The Mediterranean Basin is recognized as one of the world's most prominent biodiversity hotspots, where past climatic changes have driven range shifts, secondary contact between populations, and gene exchange. This study investigates the impact of historical introgression on the diversification of diploid members of the genus Picris (Compositae). Using nuclear and plastid genome data obtained through the Hyb-Seq approach, we assess whether introgression contributed to the evolution of the Mediterranean Picris, potentially giving rise to multiple regional endemics. We also test whether introgression was associated with the transfer of traits such as life strategy and fruit morphology, which are involved in habitat-specific adaptation. Phylogenetic network analysis revealed two major introgression events that shaped evolutionary trajectories within the genus. The earliest and most complex events involved the Turkish endemic P. campylocarpa, which hybridized with the most recent common ancestor (MRCA) of the P. cyprica-P. pauciflora lineage and with the MRCA of the B1 subclade, comprising the P. hieracioides group and the P. scaberrima-P. strigosa lineage. The latter introgression preceded shifts from iteroparity to semelparity and from heterocarpy to homocarpy, ruling out an adaptive introgression origin for these traits. Nevertheless, all detected historical introgression events contributed to the diversification of diploid Picris taxa.

Department of Biology Faculty of Science Molecular Plant Systematic Laboratory Hacettepe University Ankara Turkey

Department of Botany Faculty of Science Charles University Prague 128 01 Czechia

Department of Botany Faculty of Science İstanbul University İstanbul Turkey

Department of Botany Faculty of Science University of South Bohemia České Budějovice 370 05 Czechia

Department of Evolutionary Plant Biology Institute of Botany of the Czech Academy of Sciences Průhonice 252 43 Czechia

Department of Zoology Comenius University Bratislava Bratislava 842 15 Slovakia

Institute of Botany Plant Science and Biodiversity Centre Slovak Academy of Sciences Bratislava 845 23 Slovakia

Zobrazit více v PubMed

Agudo, A.B. , Picó, F.X. , Mateo, R.G. , Marcer, A. , Torices, R. & Álvarez, I. (2023) Unravelling plant diversification: intraspecific genetic differentiation in hybridizing PubMed DOI

Albaladejo, R.G. & Aparicio, A. (2007) Population genetic structure and hybridization patterns in the Mediterranean endemics PubMed DOI PMC

Anderson, E. (1953) Introgressive hybridization. Biological Review, 28, 280–307.

Astuti, G. , Roma‐Marzio, F. & Peruzzi, L. (2015) The genus DOI

Baskin, C. & Baskin, J.M. (2014) Seed ecology, biogeography, and evolution of dormancy and germination. San Diego: Academic Press.

Bastide, P. , Solís‐Lemus, C. , Ané, C. , Sparks, W. & Kriebel, R. (2018) Phylogenetic comparative methods on phylogenetic networks with reticulations. Systematic Biology, 67, 800–820. Available from: 10.1093/sysbio/syy033 PubMed DOI

Blanco‐Pastor, J.L. , Vargas, P. & Pfeil, B.E. (2012). Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria. PLoS ONE, 7, e39089. Available from: 10.1371/journal.pone.0039089 PubMed DOI PMC

Bolger, A.M. , Lohse, M. & Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. Available from: 10.1093/bioinformatics/btu170 PubMed DOI PMC

Borowiec, M.L. (2016) AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ, 4, e1660. Available from: 10.7717/peerj.1660 PubMed DOI PMC

Bouckaert, R. , Vaughan, T.G. , Barido‐Sottani, J. , Duchêne, S. , Fourment, M. , Gavryushkina, A. et al. (2019) BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 15, e1006650. Available from: 10.1371/journal.pcbi.1006650 PubMed DOI PMC

Bryant, D. & Moulton, V. (2004) Neighbor‐net: an agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21, 255–265. Available from: 10.1093/molbev/msh018 PubMed DOI

Cai, L. , Xi, Z. , Lemmon, E.M. , Lemmon, A.R. , Mast, A. , Buddenhagen, C.E. et al. (2021) The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales. Systematic Biology, 70, 491–507. Available from: 10.1093/sysbio/syaa083 PubMed DOI

Constantinides, B. & Robertson, D. (2017) Kindel: indel‐aware consensus for nucleotide sequence alignments. Journal of Open Source Software, 2, e282. Available from: 10.21105/joss.00282 DOI

Cowling, R.M. , Rundel, P.W. , Lamont, B.B. , Kalin Arroyo, M. & Arianoutsou, M. (1996) Plant diversity in Mediterranean‐climate regions. Trends in Ecology & Evolution, 11, 362–366. Available from: 10.1016/0169-5347(96)10044-6 PubMed DOI

Cruz‐Mazo, G. , Buide, M.L. , Samuel, R. & Narbona, E. (2009) Molecular phylogeny of PubMed DOI

Danecek, P. , Auton, A. , Abecasis, G. , Albers, C.A. , Banks, E. , DePristo, M.A. et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156–2158. Available from: 10.1093/bioinformatics/btr330 PubMed DOI PMC

Darriba, D. , Posada, D. , Kozlov, A.M. , Stamatakis, A. , Morel, B. & Flouri, T. (2020) ModelTest‐NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Molecular Biology and Evolution, 37, 291–294. Available from: 10.1093/molbev/msz189 PubMed DOI PMC

Dodd, R.S. & Afzal‐Rafii, Z. (2004) Selection and dispersal in a multispecies oak hybrid zone. Evolution, 58, 261–269. Available from: 10.1111/j.0014-3820.2004.tb01643.x PubMed DOI

Doyle, J.J. & Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11–15.

Drummond, C.S. , Eastwood, R.J. , Miotto, S.T.S. & Hughes, C.E. (2012) Multiple continental radiations and correlates of diversification in PubMed DOI PMC

Edelman, N.B. & Mallet, J. (2021) Prevalence and adaptive impact of introgression. Annual Review of Genetics, 55, 265–283. Available from: 10.1146/annurev-genet-021821-020805 PubMed DOI

Fér, T. & Schmickl, R.E. (2018) HybPhyloMaker: target enrichment data analysis from raw reads to species trees. Evolutionary Bioinformatics, 14, e1176934317742613. Available from: 10.1177/1176934317742613 PubMed DOI PMC

Fernández‐Mazuecos, A. , Jiménez‐Mejías, P. , Rotllan‐Puig, X. & Vargas, P. (2014) Narrow endemics to Mediterranean islands: moderate genetic diversity but narrow climatic niche of the ancient, critically endangered DOI

Fernández‐Mazuecos, M. & Vargas, P. (2010) Ecological rather than geographical isolation dominates quaternary formation of Mediterranean PubMed DOI

Flouri, T. , Izquierdo‐Carrasco, F. , Darriba, D. , Aberer, A.J. , Nguyen, L.T. , Minh, B.Q. et al. (2015) The phylogenetic likelihood library. Systematic Biology, 64, 356–362. Available from: 10.1093/sysbio/syu084 PubMed DOI PMC

Friedman, J. & Rubin, M.J. (2015) All in good time: understanding annual and perennial strategies in plants. American Journal of Botany, 102, 497–499. Available from: 10.3732/ajb.1500062 PubMed DOI

Galasso, G. , Conti, F. , Peruzzi, L. , Alessandrini, A. , Ardenghi, N.M.G. , Bacchetta, G. et al. (2024) A second update to the checklist of the vascular flora alien to Italy. Plant Biosystems ‐ An International Journal Dealing with all Aspects of Plant Biology, 158(2), 297–340. Available from: 10.1080/11263504.2024.2320129 DOI

García, N. , Folk, R.A. , Meerow, A.W. , Chamala, S. , Gitzendanner, M.A. , Oliveira, R.S. et al. (2017) Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain‐lilies and allies (Amaryllidaceae tribe Hippeastreae). Molecular Phylogenetics and Evolution, 111, 231–247. Available from: 10.1016/j.ympev.2017.04.003 PubMed DOI

Gizaw, A. , Gorospe, J.M. , Kandziora, M. , Chala, D. , Gustafsson, L. , Zinaw, A. et al. (2022) Afro‐alpine flagships revisited II: elucidating the evolutionary relationships and species boundaries in the giant senecios ( DOI

Gómez, J.M. , González‐Megías, A. , Lorite, J. , Abdelaziz, M. & Perfectti, F. (2015) The silent extinction: climate change and the potential hybridization‐mediated extinction of endemic high‐mountain plants. Biodiversity and Conservation, 24, 1843–1857. Available from: 10.1007/s10531-015-0909-5 DOI

Grant, V. (1981) Plant speciation, 2nd edition. New York: Columbia University Press.

Greuter, W. (1991) Med‐checklist: a critical inventory of vascular plants concerning botanical diversity, endemism, rarity, and extinction in the Mediterranean area—an analysis based on the published volumes of med‐checklist. Botanika Chronika, 10, 63–79.

Gristina, A.S. , Fici, S. , Siragusa, M. , Fontana, I. , Garfì, G. & Carimi, F. (2014) Hybridization in DOI

Gross, B.L. , Kane, N.C. , Lexer, C. , Ludwig, F. , Rosenthal, D.M. , Donovan, L.A. et al. (2004) Reconstructing the origin of PubMed DOI PMC

Holzapfel, S.A. (1994) A revision of the genus

Hudson, A.G. , Vonlanthen, P. & Seehausen, O. (2011) Rapid parallel adaptive radiations from a single hybridogenic ancestral population. Proceedings of the Royal Society B: Biological Sciences, 278, 58–66. Available from: 10.1098/rspb.2010.0925 PubMed DOI PMC

Huson, D.H. , Kloepper, T. & Bryant, D. (2008) SplitsTree 4.0: computation of phylogenetic trees and networks. Bioinformatics, 14, 68–73. Available from: 10.1093/bioinformatics/14.1.68 DOI

Imbert, E. (2002) Ecological consequences and ontogeny of seed heteromorphism. Perspectives in Plant Ecology, Evolution and Systematics, 5, 13–36. Available from: 10.1078/1433-8319-00021 DOI

Jafari, M. & Ansari‐Pour, N. (2019) Why, when and how to adjust your P values? Cell Journal, 20, 604–607. Available from: 10.22074/cellj.2019.5992 PubMed DOI PMC

Jiménez‐Mejías, P. , Fernández‐Mazuecos, M. , Amat, M.E. & Vargas, P. (2015) Narrow endemics in European mountains: high genetic diversity within the monospecific genus DOI

Jones, K.E. , Fér, T. , Schmickl, R.E. , Dikow, R.B. , Funk, V.A. , Herrando‐Moraira, S. et al. (2019) An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. Applications in Plant Sciences, 7, e11295. Available from: 10.1002/aps3.11295 PubMed DOI PMC

Joyce, D.A. , Lunt, D.H. , Genner, M.J. , Turner, G.F. , Bills, R. & Seehausen, O. (2011) Repeated colonization and hybridization in Lake Malawi cichlids. Current Biology, 21, R108–R109. Available from: 10.1016/j.cub.2010.11.029 PubMed DOI

Junier, T. & Zdobnov, E.M. (2010) The Newick utilities: high‐throughput phylogenetic tree processing in the UNIX shell. Bioinformatics, 26, 1669–1670. Available from: 10.1093/bioinformatics/btq243 PubMed DOI PMC

Kagawa, K. & Takimoto, G. (2018) Hybridization can promote adaptive radiation by means of transgressive segregation. Ecology Letters, 21, 264–274. Available from: 10.1111/ele.12891 PubMed DOI

Kandziora, M. , Sklenář, P. , Kolář, F. & Schmickl, R. (2022) How to tackle phylogenetic discordance in recent and rapidly radiating groups? Developing a workflow using PubMed DOI PMC

Kantor, A. , Kučera, J. , Šlenker, M. , Breidy, J. , Dönmez, A.A. , Marhold, K. et al. (2023) Evolution of hygrophytic plant species in the Anatolia–Caucasus region: insights from phylogenomic analyses of PubMed DOI PMC

Karimi, N. , Grover, C.E. , Gallagher, J.P. , Wendel, J.F. , Ané, C. & Baum, D.A. (2020) Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs ( PubMed DOI

Kozak, K.M. , Joron, M. , McMillan, W.O. & Jiggins, C.D. (2021) Rampant genome‐wide admixture across the PubMed DOI PMC

Kozlov, A.M. , 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. Available from: 10.1093/bioinformatics/btz305 PubMed DOI PMC

Kremer, A. & Hipp, A.L. (2020) Oaks: an evolutionary success story. New Phytologist, 226, 987–1011. Available from: 10.1111/nph.16274 PubMed DOI PMC

Lack, H.W. (1974) Die Gattung Picris L. sensu lato im ostmediterran‐westasiatischen Raum . Dissertationes der Universität Wien.

Lack, H.W. (1979) The genus DOI

Lakušić, D. , Zbiljić, M. , Šatović, Z. , Kuzmanović, N. & Liber, Z. (2024) Asymmetric introgression and cryptic natural hybridization between two species of PubMed DOI PMC

Lavergne, S. , Molofsky, J. & Schmitt, J. (2004) The biology and ecology of narrow endemic and widespread plants: a comparative study of trait variation in 20 congeneric pairs. Oikos, 107, 505–518. Available from: 10.1111/j.0030-1299.2004.13423.x DOI

Leaché, A.D. & Bouckaert, R. (2018) Species trees and species delimitation with SNAPP: a tutorial and worked example.

Leaché, A.D. , Fujita, M.K. , Minin, V.N. & Bouckaert, R.R. (2014) Species delimitation using genome‐wide SNP data. Systematic Biology, 63, 534–542. Available from: 10.1093/sysbio/syu018 PubMed DOI PMC

Lemoine, F. , Domelevo Entfellner, J.B. , Wilkinson, E. , Correia, D. , Dávila Felipe, M. , De Oliveira, T. et al. (2018) Renewing Felsenstein's phylogenetic bootstrap in the era of big data. Nature, 556, 452–456. Available from: 10.1038/s41586-018-0043-0 PubMed DOI PMC

Lexer, C. , Welch, M.E. , Raymond, O. & Rieseberg, L.H. (2003) The origin of ecological divergence in PubMed DOI

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. Available from: 10.1093/bioinformatics/btr509 PubMed DOI PMC

Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows‐Wheeler transform. Bioinformatics, 25, 1754–1760. Available from: 10.1093/bioinformatics/btp324 PubMed DOI PMC

Liu, L. , Astuti, G. , Coppi, A. & Peruzzi, L. (2022) Different chromosome numbers but slight morphological differentiation and genetic admixture among populations of the DOI

Lopez‐Alvarado, J. & Farris, E. (2022) Ecology and evolution of plants in the Mediterranean Basin: perspectives and challenges. Plants, 11, e1584. Available from: 10.3390/plants11121584 PubMed DOI PMC

Malinsky, M. , Matschiner, M. & Svardal, H. (2021) Dsuite – fast PubMed DOI PMC

Malinsky, M. , Svardal, H. , Tyers, A.M. , Miska, E.A. , Genner, M.J. , Turner, G.F. et al. (2018) Whole‐genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nature Ecology & Evolution, 2, 1940–1955. Available from: 10.1038/s41559-018-0717-x PubMed DOI PMC

Mandel, J.R. , Dikow, R.B. , Funk, V.A. , Masalia, R.R. , Staton, S.E. , Kozik, A. et al. (2014) A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae. Applications in Plant Sciences, 2, 1300085. Available from: 10.3732/apps.1300085 PubMed DOI PMC

Marques, I. , Loureiro, J. , Draper, D. , Castro, O. & Castro, S. (2018) How much do we know about the frequency of hybridization and polyploidy in the Mediterranean region? Plant Biology, 20(Suppl. 1), 21–37. Available from: 10.1111/plb.12639 PubMed DOI

Martin, S.H. & Van Belleghem, S.M. (2017) Exploring evolutionary relationships across the genome using topology weighting. Genetics, 206, 429–438. Available from: 10.1534/genetics.116.194720 PubMed DOI PMC

Maurin, K.J.L. (2020) An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood framework. arXiv. Available from: https://arxiv.org/abs/2008.07054

McVay, J.D. , Hipp, A.L. & Manos, P.S. (2017) A genetic legacy of introgression confounds phylogeny and biogeography in oaks. Proceedings of the Royal Society B: Biological Sciences, 284, e20170300. Available from: 10.1098/rspb.2017.0300 PubMed DOI PMC

Médail, F. & Diadema, K. (2009) Glacial refugia influence plant diversity patterns in the Mediterranean Basin. Journal of Biogeography, 36, 1333–1345. Available from: 10.1111/j.1365-2699.2008.02051.x DOI

Meier, J.I. , Marques, D.A. , Mwaiko, S. , Wagner, C.E. , Excoffier, L. & Seehausen, O. (2017) Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nature Communications, 8, e14363. Available from: 10.1038/ncomms14363 PubMed DOI PMC

Morales‐Briones, D.F. , Kadereit, G. , Tefarikis, D.T. , Moore, M.J. , Smith, S.A. , Brockington, S.F. et al. (2021) Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae s.l. Systematic Biology, 70, 219–235. Available from: 10.1093/sysbio/syaa066 PubMed DOI PMC

Nieto Feliner, G. (2014) Patterns and processes in plant phylogeography in the Mediterranean Basin: a review. Perspectives in Plant Ecology, Evolution and Systematics, 16, 265–278. Available from: 10.1016/j.ppees.2014.07.002 DOI

Nieto Feliner, G. , Cellinese, N. , Crowl, A.A. & Frajman, B. (2023) Editorial: understanding plant diversity and evolution in the Mediterranean Basin. Frontiers in Plant Science, 14, 1152340. Available from: 10.3389/fpls.2023.1152340 PubMed DOI PMC

Owens, G.L. , Huang, K. , Todesco, M. & Rieseberg, L.H. (2023) Re‐evaluating homoploid reticulate evolution in PubMed DOI PMC

Page, A.J. , Taylor, B. , Delaney, A.J. , Soares, J. , Seemann, T. , Keane, J.A. et al. (2016) SNP‐sites: rapid efficient extraction of SNPs from multi‐FASTA alignments. Microbial Genomics, 2, e000056. Available from: 10.1099/mgen.0.000056 PubMed DOI PMC

Paradis, E. & Schliep, K. (2019) Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526–528. Available from: 10.1093/bioinformatics/bty633 PubMed DOI

Peruzzi, L. , Bedini, G. & Andreucci, A. (2011) Homoploid hybrid speciation in DOI

Postigo Mijarra, J.M. , Barrón, E. , Gómez Manzaneque, F. & Morla, C. (2009) Floristic changes in the Iberian Peninsula and Balearic Islands (south‐west Europe) during the Cenozoic. Journal of Biogeography, 36, 2025–2043. Available from: 10.1111/j.1365-2699.2009.02142.x DOI

Qian, Y. , Meng, M. , Zhou, C. , Liu, H. , Jiang, H. , Xu, Y. et al. (2023) The role of introgression during the radiation of endemic fishes adapted to extreme altitudes in the Tibetan plateau. Molecular Biology and Evolution, 40, msad129. Available from: 10.1093/molbev/msad129 PubMed DOI PMC

R Core Team . (2022) R: a language and environment for statistical computing, version 4.2.0. Vienna: R Foundation for Statistical Computing. Available from: https://www.r‐project.org/

Radosavljević, I. , Bogdanović, S. , Celep, F. , Filipović, M. , Satovic, Z. , Surina, B. et al. (2019) Morphological, genetic and epigenetic aspects of homoploid hybridization between PubMed DOI PMC

Rambaut, A. , Drummond, A.J. , Xie, D. , Baele, G. & Suchard, M.A. (2018) Posterior summarization in Bayesian phylogenetics using tracer 1.7. Systematic Biology, 67, 901–904. Available from: 10.1093/sysbio/syy032 PubMed DOI PMC

Rendón‐Anaya, M. , Wilson, J. , Sveinsson, S. , Fedorkov, A. , Cottrell, J. , Bailey, M.E.S. et al. (2021) Adaptive introgression facilitates adaptation to high latitudes in European aspen ( PubMed DOI PMC

Rieseberg, L.H. , Archer, M.A. & Wayne, R.K. (1999) Transgressive segregation, adaptation, and speciation. Heredity, 83, 363–372. Available from: 10.1038/sj.hdy.6886170 PubMed DOI

Rivas‐Martinez, S. & Rivas‐Saenz, S. (2016) Worldwide bioclimatic classification system, 1996–2016. Madrid: Phytosociological Research Center, University Complutense of Madrid. Available from: http://www.globalbioclimatics.org

Rose, J.P. , Toledo, C.A.P. , Moriarty Lemmon, E. , Lemmon, A.R. & Sytsma, K.J. (2021) Out of sight, out of mind: widespread nuclear and plastid‐nuclear discordance in the flowering plant genus PubMed DOI

Rosenthal, D.M. , Schwarzbach, A.E. , Donovan, L.A. , Raymond, O. & Rieseberg, L.H. (2002) Phenotypic differentiation between three ancient hybrid taxa and their parental species. International Journal of Plant Sciences, 163, 387–398. Available from: 10.1086/339237 DOI

Rundle, H.D. & Nosil, P. (2005) Ecological speciation. Ecology Letters, 8, 336–352. Available from: 10.1111/j.1461-0248.2004.00715.x DOI

Sanderson, M.J. (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101–109. Available from: 10.1093/oxfordjournals.molbev.a003974 PubMed DOI

Schluter, D. (2009) Evidence for ecological speciation and its alternative. Science, 323, 737–741. Available from: 10.1126/science.1160006 PubMed DOI

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. Available from: 10.1093/jxb/erx297 PubMed DOI

Schmickl, R. & Yant, L. (2021) Adaptive introgression: how polyploidy reshapes gene flow landscapes. New Phytologist, 230, 457–461. Available from: 10.1111/nph.17204 PubMed DOI

Schönswetter, P. , Tribsch, A. , Barfuss, M. & Niklfeld, H. (2002) Several Pleistocene refugia detected in the high alpine plant PubMed DOI

Sell, P.D. (1976) Picris L. In: Tutin, T.G. , Heywood, V.H. , Burges, N.A. , Moore, D.M. , Valentine, D.A. & Walters, S.M. (Eds.) Flora Europaea, volume 4. Cambridge: Cambridge University Press, pp. 159–160.

Skopalíková, J. , Leong‐Škorničková, J. , Šída, O. , Newman, M. , Chumová, Z. , Fér, T. et al. (2023) Ancient hybridization in PubMed DOI

Skubic, M. , Záveská, E. & Frajman, B. (2023) Meeting in Liguria: hybridization between Apennine endemic PubMed DOI

Šlenker, M. , Kantor, A. , Marhold, K. , Schmickl, R. , Mandáková, T. , Lysak, M.A. et al. (2021) Allele sorting as a novel approach to resolving the origin of allotetraploids using Hyb‐Seq data: a case study of the Balkan mountain endemic PubMed DOI PMC

Slovák, M. , Kučera, J. , Lack, H.W. , Ziffer‐Berger, J. , Melicharková, A. , Záveská, E. et al. (2018) Diversification dynamics and transoceanic Eurasian‐Australian disjunction in the genus PubMed DOI

Slovák, M. , Kučera, J. , Marhold, K. & Zozomová‐Lihová, J. (2012) The morphological and genetic variation in the polymorphic species DOI

Slovák, M. , Kučera, J. , Záveská, E. & Vďačný, P. (2014) Dealing with discordant genetic signals caused by hybridization, incomplete lineage sorting, and paucity of primary nucleotide homologies: a case study of closely related members of the genus PubMed DOI PMC

Slovák, M. , Melichárková, A. , Gbúrová Štubňová, E. , Kučera, J. , Mandáková, T. , Smyčka, J. et al. (2023) Pervasive introgression during rapid diversification of the European mountain genus PubMed DOI PMC

Slovák, M. , Šingliarová, B. & Mráz, P. (2007) Chromosome numbers and mode of reproduction in DOI

Slovák, M. , Urfus, T. , Vít, P. & Marhold, K. (2009) The Balkan endemic DOI

Slovák, M. , Vít, P. , Urfus, T. & Suda, J. (2009) Complex pattern of genome size variation in a polymorphic member of the Asteraceae. Journal of Biogeography, 36, 372–384. Available from: 10.1111/j.1365-2699.2008.02005.x DOI

Smalla, M. (2000) Studies in the Compositae of the Arabian peninsula and Socotra—6. The Hypochaeridinae (Lactuceae) in the Arabian peninsula. Willdenowia, 30, 315–337.

Smith, S.A. , Moore, M.J. , Brown, J.W. & Yang, Y. (2015) Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology, 15, e150. Available from: 10.1186/s12862-015-0423-0 PubMed DOI PMC

Smith, S.A. & O'Meara, B.C. (2012) TreePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics, 28, 2689–2690. Available from: 10.1093/bioinformatics/bts492 PubMed DOI

Solís‐Lemus, C. & Ané, C. (2016) Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genetics, 12, e1005896. Available from: 10.1371/journal.pgen.1005896 PubMed DOI PMC

Solís‐Lemus, C. , Bastide, P. & Ané, C. (2017) PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution, 34, 3292–3298. Available from: 10.1093/molbev/msx235 PubMed DOI

Souissi, A. , Gagnaire, P.A. , Bonhomme, F. & Bahri‐Sfar, L. (2016) Introgressive hybridization and morphological transgression in the contact zone between two Mediterranean PubMed DOI PMC

Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post‐analysis of large phylogenies. Bioinformatics, 30, 1312–1313. Available from: 10.1093/bioinformatics/btu033 PubMed DOI PMC

Stankowski, S. & Streisfeld, M.A. (2015) Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers. Proceedings of the Royal Society B: Biological Sciences, 282, e20151666. Available from: 10.1098/rspb.2015.1666 PubMed DOI PMC

Stebbins, G.L. (1959) The role of hybridization in evolution. Proceedings of the American Philosophical Society, 103, 231–251.

Stull, G.W. , Pham, K.K. , Soltis, P.S. & Soltis, D.E. (2023) Deep reticulation: the long legacy of hybridization in vascular plant evolution. Plant Journal, 114, 743–766. Available from: 10.1111/tpj.16142 PubMed DOI

Suárez‐González, A. , Lexer, C. & Cronk, Q.C.B. (2018) Adaptive introgression: a plant perspective. Biology Letters, 14, e20170688. Available from: 10.1098/rsbl.2017.0688 PubMed DOI PMC

Suc, J.P. (1984) Origin and evolution of the Mediterranean vegetation and climate in Europe. Nature, 307, 429–432. Available from: 10.1038/307429a0 DOI

Suchard, M.A. , Lemey, P. , Baele, G. , Ayres, D.L. , Drummond, A.J. & Rambaut, A. (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4, vey016. Available from: 10.1093/ve/vey016 PubMed DOI PMC

Sun, M. , Soltis, D.E. , Soltis, P.S. , Zhu, X. , Burleigh, J.G. & Chen, Z. (2015) Deep phylogenetic incongruence in the angiosperm clade Rosidae. Molecular Phylogenetics and Evolution, 83, 156–166. Available from: 10.1016/j.ympev.2014.11.003 PubMed DOI

Svardal, H. , Quah, F.X. , Malinsky, M. , Ngatunga, B.P. , Miska, E.A. , Salzburger, W. et al. (2020) Ancestral hybridization facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation. Molecular Biology and Evolution, 37, 1100–1113. Available from: 10.1093/molbev/msz294 PubMed DOI PMC

Tavşanoğlu, Ç. & Pausas, J. (2018) A functional trait database for Mediterranean Basin plants. Scientific Data, 5, e180135. Available from: 10.1038/sdata.2018.135 PubMed DOI PMC

Thompson, J.D. (2020) Plant evolution in the Mediterranean: insights for conservation, 2nd edition. Oxford: Oxford University Press. Available from: 10.1093/oso/9780198835141.001.000 DOI

Thompson, J.D. , Lavergne, S. , Affre, L. , Gaudeul, M. & Debussche, M. (2005) Ecological differentiation of Mediterranean endemic plants. Taxon, 54, 967–976. Available from: 10.2307/25065481 DOI

Tiburtini, M. , Tomasello, S. , Manzo, E. , Sandroni, L. , Abeli, T. & Peruzzi, L. (2025) Are Ophiolitic substrates drivers for reticulate evolution in PubMed DOI PMC

Tremetsberger, K. , Gemeinholzer, B. , Zetzsche, H. , Blackmore, S. , Kilian, N. & Talavera, S. (2013) Divergence time estimation in DOI

Ufimov, R. , Gorospe, J.M. , Fér, T. , Kandziora, M. , Salomon, L. , van Loo, M. et al. (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. Available from: 10.1111/1755-0998.13684 PubMed DOI

Valdés‐Florido, A. , González‐Toral, C. , Maguilla, E. , Cires, E. , Díaz‐Lifante, Z. , Andrés‐Camacho, C. et al. (2024) Polyploidy and hybridization in the Mediterranean: unraveling the evolutionary history of PubMed DOI PMC

Vargas, P. (2020) The Mediterranean floristic region: high diversity of plants and vegetation types. In: Goldstein, M.I. & DellaSala, D.A. (Eds.) Encyclopedia of the world's biomes, volume 3. Oxford, UK: Elsevier, pp. 602–616. Available from: 10.1016/B978-0-12-409548-9.12097-4 DOI

Vargas, P. , Fernández‐Mazuecos, M. & Heleno, R. (2018) Phylogenetic evidence for a Miocene origin of Mediterranean lineages: species diversity, reproductive traits, and geographical isolation. Plant Biology, 20, 157–165. Available from: 10.1111/plb.12626 PubMed DOI

Warnes, G. , Bolker, B. , Bonebakker, L. , Gentleman, R. , Huber, W. , Liaw, A. et al. (2024)

Xu, H. , Luo, X. , Qian, J. , Pang, X. , Song, J. , Qian, G. et al. (2012) FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS One, 7, e52249. Available from: 10.1371/journal.pone.0052249 PubMed DOI PMC

Yakimowski, S.B. & Rieseberg, L.H. (2014) The role of homoploid hybridization in evolution: a century of studies synthesizing genetics and ecology. American Journal of Botany, 101, 1247–1258. Available from: 10.3732/ajb.1400201 PubMed DOI

Yang, W. , Feiner, N. , Pinho, C. , While, G.M. , Kaliontzopoulou, A. , Harris, D.J. et al. (2021) Extensive introgression and mosaic genomes of Mediterranean endemic lizards. Nature Communications, 12, e2762. Available from: 10.1038/s41467-021-22949-9 PubMed DOI PMC

Zhang, C. , Rabiee, M. , Sayyari, E. & Mirarab, S. (2018) ASTRAL‐III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19, e153. Available from: 10.1186/s12859-018-2129-y PubMed DOI PMC