: historical and biogeographical analysis of Myrtaceae, Vochysiaceae, and relatives in the Southern Hemisphere. Int. J. Plant Sci. 165 (2004), S85–S105.
Thorne, R.F., Floristic relationships between tropical Africa and tropical America. Meggers, B.J., Ayensu, E.S., Duckworth, W.D., (eds.) Tropical Forest Ecosystems in Africa and South America: A Comparative Review, 1973, Smithsonian Instn. Press, Washington, 27–47.
Tiffney, B.H., The Eocene North Atlantic land bridge: its importance in Tertiary and modern phytogeography of the Northern Hemisphere. J. Arnold Arbor. 66:2 (1985), 243–273.
Tiffney, B.H., Manchester, S.R., The use of geological and paleontological evidence in evaluating plant phylogeographic hypotheses in the Northern Hemisphere Tertiary. Int. J. Plant Sci. 162 (2001), S3–S17.
Tosso, F., Daïnou, K., Hardy, O.J., Sinsin, B., Doucet, J.-L., Le genre Guibourtia Benn., un taxon à haute valeur commerciale et sociétale (synthèse bibliographique). Biotechnol. Agron. Soc. Environ. 19 (2015), 71–88.
Uribe-Convers, S., Duke, J.R., Moore, M.J., Tank, D.C., A long PCR-based approach for DNA enrichment prior to next-generation sequencing for systematic studies. Appl. Plant Sci., 2, 2014, 1300063.
Williams, A.V., Miller, J.T., Small, I., Nevill, P.G., Boykin, L.M., Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia. Mol. Phylogenet. Evol. 96 (2016), 1–8.
Zerega, N.J.C., Clement, W.L., Datwyler, S.H., Weiblen, G.D., Biogeography and divergence times in the mulberry family (Moraceae). Mol. Phylogenet. Evol. 37 (2005), 402–416.