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Genetic variation among and within Lithops species in Namibia


The dwarf succulent genus Lithops is endemic to Southern Africa and of considerable conservation concern. Species delimitation is often problematic and based mainly on leaf morphology, which is strongly associated with habitat. Relationships between taxa and populations in Namibia were studied with amplified fragment length polymorphisms using 44 wild Lithops populations representing 15 species and 23 taxa. Four primer pairs produced 92 polymorphic bands in the 223 samples. Expected heterozygosity (He) within taxa ranged from 0.086 to 0.450. Genetic and geographic distances were correlated according to a Mantel test. Analysis of molecular variance showed only 23% variation among the 15 investigated species. Genetic differentiation and structuring were investigated with a principal coordinate analysis, a neighbour-joining and a Bayesian phylogeny, a Bayesian clustering analysis and a discriminant analysis of principal components. In all five analyses, L. optica and L. herrei, which differ only in flower colour, clustered closely together and are here combined under L. optica. The morphologically similar species L. amicorum and L. karasmontana clustered together. Lithops amicorum is therefore reduced to subspecific level: L. karasmontana subsp. amicorum, comb. nov. Subspecific taxa overlapped to a large extent except in L. karasmontana where 13% of the variability resided among subspecies, whereas the nominal subspecies differed from subsp. bella and subsp. eberlanzii; the latter two could not be separated and are here combined under L. karasmontana subsp. bella.

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Adapted from Irish (1994). Mapping done with QGIS version 2.18.25

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Financial support was received from the SADC Plant Genetic Resources Centre (SPGRC) in Lusaka, Zambia and the Swedish International Development and Cooperation Agency (Sida). Technical support was received from the Senckenberg Biodiversitäts- und Klimaforschungszentrum, Germany (SBik-F) and assistance with statistical analyses from V. Herklotz and advices in taxonomic treatments from V. Otte (Senckenberg Museum of Natural History Görlitz, Germany). Technical, administrative and financial support was received from the Ministry of Agriculture, Water and Forestry of Namibia and especially staff at the National Botanical Research Institute (Windhoek, Namibia). The Ministry of Environment and Tourism of Namibia granted research and entry permits into National Parks. Rössing Uranium Mine, Husab Uranium mine, Langer Heinrich Mine, Namdeb Diamond mine and Scorpion Zinc mine granted access and assistance in their license areas. The late Tok Schoeman, Hilde and Frikkie Mouton (Namibia), Roy Earle (UK) and Keith Green (UK) provided information about localities. Lize von Staden of the South African National Biodiversity Institute (SANBI) and the Threatened Species Programme, Pieter van Wyk from South African National Parks (SANParks) and the Custodians of Rare and Endangered Wildlife (CREW), South Africa, are acknowledged for data to re-assess Lithops optica/L. herrei. This work would not have been possible without the Namibian farm owners who granted access to their farms and provided assistance: Mr and Ms G.S. Berg, Ms B. Boehm-Erni, C. Buhrman, W. Diergaardt, L. Gessert, J. and S. Hopkins, B. and L. Eksteen, H. Esterhuizen, W. Itzko, Ms. Koch, A. Louw, J. and J. van Niekerk, Mr. I and Ms. du Plooy (Farm Garub), N. and C. Pretorius, H and O. Pretorius, A. Rusch, F. Snyman, B.N. and J. Steyn, P. and W. Swiegers, W. Teubner, G.G. Viviers, D. De Wet, R. and R. von Wielich.

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Correspondence to Sonja Loots.

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Information on Electronic Supplementary Material

Online Resource 1. Description of each population of Lithops in Namibia from which material for DNA samples was collected.

Online Resource 2. List of voucher specimens collected from populations where DNA collections were made.

Online Resource 3. Distribution of log likelihood of ten replicates across different models (K = 1–15) computed with Bayesian clustering (a), distribution of ΔK based on the rate of change in log probability according to the method described by Evanno et al. (2005) (b), and the Bayesian information criterion (BIC) across different models of the DAPC analysis (c).

Online Resource 4. Unrooted Bayesian phylogeny of Lithops based on 92 polymorphic AFLP fragments.

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Loots, S., Nybom, H., Schwager, M. et al. Genetic variation among and within Lithops species in Namibia. Plant Syst Evol 305, 985–999 (2019).

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  • Aizoaceae
  • Molecular marker
  • Phylogenetics
  • Succulent
  • Taxonomy