References
- Bandelt, HJ, P Forster, A Röhl. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16(1):37–48. doi:https://doi.org/10.1093/oxfordjournals.molbev.a026036.
- Belkhir, K, P Borsa, L Chikhi, N Raufaste, F Bonhomme. 2004. Genetix 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France http://www.genetix.univmontp2.fr/genetix/intro.htm
- Besnard, G, D Baali-Cherif. 2009. Coexistence of diploids and triploids in a Saharan relict olive: evidence from nuclear microsatellite and flow cytometry analyses. C R Bio. 332(12):1115–1120. doi:https://doi.org/10.1016/j.crvi.2009.09.014.
- Besnard, G, C García-Verdugo, R Rubio De Casas, UA Treier, N Galland, P Vargas. 2008. Polyploidy in the olive complex (Olea europaea L.): evidence from flow cytometry and nuclear microsatellite analyses. Ann Bot. 101(1):25–30. doi:https://doi.org/10.1093/aob/mcm275.
- Besnard, G, P Hernández, B Khadari, G Dorado, V Savolainen. 2011. Genomic profiling of plastid DNA variation in the Mediterranean olive tree. BMC Plant Biol. 11(1):80. doi:https://doi.org/10.1186/1471-2229-11-80.
- CABI. 2020. Noronhia emarginata (Madagascar olive). In Invasive species compendium. Wallingford (UK): CAB International. https://www.cabi.org/isc/datasheet/19708471
- Caetano Wyler, S, Y Naciri. 2016. Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species. BMC Evol Biol. 16(1):103. doi:https://doi.org/10.1186/s12862-016-0678-0.
- Callmander, MW, PB Phillipson, GE Schatz, S Andriambololonera, M Rabarimanarivo, N Rakotonirina, J Raharimampionona, C Chatelain, L Gautier, PP Lowry II. 2011. The endemic and non-endemic vascular flora of Madagascar updated. Plant Ecol Evol. 144(2):121–125. doi:https://doi.org/10.5091/plecevo.2011.513.
- Clauss, MJ, H Cobban, T Mitchell-Olds. 2002. Cross-species microsatellite markers for elucidating population genetic structure in Arabidopsis and Arabis (Brassicaeae). Mol Ecol. 11(3):591–601. doi:https://doi.org/10.1046/j.0962-1083.2002.01465.x.
- Díaz-Rueda, P, JD Franco Navarro, R Messora, J Espartero, C Rivero, P Aleza, N Capote, M Cantos-Barragán, JL García-Fernández, de A Cires, et al. 2020. SILVOLIVE, a germplasm collection of wild subspecies with high genetic variability as a source of rootstocks and resistance genes for olive breeding. Front Plant Sci. 11:629. doi:https://doi.org/10.3389/fpls.2020.00629.
- Díaz Martínez, S, C Boedeker, GC Zuccarello. 2020. Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock. Phycologia. 59(4):355–364. doi:https://doi.org/10.1080/00318884.2020.1771524.
- Dray, S, A Dufour. 2007. The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 22(4):1–20. doi:https://doi.org/10.18637/jss.v022.i04.
- Duminil, J, M Di Michele. 2009. Plant species delimitation: a comparison of morphological and molecular markers. Plant Biosyst. 143:528–542. doi:https://doi.org/10.1080/11263500902722964.
- Feng, B, SV Yi, M Zhang, X Zhou, T-Y Chiang. 2018. Development of novel EST-SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus. PLoS ONE. 13:e0195829. doi:https://doi.org/10.1371/journal.pone.0195829.
- Freudenstein, JV, MB Broe, RA Folk, BT Sinn. 2017. Biodiversity and the species concept: lineages are not enough. Syst Biol. 66:644–656. doi:https://doi.org/10.1093/sysbio/syw098.
- Ganzhorn, JU, PP Lowry II, GE Schatz, S Sommer. 2008. The biodiversity of Madagascar: one of the world’s hottest hotspots on its way out. Oryx. 35:346–348. doi:https://doi.org/10.1046/j.1365-3008.2001.00201.x.
- García-Verdugo, C, MF Fay, C Granado-Yela, R Rubio De Casas, L Balaguer, G Besnard, P Vargas. 2009. Genetic diversity and differentiation processes in the ploidy series of Olea europaea: a multiscale approach from subspecies to insular populations. Mol Ecol. 18:454–467. doi:https://doi.org/10.1111/j.1365-294X.2008.04027.x.
- Goudet, J, M Raymond, T De Meeüs, F Rousset. 1996. Testing differentiation in diploid populations. Genetics. 144:1933–1940. doi:https://doi.org/10.1093/genetics/144.4.1933.
- Goyder, D, WJ Baker, G Besnard, J Dransfield, L Gardiner, J Moat, D Rabehevitra, L Rajaovelona, S Rakotoarisoa, F Rakotonasolo, et al. 2017. Country focus - status of knowledge of Madagascan plants. In KJ Willis, editor. State of the world’s plants 2017. Kew: Royal Botanic Gardens; p. 36–41. Chap. 6.
- Hagl, A, R Gargiulo, MF Fay, C Solofondranohatra, J Salmona, U Suescun, N Rakotomalala, CER Lehmann, G Besnard, AST Papadopoulos, et al. 2021. Geographical structure of genetic diversity in Loudetia simplex (Poaceae) in Madagascar and South Africa. Bot J Linn Soc. 196(1):81-99. doi:https://doi.org/10.1093/botlinnean/boaa098.
- Hardy, OJ, X Vekemans. 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes. 2:618–620. doi:https://doi.org/10.1046/j.1471-8286.2002.00305.x.
- Hong-Wa, C. 2016. A taxonomic revision of the genus Noronhia Stadtm. ex Thouars (Oleaceae) in Madagascar and the Comoro Islands. In MW Callmander, PP Lowry II, editors. Boissiera. Vol. 70. Geneva: Conservatoire et Jardin Botanique, 291 pages.
- Hong-Wa, C, G Besnard. 2013. Intricate patterns of relationships in the olive family as inferred from multi-locus plastid and nuclear DNA sequence analyses: a close-up on Chionanthus and Noronhia (Oleaceae). Mol Phylogenet Evol. 67:367–378. doi:https://doi.org/10.1016/j.ympev.2013.02.003.
- Hong-Wa, C, G Besnard. 2014. Diversification and species limits in the Madagascar olive. Bot J Linn Soc. 174:141–161. doi:https://doi.org/10.1111/boj.12112.
- Hurlbert, SH. 1971. The nonconcept of species diversity: a critique and alternative parameters. Ecology. 52:577–586. doi:https://doi.org/10.2307/1934145.
- Husband, BC, SJ Baldwin, J Suda. 2013. The incidence of polyploidy in natural plant populations: major patterns and evolutionary processes. In J Greilhuber, J Doležel, JF Wendel, editors. Plant genome diversity. Vol. 2. Vienna: Springer; p. 255–276.
- Jombart, T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 24:1403–1405. doi:https://doi.org/10.1093/bioinformatics/btn129.
- Kearse, M, R Moir, A Wilson, S Stones-Havas, M Cheung, S Sturrock, S Buxton, A Cooper, S Markowitz, C Duran, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28:1647–1649. doi:https://doi.org/10.1093/bioinformatics/bts199.
- Kpatènon, MJ, KV Salako, S Santoni, L Zekraoui, M Latreille, C Tollon-Cordet, C Mariac, E Jaligot, T Beulé, K Adéoti. 2020. Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin. BMC Genet. 21:145. doi:https://doi.org/10.1186/s12863-020-00955-y.
- Liang, T, W Sun, H Ren, I Ahmad, N Vu, J Huang, J Huang. 2019. Genetic diversity of Ziziphus mauritiana germplasm based on SSR markers and ploidy level estimation. Planta. 249:1875–1887. doi:https://doi.org/10.1007/s00425-019-03133-2.
- Linan, AG, GE Schatz, PP Lowry II, A Miller, CE Edwards. 2019. Ebony and the Mascarenes: the evolutionary relationships and biogeography of Diospyros (Ebenaceae) in the western Indian Ocean. Bot J Linn Soc. 190:359–373. doi:https://doi.org/10.1093/botlinnean/boz034.
- Loiselle, BA, VA Sork, J Nason, C Graham. 1995. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot. 82:1420–1425. doi:https://doi.org/10.1002/j.1537-2197.1995.tb12679.x.
- Maduna, SN, C Rossouw, C Da Silva, M Soekoe, ZE Bester-Van Der Merwe. 2017. Species identification and comparative population genetics of four coastal houndsharks based on novel NGS‐mined microsatellites. Ecol Evol. 7:1462–1486. doi:https://doi.org/10.1002/ece3.2770.
- McKendrick, L, J Provan, Ú Fitzpatrick, MJF Brown, TE Murray, E Stolle, RJ Paxton. 2017. Microsatellite analysis supports the existence of three cryptic species within the bumble bee Bombus lucorum sensu lato. Conserv Genet. 18:573–584. doi:https://doi.org/10.1007/s10592-017-0965-3.
- Perrier De La Bâthie, H. 1949. Révision des Oléacées de Madagascar et des Comores. Mémoires de l’Institut Scientifique de Madagascar, Série B, Biologie Végétale. 2:275–310.
- Perrier De La Bâthie, H. 1952. Oléacées. 166ème famille. In H Humbert, editor. Flore de Madagascar et des Comores. Paris: Muséum National d’Histoire Naturelle, 89 pages.
- R Development Core Team. 2014. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
- Raymond, M, F Rousset. 1995. Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J Hered. 86:248–249. doi:https://doi.org/10.1093/oxfordjournals.jhered.a111573.
- Ritland, K. 1996. Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res. 67:175–185. doi:https://doi.org/10.1017/S0016672300033620.
- Rohwer, JG. 1995. From flower to fruit in Noronhia emarginata (Lam.) Thouars (Oleaceae). Flora. 190:35–43. doi:https://doi.org/10.1016/S0367-2530(17)30624-2.
- Salmona, J, A Dresen, AE Ranaivoson, S Manzi, B Le Pors, C Hong-Wa, J Razanatsoa, NV Andriaholinirina, S Rasoloharijaona, ME Vavistara, et al. 2020a. How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree. bioRxiv. doi:https://doi.org/10.1101/2020.11.25.394544.
- Salmona, J, JK Olofsson, C Hong-Wa, J Razanatosa, F Rakotonasolo, H Ralimanana, T Randriamboavonjy, U Suescun, MS Vorontsova, G Besnard. 2020b. Late Miocene origin and recent population collapse of the savanna Malagasy olive (Noronhia lowryi). Biol J Linn Soc. 129:227–243. doi:https://doi.org/10.1093/biolinnean/blz164.
- Schwarz, GE. 1978. Estimating the dimension of a model. Ann Stat. 6:461–464. doi:https://doi.org/10.1214/aos/1176344136.
- Singh, HK, I Parveen, S Raghuvanshi, SB Babbar. 2012. The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species. BMC Res Notes. 5:42. doi:https://doi.org/10.1186/1756-0500-5-42.
- Skema, C. 2012. Toward a new circumscription of Dombeya (Malvales: dombeyaceae): a molecular phylogenetic and morphological study of Dombeya of Madagascar and a new segregate genus, Andringitra. Taxon. 61:612–628. doi:https://doi.org/10.1002/tax.613010.
- Tonkin-Hill, G, JA Lees, SD Bentley, SDW Frost, J Corander. 2019. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Res. 47:5539–5549. doi:https://doi.org/10.1093/nar/gkz361.
- Viruel, J, M Conejero, O Hidalgo, L Pokorny, RF Powell, F Forest, MB Kantar, M Soto Gomez, SW Graham, B Gravendeel, et al. 2019. A target capture-based method to estimate ploidy from herbarium specimens. Front Plant Sci. 10:937. doi:https://doi.org/10.3389/fpls.2019.00937.
- Wang, H, J Yang, L Boykin, QY Zhao, YJ Wang, SS Liu, XW Wang. 2014. Developing conversed microsatellite markers and their implications in evolutionary analysis of the Bemisia tabaci complex. Sci Rep. 4:6351. doi:https://doi.org/10.1038/srep06351.
- Weir, B, C Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution. 38:1358–1370. doi:https://doi.org/10.1111/j.1558-5646.1984.tb05657.x.
- Willis, KJ, L Gillson, S Knapp. 2007. Biodiversity hotspots through time: an introduction. Philos Trans R Soc B. 362:169–174. doi:https://doi.org/10.1098/rstb.2006.1976.