Mountains have highly heterogeneous environments that generate ample opportunities for lineage differentiation through ecological adaptation, geographic isolation and secondary contact. The geographic and ecological isolation of the afroalpine vegetation fragments on the East African mountain tops makes them an excellent system to study speciation. The initial diversification within the afroalpine endemic genus Dendrosenecio was shown to occur via allopatric divergence among four isolated mountain groups, but the potential role of ecological speciation within these groups and the role of gene flow in speciation remained uncertain. Here we extend the sampling of Dendrosenecio and use phylogenomics to assess the importance of gene flow in the diversification of the genus. Then, population genomics, demographic modelling and habitat differentiation analyses are used to study ecological speciation in two sister species occurring on Mount Kenya. We found that two sympatric sister species on Mt Kenya occupy distinct microhabitats, and our analyses support that they originated in situ via ecological speciation with gene flow. In addition, we obtained signals of admixture history between mountain groups. Taken together, these results suggest that geographic isolation shaped main lineages, while ecologically mediated speciation occurred within a single mountain.

Department of Botany Faculty of Science Charles University Benátská 2 Prague 12801 Czech Republic

Department of Evolutionary Plant Biology Institute of Botany of the Czech Academy of Sciences Zámek 1 Průhonice 25243 Czech Republic

Department of Forestry Biodiversity and Tourism Makerere University PO Box 7062 Kampala Uganda

Department of Urban Greening and Vegetation Ecology Norwegian Institute of Bioeconomy Research PO Box 115 Ås NO 1431 Norway

Department of Zoology Faculty of Science University of South Bohemia Branišovská 1645 31a České Budějovice 37005 Czech Republic

Natural History Museum University of Oslo PO Box 1172 Blindern Oslo NO 0318 Norway

Zobrazit více v PubMed

Alvarez N, Thiel‐Egenter C, Tribsch A, Holderegger R, Manel S, Schönswetter P, Taberlet P, Brodbeck S, Gaudeul M, Gielly L et al. 2009. History or ecology? Substrate type as a major driver of spatial genetic structure in alpine plants. Ecology Letters 12: 632–640.

Anacker BL, Strauss SY. 2014. The geography and ecology of plant speciation: range overlap and niche divergence in sister species. Proceedings of the Royal Society B: Biological Sciences 281: 2980.

Assefa A, Ehrich D, Taberlet P, Nemomissa S, Brochmann C. 2007. Pleistocene colonization of afro‐alpine ‘sky islands’ by the arctic‐alpine Arabis alpina. Heredity 99: 133–142.

Baldwin BG. 1997. Adaptive radiation of the Hawaiian silversword alliance: congruence and conflict of phylogenetic evidence from molecular and non‐molecular investigations. In: Givnish TJ, Sytsma KJ, eds. Molecular evolution and adaptive radiation. Cambridge, UK: Cambridge University Press, 103–128.

Beck E, Rehder H, Pongratz P, Scheibe R, Senser M. 1981. Ecological analysis of the boundary between the afroalpine vegetation types ‘Dendrosenecio woodlands’ and ‘Senecio brasiica‐Lobelia keniensis community’ on Mt. Kenya. Journal of the East Africa and Uganda Natural History Society 172: 1–11.

Beck E, Scheibe R, Schlütter I, Sauer W. 1992. Senecio × saundersii Sauer and Beck (Asteraceae), an intermediate hybrid between S. keniodendron and S. keniensis of Mt. Kenya. Phyton 32: 9–37.

Beck E, Schlüter I, Scheibe R, Schulze E. 1984. Growth rates and population rejuvenation of East African giant groundsels (Dendrosenecio keniodendron). Flora 175: 243–248.

Blanco‐Gavaldà C, Galbany‐Casals M, Susanna A, Andrés‐Sánchez S, Bayer RJ, Brochmann C, Cron GV, Bergh NG, Garcia‐Jacas N, Gizaw A et al. 2023. Repeatedly northwards and upwards: southern African grasslands fuel the colonization of the African sky islands in Helichrysum (Compositae). Plants 12: 2213.

Brochmann C, Gizaw A, Chala D, Kandziora M, Eilu G, Popp M, Pirie MD, Gehrke B. 2022. History and evolution of the afroalpine flora: in the footsteps of Olov Hedberg. Alpine Botany 132: 65–87.

Burnham KP, Anderson DR. 2002. Model selection and multimodel inference: a practical information‐theoretic approach. New York, NY, USA: Springer.

Campbell CR, Poelstra JW, Yoder AD. 2018. What is speciation genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biological Journal of the Linnean Society 124: 561–583.

Campbell DR. 2004. Natural selection in Ipomopsis hybrid zones: implications for ecological speciation. New Phytologist 161: 83–90.

Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. 2011. Stacks: building and genotyping loci de novo from short‐read sequences. G3: Genes, Genomes, Genetics 1: 171–182.

Chala D, Zimmermann NE, Brochmann C, Bakkestuen V. 2017. Migration corridors for alpine plants among the ‘sky islands’ of eastern Africa: do they, or did they exist? Alpine Botany 127: 133–144.

Clark LV, Lipka AE, Sacks EJ. 2019. POLYRAD: genotype calling with uncertainty from sequencing data in polyploids and diploids. G3: Genes, Genomes, Genetics 9: 663–673.

Clark LV, Mays W, Lipka AE, Sacks EJ. 2022. A population‐level statistic for assessing Mendelian behavior of genotyping‐by‐sequencing data from highly duplicated genomes. BMC Bioinformatics 23: 101.

Cortés AJ, Garzón LN, Valencia JB, Madriñán S. 2018. On the causes of rapid diversification in the Páramos: isolation by ecology and genomic divergence in Espeletia. Frontiers in Plant Science 9: 1025.

Cortés AJ, Wheeler JA. 2018. The environmental heterogeneity of mountains at a fine scale in a changing world. In: Hoorn C, Perrigo A, Antonelli A, eds. Mountains, climate and biodiversity. New York, NY, USA: John Wiley & Sons, 187–199.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST et al. 2011. The variant call format and VCFtools. Bioinformatics 27: 2156–2158.

Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14: 2611–2620.

Fér T, Schmickl RE. 2018. HybPhyloMaker: target enrichment data analysis from raw reads to species trees. Evolutionary Bioinformatics 14: 2613.

Ferrer Obiol J, James HF, Chesser RT, Bretagnolle V, González‐Solís J, Rozas J, Riutort M, Welch AJ. 2021. Integrating sequence capture and restriction site‐associated DNA sequencing to resolve recent radiations of pelagic seabirds. Systematic Biology 70: 976–996.

Flantua SGA, Hooghiemstra H. 2018. Historical connectivity and mountain biodiversity. In: Hoorn C, Perrigo A, Antonelli A, eds. Mountains, climate and biodiversity. Oxford, UK: John Wiley & Sons, 171–185.

Friar EA, Prince LM, Roalson EH, McGlaughlin ME, Cruse‐Sanders JM, Groot SJD, Porter JM. 2006. Ecological speciation in the East Maui‐endemic Dubautia (Asteraceae) Species. Evolution 60: 1777–1792.

Funk DJ, Nosil P, Etges WJ. 2006. Ecological divergence exhibits consistently positive associations with reproductive isolation across disparate taxa. Proceedings of the National Academy of Sciences, USA 103: 3209–3213.

Gehrke B, Kandziora M, Pirie MD. 2016. The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa. Annals of Botany 117: 121–131.

Gehrke B, Linder HP. 2014. Species richness, endemism and species composition in the tropical afroalpine flora. Alpine Botany 124: 165–177.

Gichira AW, Chen L, Li Z, Hu G, Saina JK, Gituru RW, Wang Q, Chen J. 2021. Plastid phylogenomics and insights into the inter‐mountain dispersal of the Eastern African giant senecios (Dendrosenecio, Asteraceae). Molecular Phylogenetics and Evolution 164: 107271.

Givnish TJ. 2010. Ecology of plant speciation. Taxon 59: 1326–1366.

Gizaw A, Brochmann C, Nemomissa S, Wondimu T, Masao CA, Tusiime FM, Abdi AA, Oxelman B, Popp M, Dimitrov D. 2016a. Colonization and diversification in the African ‘sky islands’: insights from fossil‐calibrated molecular dating of Lychnis (Caryophyllaceae). New Phytologist 211: 719–734.

Gizaw A, Gorospe JM, Kandziora M, Chala D, Gustafsson L, Zinaw A, Salomón L, Eilu G, Brochmann C, Kolář F et al. 2022. Afro‐alpine flagships revisited II: elucidating the evolutionary relationships and species boundaries in the giant senecios (Dendrosenecio, Asteraceae). Alpine Botany 132: 1–17.

Gizaw A, Wondimu T, Mugizi TF, Masao CA, Abdi AA, Popp M, Ehrich D, Nemomissa S, Brochmann C. 2016b. Vicariance, dispersal, and hybridization in a naturally fragmented system: the afro‐alpine endemics Carex monostachya and C. runssoroensis (Cyperaceae). Alpine Botany 126: 59–71.

Grant BR, Grant PR. 1979. Darwin's finches: population variation and sympatric speciation. Proceedings of the National Academy of Sciences, USA 76: 2359–2363.

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genetics 5: e1000695.

Hatfield T, Schluter D. 1999. Ecological speciation in sticklebacks: environment‐dependent hybrid fitness. Evolution 53: 866–873.

Hedberg O. 1957. Afroalpine vascular plants. Symbolae Botanicae Upsalienses 15: 1–411.

Hedberg O. 1961. The phytogeographical position of the afroalpine flora. Recent Advances in Botany 20: 914–919.

Hedberg O. 1962. Intercontinental crosses in Arabis alpina L. Caryologia 15: 253–260.

Hedberg O. 1964. Features of afroalpine plant ecology. Acta Phytogeographica Suecica 49: 1–144.

Hedberg O. 1969a. Evolution and speciation in a tropical high mountain flora. Biological Journal of the Linnean Society 1: 135–148.

Hedberg O. 1969b. Growth rate of the East African giant senecios. Nature 222: 163–164.

Hedberg O. 1970. Evolution of the afroalpine flora. Biotropica 2: 16.

Hedberg O. 1986. Origins of the afroalpine flora. In: Vuilleumier F, Monasterio M, eds. High altitude tropical biogeography. New York, NY, USA: Oxford University Press, 443–468.

Hernández‐Hernández T, Miller EC, Román‐Palacios C, Wiens JJ. 2021. Speciation across the Tree of Life. Biological Reviews 96: 1205–1242.

Hooghiemstra H, Van der Hammen T. 2004. Quaternary ice‐age dynamics in the Colombian Andes: developing an understanding of our legacy. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359: 173–181.

Inouye DW. 2020. Effects of climate change on alpine plants and their pollinators. Annals of the New York Academy of Sciences 1469: 26–37.

Jafari M, Ansari‐Pour N. 2019. Why, when and how to adjust your P values? Cell Journal (Yakhteh) 20: 604–607.

Jombart T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403–1405.

Jonsell B. 1982. Cruciferae. In: Polhill RM, ed. Flora of tropical East Africa. London, UK: Royal Botanical Gardens Kew.

Kandziora M, Gehrke B, Popp M, Gizaw A, Brochmann C, Pirie MD. 2022. The enigmatic tropical alpine flora on the African sky islands is young, disturbed, and unsaturated. Proceedings of the National Academy of Sciences, USA 119: e2112737119.

Kandziora M, Gorospe JM, Salomon L, Vásquez DLA, Vargas MP, Kolář F, Sklenář P, Schmickl R. 2024. The ghost of past climate acting on present‐day plant diversity: Lessons from a climate‐based delimitation of the tropical alpine ecosystem. Journal of Systematics and Evolution 62: 275–290.

Knox EB. 2005. Dendrosenecio. In: Beentje H, ed. Flora of tropical East Africa, compositae (part 3). London, UK: Royal Botanical Gardens Kew, 548–563.

Knox EB, Kowal RR. 1993. Chromosome numbers of the East African giant senecios and giant lobelias and their evolutionary significance. American Journal of Botany 80: 847–853.

Knox EB, Palmer JD. 1998. Chloroplast DNA evidence on the origin and radiation of the giant lobelias in eastern Africa. Systematic Botany 23: 109.

Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I. 2015. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15: 1179–1191.

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML‐NG: a fast, scalable and user‐friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35: 4453–4455.

Lagomarsino LP, Condamine FL, Antonelli A, Mulch A, Davis CC. 2016. The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae). New Phytologist 210: 1430–1442.

Levin DA. 2012. The long wait for hybrid sterility in flowering plants. New Phytologist 196: 666–670.

Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27: 2987–2993.

Li J‐L, Zhong L‐L, Wang J, Ma T, Mao K‐S, Zhang L. 2021. Genomic insights into speciation history and local adaptation of an alpine aspen in the Qinghai–Tibet Plateau and adjacent highlands. Journal of Systematics and Evolution 59: 1220–1231.

Lisiecki LE, Raymo ME. 2005. A Pliocene‐Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20: 1–17.

Liu J, Möller M, Provan J, Gao L‐M, Poudel RC, Li D‐Z. 2013. Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot. New Phytologist 199: 1093–1108.

Lowry DB, Rockwood RC, Willis JH. 2008. Ecological reproductive isolation of coast and inland races of Mimulus guttatus. Evolution 62: 2196–2214.

Mabberley DJ. 1973. Evolution in the giant groundsels. Kew Bulletin 28: 61–96.

Mairal M, Namaganda M, Gizaw A, Chala D, Brochmann C, Catalán P. 2021. Multiple mountain‐hopping colonization of sky‐islands on the two sides of Tropical Africa during the Pleistocene: the afroalpine Festuca grasses. Journal of Biogeography 48: 1858–1874.

Malinsky M, Matschiner M, Svardal H. 2021. DSUITE–FastD‐statistics and related admixture evidence from VCF files. Molecular Ecology Resources 21: 584–595.

Mallet J. 2007. Hybrid speciation. Nature 446: 279–283.

Mandel JR, Dikow RB, Funk VA, Masalia RR, Staton SE, Kozik A, Michelmore RW, Rieseberg LH, Burke JM. 2014. A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae. Applications in Plant Sciences 2: 1300085.

Masao CA, Gizaw A, Piñeiro R, Tusiime FM, Wondimu T, Abdi AA, Popp M, Gussarova G, Lye KA, Munishi P et al. 2013. Phylogeographic history and taxonomy of some afro‐alpine grasses assessed based on AFLPs and morphometry: Deschampsia cespitosa, D. angusta and Koeleria capensis. Alpine Botany 123: 107–122.

Maurin KJL. 2020. An empirical guide for producing a dated phylogeny with TREEPL in a maximum likelihood framework. arXiv. doi: 10.48550/arXiv.2008.07054.

McLaughlin JF, Winker K. 2020. An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data. PeerJ 8: e9939.

Meirmans PG. 2020. Genodive v.3.0: Easy‐to‐use software for the analysis of genetic data of diploids and polyploids. Molecular Ecology Resources 20: 1126–1131.

Milne‐Redhead E. 2000. Ranunculaceae. In: Turrill WB, ed. Flora of tropical East Africa. London, UK: Royal Botanic Gardens Kew.

Mizuno K. 2005. Glacial fluctuation and vegetation succession on Tyndall Glacier, Mt. Kenya. Mountain Research and Development 25: 68–75.

Mizuno K, Fujita T. 2014. Vegetation succession on Mt. Kenya in relation to glacial fluctuation and global warming. Journal of Vegetation Science 25: 559–570.

Momigliano P, Florin A‐B, Merilä J. 2021. Biases in demographic modeling affect our understanding of recent divergence. Molecular Biology and Evolution 38: 2967–2985.

Nevado B, Contreras‐Ortiz N, Hughes C, Filatov DA. 2018. Pleistocene glacial cycles drive isolation, gene flow and speciation in the high‐elevation Andes. New Phytologist 219: 779–793.

Noor MAF. 1999. Reinforcement and other consequences of sympatry. Heredity 83: 503–508.

Nosil P. 2008. Speciation with gene flow could be common. Molecular Ecology 17: 2103–2106.

Nosil P, Vines TH, Funk DJ. 2005. Reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution 59: 705–719.

O'Dea A, Lessios HA, Coates AG, Eytan RI, Restrepo‐Moreno SA, Cione AL, Collins LS, de Queiroz A, Farris DW, Norris RD et al. 2016. Formation of the Isthmus of Panama. Science Advances 2: e1600883.

Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin P, O'Hara R, Simpson G, Solymos P et al. 2022. vegan community ecology package v.2.6‐4. [WWW document] URL https://CRAN.R‐project.org/package=vegan.

Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR. 2016. SNP‐sites: rapid efficient extraction of SNPs from multi‐FASTA alignments. Microbial Genomics 2: e000056.

Papadopulos AST, Baker WJ, Crayn D, Butlin RK, Kynast RG, Hutton I, Savolainen V. 2011. Speciation with gene flow on Lord Howe Island. Proceedings of the National Academy of Sciences, USA 108: 13188–13193.

Paton AJ, Bramley G, Ryding O, Polhill RM, Harvey YB, Iwarsson M, Willis F, Phillipson PB, Balkwill K, Lukhoba CW et al. 2009. Lamiaceae (Labiatae). In: Beentje HJ, Ghazanfar SA, Polhill RM, eds. Flora of tropical East Africa. London, UK: Royal Botanic Gardens Kew.

Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. 2012. Ancient admixture in human history. Genetics 192: 1065–1093.

Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non‐model species. PLoS ONE 7: e37135.

Piálek L, Burress E, Dragová K, Almirón A, Casciotta J, Říčan O. 2019. Phylogenomics of pike cichlids (Cichlidae: Crenicichla) of the C. mandelburgeri species complex: rapid ecological speciation in the Iguazú River and high endemism in the Middle Paraná basin. Hydrobiologia 832: 355–375.

Podos J, Dybboe R, Jensen MO. 2013. Ecological speciation in Darwin's finches: parsing the effects of magic traits. Current Zoology 59: 8–19.

Portik DM, Leaché AD, Rivera D, Barej MF, Burger M, Hirschfeld M, Rödel M‐O, Blackburn DC, Fujita MK. 2017. Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection. Molecular Ecology 26: 5245–5263.

Pouchon C, Lavergne S, Fernández Á, Alberti A, Aubert S, Mavárez J. 2021. Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia. American Journal of Botany 108: 113–128.

Powell CLE, Waskin S, Battistuzzi FU. 2020. Quantifying the error of secondary vs. distant primary calibrations in a simulated environment. Frontiers in Genetics 11: 5268.

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

Pyron RA, Burbrink FT. 2010. Hard and soft allopatry: physically and ecologically mediated modes of geographic speciation. Journal of Biogeography 37: 2005–2015.

de Queiroz K. 2007. Species concepts and species delimitation. Systematic Biology 56: 879–886.

R Core Team. 2018. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.

Rabiee M, Sayyari E, Mirarab S. 2019. Multi‐allele species reconstruction using ASTRAL. Molecular Phylogenetics and Evolution 130: 286–296.

Rahbek C, Borregaard MK, Antonelli A, Colwell RK, Holt BG, Nogues‐Bravo D, Rasmussen CMØ, Richardson K, Rosing MT, Whittaker RJ et al. 2019. Building mountain biodiversity: Geological and evolutionary processes. Science 365: 1114–1119.

Ramsey J, Bradshaw JR, Schemske DW. 2003. Components of reproductive isolation between the monkeyflowers Mimulus lewisii and M. cardinalis (Phrymaceae). Evolution 57: 1520–1534.

Richards TJ, Ortiz‐Barrientos D. 2016. Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus. Evolution 70: 1239–1248.

Robbins EHJ, Kelly S. 2023. The evolutionary constraints on Angiosperm chloroplast adaptation. Genome Biology and Evolution 15: evad101.

Robinson JD, Coffman AJ, Hickerson MJ, Gutenkunst RN. 2014. Sampling strategies for frequency spectrum‐based population genomic inference. BMC Evolutionary Biology 14: 254.

Rochette NC, Rivera‐Colón AG, Catchen JM. 2019. STACKS2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Molecular Ecology 28: 4737–4754.

Ronfort J, Jenczewski E, Bataillon T, Rousset F. 1998. Analysis of population structure in autotetraploid species. Genetics 150: 921–930.

Rundle HD, Nosil P. 2005. Ecological speciation. Ecology Letters 8: 336–352.

Sanderson MJ. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19: 101–109.

Sang T, Crawford DJ, Stuessy TF, Silva M. 1995. ITS sequences and the phylogeny of the genus Robinsonia (Asteraceae). Systematic Botany 20: 55–64.

Savolainen V, Anstett M‐C, Lexer C, Hutton I, Clarkson JJ, Norup MV, Powell MP, Springate D, Salamin N, Baker WJ. 2006. Sympatric speciation in palms on an oceanic Island. Nature 441: 210–213.

Sayyari E, Mirarab S. 2016. Fast coalescent‐based computation of local branch support from quartet frequencies. Molecular Biology and Evolution 33: 1654–1668.

Schenk JJ. 2016. Consequences of secondary calibrations on divergence time estimates. PLoS ONE 11: e0148228.

Schluter D. 2009. Evidence for ecological speciation and its alternative. Science 323: 737–741.

Schluter D, Conte GL. 2009. Genetics and ecological speciation. Proceedings of the National Academy of Sciences, USA 106: 9955–9962.

Schmickl R, Marburger S, Bray S, Yant L. 2017. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. Journal of Experimental Botany 68: 5453–5470.

Seehausen O, Takimoto G, Roy D, Jokela J. 2008. Speciation reversal and biodiversity dynamics with hybridization in changing environments. Molecular Ecology 17: 30–44.

Smith AP, Young TP. 1982. The cost of reproduction in Senecio keniodendron, a giant rosette species of Mt. Kenya. Oecologia 55: 243–247.

Smith AP, Young TP. 1994. Population biology of Senecio keniodendron (Asteraceae), an afroalpine giant rosette plant. In: Smith AP, Meinzer FC, Rundel PW, eds. Tropical alpine environments: plant form and function. Cambridge, UK: Cambridge University Press, 273–294.

Smith SA, O'Meara BC. 2012. TREEPL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28: 2689–2690.

Spiess A‐N. 2018. qpcR: modelling and analysis of real‐time PCR data v. 1.4. [WWW document] URL https://CRAN.R‐project.org/package=qpcR.

Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. 2018. Bayesian phylogenetic and phylodynamic data integration using beast 1.10. Virus Evolution 4: vey016.

Suvorov A, Kim BY, Wang J, Armstrong EE, Peede D, D'Agostino ERR, Price DK, Waddell PJ, Lang M, Courtier‐Orgogozo V et al. 2022. Widespread introgression across a phylogeny of 155 Drosophila genomes. Current Biology 32: 111–123.

Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.

Taylor P. 1989. Primulaceae. In: Hubbard CE, Milne‐Redhead E, eds. Flora of tropical East Africa. London, UK: Royal Botanic Gardens Kew.

Totland Ø. 2001. Environment‐dependent pollen limitation and selection on floral traits in an alpine species. Ecology 82: 2233–2244.

Turelli M, Barton NH, Coyne JA. 2001. Theory and speciation. Trends in Ecology & Evolution 16: 330–343.

Turrill WB. 1956. Caryophyllaceae. In: Polhill RM, Milne‐Redhead E, eds. Flora of tropical East Africa. London, UK: Royal Botanic Gardens Kew.

Tusiime FM, Gizaw A, Gussarova G, Nemomissa S, Popp M, Masao CA, Wondimu T, Abdi AA, Mirré V, Muwanika V et al. 2020. Afro‐alpine flagships revisited: parallel adaptation, intermountain admixture and shallow genetic structuring in the giant senecios (Dendrosenecio). PLoS ONE 15: e0228979.

Ufimov R, Gorospe JM, Fér T, Kandziora M, Salomon L, van Loo M, Schmickl R. 2022. Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data. Molecular Ecology Resources 22: 3018–3034.

Verdcourt B. 1994. Lythraceae. In: Polhill RM, ed. Flora of tropical East Africa. London, UK: Royal Botanic Gardens Kew.

Waser NM, Campbell DR. 2004. Ecological speciation in flowering plants. In: Adaptive speciation. Cambridge, UK: Cambridge University Press, 264–277.

Wichura H, Jacobs LL, Lin A, Polcyn MJ, Manthi FK, Winkler DA, Strecker MR, Clemens M. 2015. A 17‐Myr‐old whale constrains onset of uplift and climate change in East Africa. Proceedings of the National Academy of Sciences, USA 112: 3910–3915.

Wondimu T, Gizaw A, Tusiime FM, Masao CA, Abdi AA, Gussarova G, Popp M, Nemomissa S, Brochmann C. 2014. Crossing barriers in an extremely fragmented system: two case studies in the afro‐alpine sky Island flora. Plant Systematics and Evolution 300: 415–430.

Young TP, Peacock MM. 1992. Giant senecios and alpine vegetation of Mount Kenya. Journal of Ecology 80: 141–148.

Zhang C, Rabiee M, Sayyari E, Mirarab S. 2018. astral‐iii: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19: 153.

Zhao S‐Y, Chen L‐Y, Muchuku JK, Hu G‐W, Wang Q‐F. 2016. Genetic adaptation of giant lobelias (Lobelia aberdarica and Lobelia telekii) to different altitudes in East African mountains. Frontiers in Plant Science 7: 488.