Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of Cardamine (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic in situ hybridization (GISH), to resolve the origin of tetraploid Cardamine barbaraeoides endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for C. barbaraeoides, which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.

Central European Institute of Technology Masaryk University Brno Czechia

Department of Botany Faculty of Science Charles University Prague Czechia

Department of Experimental Biology Faculty of Science Masaryk University Brno Czechia

Independent Researcher Žibritov Slovakia

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

Institute of Botany The Czech Academy of Sciences Průhonice Czechia

National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czechia

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Álvarez I., Wendel J. F. (2003). Ribosomal ITS sequences and plant phylogenetic inference. PubMed DOI

Ančev M., Yurukova-Grancharova P., Ignatova P., Goranova V., Stoyanov S., Yankova-Tsvetkova E., et al. (2013).

Andermann T., Fernandes A. M., Olsson U., Töpel M., Pfeil B., Oxelman B., et al. (2019). Allele phasing greatly improves the phylogenetic utility of ultraconserved elements. PubMed DOI PMC

Ansell S. W., Stenøien H. K., Grundmann M., Russell S. J., Koch M. A., Schneider H., et al. (2011). The importance of Anatolian mountains as the cradle of global diversity in PubMed DOI PMC

Arcila D., Ortí G., Vari R., Armbruster J. W., Stiassny M. L. J., Ko K. D., et al. (2017). Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life. PubMed DOI

Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. PubMed DOI PMC

Bastkowski S., Mapleson D., Spillner A., Wu T., Balvociute M., Moulton V. (2018). SPECTRE: a suite of phylogenetic tools for reticulate evolution. PubMed DOI PMC

Bilgin R. (2011). Back to the suture: the distribution of intraspecific genetic diversity in and around Anatolia. PubMed DOI PMC

Blanco-Pastor J. L., Vargas P., Pfeil B. E. (2012). Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean PubMed DOI PMC

Bolger A. M., Lohse M., Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. PubMed DOI PMC

Borowiec M. L. (2016). AMAS: a fast tool for alignment manipulation and computing of summary statistics. PubMed DOI PMC

Brandrud M. K., Baar J., Lorenzo M. T., Athanasiadis A., Bateman R. M., Chase M. W., et al. (2020). Phylogenomic relationships of diploids and the origins of allotetraploids in PubMed DOI PMC

Brassac J., Blattner F. R. (2015). Species-level phylogeny and polyploid relationships in PubMed DOI PMC

Brysting A. K., Oxelman B., Huber K. T., Moulton V., Brochmann C. (2007). Untangling complex histories of genome mergings in high polyploids. PubMed DOI

Caković D., Stešević D., Schönswetter P., Frajman B. (2015). How many taxa? Spatiotemporal evolution and taxonomy of DOI

Cao Z., Liu X., Ogilvie H. A., Yan Z., Nakhleh L. (2019). DOI

Carlsen T., Bleeker W., Hurka H., Elven R., Brochmann C. (2009). Biogeography and phylogeny of DOI

Carter K. A., Liston A., Bassil N. V., Alice L. A., Bushakra J. M., Sutherland B. L., et al. (2019). Target capture sequencing unravels PubMed DOI PMC

Chen H., German D. A., Al-Shehbaz I. A., Yue J., Sun H. (2020). Phylogeny of Euclidieae (Brassicaceae) based on plastome and nuclear ribosomal DNA data. PubMed DOI

Chernomor O., von Haeseler A., Minh B. Q. (2016). Terrace aware data structure for phylogenomic inference from supermatrices. PubMed DOI PMC

Cires E., Baltisberger M., Cuesta C., Vargas P., Prieto J. A. F. (2014). Allopolyploid origin of the Balkan endemic DOI

Crowl A. A., Myers C., Cellinese N. (2017). Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean PubMed DOI PMC

Dauphin B., Grant J. R., Farrar D. R., Rothfels C. J. (2018). Rapid allopolyploid radiation of moonwort ferns ( PubMed DOI

Degnan J. H., Rosenberg N. A. (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. PubMed DOI

del Valle J. C., Casimiro-Soriguer I., Buide M. L., Narbona E., Whittall J. B. (2019). Whole plastome sequencing within PubMed DOI PMC

Doležel J., Greilhuber J., Suda J. (2007). Estimation of nuclear DNA content in plants using flow cytometry. PubMed DOI

Durović S., Schönswetter P., Niketić M., Tomović G., Frajman B. (2017). Disentangling relationships among the members of the DOI

Eriksson J. S., de Sousa F., Bertrand Y. J. K., Antonelli A., Oxelman B., Pfeil B. E. (2018). Allele phasing is critical to revealing a shared allopolyploid origin of PubMed DOI PMC

Evanno G., Regnaut S., Goudet J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. PubMed DOI

Fonseca L. H. M., Lohmann L. G. (2019). Exploring the potential of nuclear and mitochondrial sequencing data generated through genome-skimming for plant phylogenetics: a case study from a clade of neotropical lianas. DOI

Freyman W. A., Johnson M. G., Rothfels C. J. (2020). Homologizer: phylogenetic phasing of gene copies into polyploid subgenomes. PubMed DOI

Georghiou K., Delipetrou P. (2010). Patterns and traits of the endemic plants of Greece. DOI

Gonçalves D. J. P., Simpson B. B., Ortiz E. M., Shimizu G. H., Jansen R. K. (2019). Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. PubMed DOI

Grover C. E., Gallagher J. P., Jareczek J. J., Page J. T., Udall J. A., Gore M. A., et al. (2015). Re-evaluating the phylogeny of allopolyploid PubMed DOI

Grünewald S., Spillner A., Bastkowski S., Bögershausen A., Moulton V. (2013). SuperQ: computing super networks from quartets. PubMed DOI

Harrison S., Noss R. (2017). Endemism hotspots are linked to stable climatic refugia. PubMed DOI PMC

Heibl C. (2008).

Hewitt G. M. (2011). “Mediterranean peninsulas: the evolution of hotspots,” in DOI

Huang X. C., German D. A., Koch M. A. (2020). Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. PubMed DOI PMC

Jakobsson M., Rosenberg N. A. (2007). CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. PubMed DOI

Jalas J., Suominen J. (1994).

Johnson M. G., Gardner E. M., Liu Y., Medina R., Goffinet B., Shaw A. J., et al. (2016). HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. PubMed DOI PMC

Jones B. M. G., Akeroyd J. R. (1993). “

Junier T., Zdobnov E. M. (2010). The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. PubMed DOI PMC

Kalyaanamoorthy S., Minh B. Q., Wong T. K., von Haeseler A., Jermiin L. S. (2017). Model finder: fast model selection for accurate phylogenetic estimates. PubMed DOI PMC

Kamneva O. K., Syring J., Liston A., Rosenberg N. A. (2017). Evaluating allopolyploid origins in strawberries ( PubMed DOI PMC

Karbstein K., Tomasello S., Hodač L., Dunkel F. G., Daubert M., Hörandl E. (2020). Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic DOI

Kates H. R., Johnson M. G., Gardner E. M., Zerega N. J. C., Wickett N. J. (2018). Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of PubMed DOI

Katoh K., Standley D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. PubMed DOI PMC

Kaya S., Çiplak B. (2017). Phylogeography and taxonomy of the DOI

Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., et al. (2012). Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. PubMed DOI PMC

Koch M. A., Karl R., German D. A. (2017). Underexplored biodiversity of Eastern Mediterranean biota: systematics and evolutionary history of the genus PubMed DOI PMC

Konowalik K., Wagner F., Tomasello S., Vogt R., Oberprieler C. (2015). Detecting reticulate relationships among diploid PubMed DOI

Kougioumoutzis K., Kokkoris I. P., Panitsa M., Kallimanis A., Strid A., Dimopoulos P. (2021). Plant endemism centres and biodiversity hotspots in Greece. 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. PubMed DOI PMC

Krak K., Caklová P., Chrtek J., Fehrer J. (2013). Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation ( PubMed DOI PMC

Kučera J., Lihová J., Marhold K. (2006). Taxonomy and phylogeography of DOI

Kučera J., Marhold K., Lihová J. (2010). DOI

Kučera J., Valko I., Marhold K. (2005). On-line database of the chromosome numbers of the genus

Kyriakidou M., Tai H. H., Anglin N. L., Ellis D., Strömvik M. V. S. (2018). Current strategies of polyploid plant genome sequence assembly. PubMed DOI PMC

Langmead B., Salzberg S. L. (2012). Fast gapped-read alignment with Bowtie 2. PubMed DOI PMC

Larridon I., Villaverde T., Zuntini A. R., Pokorny L., Brewer G. E., Epitawalage N., et al. (2020). Tackling rapid radiations with targeted sequencing. PubMed DOI PMC

Lautenschlager U., Wagner F., Oberprieler C. (2020). AllCoPol: inferring allele co-ancestry in polyploids. PubMed DOI PMC

Li H., Durbin R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. PubMed DOI PMC

Lihová J., Fuertes Aguilar J., Marhold K., Nieto Feliner G. (2004a). Origin of the disjunct tetraploid PubMed DOI

Lihová J., Marhold K. (2006). “Phylogenetic and diversity patterns in

Lihová J., Shimizu K. K., Marhold K. (2006). Allopolyploid origin of PubMed DOI

Lihová J., Tribsch A., Marhold K. (2003). The DOI

Lihová J., Tribsch A., Stuessy T. F. (2004b). DOI

López-González N., Bobo-Pinilla J., Padilla-García N., Loureiro J., Castro S., Rojas-Andrés B. M., et al. (2021). Genetic similarities versus morphological resemblance: unraveling a polyploid complex in a Mediterranean biodiversity hotspot. PubMed DOI

López-Vinyallonga S., López-Pujol J., Constantinidis T., Susanna A., Garcia-Jacas N. (2015). Mountains and refuges: genetic structure and evolutionary history in closely related, endemic PubMed DOI

Lövkvist B. (1956). The

Maddison W. P. (1997). Gene trees in species trees. DOI

Madlung A., Wendel J. F. (2013). Genetic and epigenetic aspects of polyploid evolution in plants. PubMed DOI

Maguilla E., Escudero M., Hipp A. L., Luceño M. (2017). Allopatric speciation despite historical gene flow: divergence and hybridization in PubMed DOI

Mandáková T., Kovařík A., Zozomová-Lihová J., Shimizu-Inatsugi R., Shimizu K. K., Mummenhoff K., et al. (2013). The more the merrier: recent hybridization and polyploidy in PubMed DOI PMC

Mandáková T., Lysak M. A. (2016a). Chromosome preparation for cytogenetic analyses in PubMed DOI

Mandáková T., Lysak M. A. (2016b). Painting of PubMed DOI

Mandáková T., Marhold K., Lysak M. A. (2014). The widespread crucifer species PubMed DOI

Mandáková T., Zozomová-Lihová J., Kudoh H., Zhao Y., Lysak M. A., Marhold K. (2019). The story of promiscuous crucifers: origin and genome evolution of an invasive species, PubMed DOI PMC

Marhold K., Ančev M. E. (1999).

Marhold K., Ančev M. E., Tan K. (1996). A new subspecies of

Marhold K., Kudoh H., Pak J. H., Watanabe K., Španiel S., Lihová J. (2010). Cytotype diversity and genome size variation in eastern Asian polyploid PubMed DOI PMC

Marhold K., Lihová J., Perný M., Bleeker W. (2004). Comparative ITS and AFLP analysis of diploid PubMed DOI PMC

Marhold K., Lihová J., Perný M., Grupe R., Neuffer B. (2002). Natural hybridization in DOI

Marhold K., Šlenker M., Zozomová-Lihová J. (2018). Polyploidy and hybridization in the Mediterranean and neighbouring areas towards the north: examples from the genus DOI

Marhold K., Tan K. (2000). The distribution of

Marques I., Loureiro J., Draper D.,, Castro O., Castro S. (2018). How much do we know about the frequency of hybridisation and polyploidy in the Mediterranean region? PubMed DOI

Martin M., Patterson M., Garg S., Fischer S., Pisanti N., Klau G. W., et al. (2016). DOI

Médail F., Diadema K. (2009). Glacial refugia influence plant diversity patterns in the Mediterranean Basin. DOI

Médail F., Quézel P. (1997). Hot-spots analysis for conservation of plant biodiversity in the Mediterranean Basin. DOI

Melichárková A., Šlenker M., Zozomová-Lihová J., Skokanová K., Šingliarová B., Kačmárová T., et al. (2020). So closely related and yet so different: Strong contrasts between the evolutionary histories of species of the PubMed DOI PMC

Melichárková A., Španiel S., Brišková D., Marhold K., Zozomová-Lihová J. (2017). Unravelling allopolyploid origins in the DOI

Melichárková A., Španiel S., Marhold K., Hurdu B. I., Drescher A., Zozomová-Lihová J. (2019). Diversification and independent polyploid origins in the disjunct species PubMed DOI

Morales-Briones D. F., Liston A., Tank D. C. (2018). Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus PubMed DOI

Muellner-Riehl A. N., Schnitzler J., Kissling W. D., Mosbrugger V., Rijsdijk K. F., Seijmonsbergen A. C., et al. (2019). Origins of global mountain plant biodiversity: testing the ‘mountain-geobiodiversity hypothesis’. DOI

Myers N., Mittermeier R. A., Mittermeier C. G., da Fonseca G. A., Kent J. (2000). Biodiversity hotspots for conservation priorities. PubMed DOI

Naciri Y., Linder H. P. (2015). Species delimitation and relationships: The dance of the seven veils. DOI

Nieto Feliner G. (2014). Patterns and processes in plant phylogeography in the Mediterranean Basin. A review. DOI

Nieto Feliner G., Rosselló J. A. (2012). “Concerted evolution of multigene families and homoeologous recombination,” in DOI

Nikolov L. A., Shushkov P., Nevado B., Gan X., Al-Shehbaz I. A., Filatov D., et al. (2019). Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. PubMed DOI

Oberprieler C., Wagner F., Tomasello S., Konowalik K. (2017). A permutation approach for inferring species networks from gene trees in polyploid complexes by minimising deep coalescences. DOI

Olšavská K., Slovák M., Marhold K., Štubňová E., Kučera J. (2016). On the origins of Balkan endemics: the complex evolutionary history of the PubMed DOI PMC

Oxelman B., Brysting A. K., Jones G. R., Marcussen T., Oberprieler C., Pfeil B. E. (2017). Phylogenetics of allopolyploids.

Özüdoğru B., Mummenhoff K. (2020). Phylogenetic and biogeographical history confirm the Anatolian origin of DOI

Page J. T., Gingle A. R., Udall J. A. (2013). PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms. PubMed DOI PMC

Panitsa M., Kagiampaki A., Kougioumoutzis K. (2018). “Plant diversity and biogeography of the Aegean Archipelago: a new synthesis,” in

Pease J. B., Brown J. W., Walker J. F., Hinchliff C. E., Smith S. A. (2018). Quartet sampling distinguishes lack of support from conflicting support in the green plant tree of life. PubMed DOI

Perný M., Tribsch A., Anchev M. E. (2004). Infraspecific differentiation in the Balkan diploid DOI

Perný M., Tribsch A., Stuessy T. F., Marhold K. (2005a). Allopolyploid origin of DOI

Perný M., Tribsch A., Stuessy T. F., Marhold K. (2005b). Taxonomy and cytogeography of DOI

Perrigo A., Hoorn C., Antonelli A. (2020). Why mountains matter for biodiversity. DOI

Pritchard J. K., Stephens M., Donnelly P. (2000). Inference of population structure using multilocus genotype data. PubMed PMC

R Core Team (2019).

Robinson J. T., Thorvaldsdóttir H., Winckler W., Guttman M., Lander E. S., Getz G., et al. (2011). Integrative genomics viewer. PubMed DOI PMC

Roces-Díaz J. V., Jiménez-Alfaro B., Chytrý M., Díaz-Varela E. R., Álvarez-Álvarez P. (2018). Glacial refugia and mid-Holocene expansion delineate the current distribution of DOI

Rosenberg N. A. (2004). DISTRUCT: a program for the graphical display of population structure. DOI

Rothfels C. J. (2021). Polyploid phylogenetics. PubMed DOI

Rothfels C. J., Pryer K. M., Li F. W. (2017). Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. PubMed DOI

Rousseau-Gueutin M., Gaston A., Aïnouche A., Aïnouche M. L., Olbricht K., Staudt G., et al. (2009). Tracking the evolutionary history of polyploidy in PubMed DOI

Schmickl R., Liston A., Zeisek V., Oberlander K., Weitemier K., Straub S. C. K., et al. (2016). Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African PubMed DOI

Schönswetter P., Suda J., Popp M., Weiss-Schneeweiss H., Brochmann C. (2007). Circumpolar phylogeography of PubMed DOI

Schrinner S. D., Serra Mari R., Ebler J., Rautiainen M., Seillier L., Reimer J. J., et al. (2020). Haplotype threading: accurate polyploid phasing from long reads. PubMed DOI PMC

Shimodaira H. (2002). An approximately unbiased test of phylogenetic tree selection. PubMed DOI

Shimodaira H., Hasegawa M. (2001). CONSEL: for assessing the confidence of phylogenetic tree selection. PubMed DOI

Silva G. S., Souza M. M. (2013). Genomic in situ hybridization in plants. PubMed DOI

Slater G. S., Birney E. (2005). Automated generation of heuristics for biological sequence comparison. PubMed DOI PMC

Small R. L., Cronn R. C., Wendel J. F. (2004). Use of nuclear genes for phylogeny reconstruction in plants. DOI

Soltis D. E., Visger C. J., Soltis P. S. (2014). The polyploidy revolution then…and now: Stebbins revisited. PubMed DOI

Soltis P. S., Soltis D. E. (2009). The role of hybridization in plant speciation. PubMed DOI

Španiel S., Marhold K., Zozomová-Lihová J. (2017). The polyploid DOI

Stevanović V., Tan K., Petrova A. (2007). Mapping the endemic flora of the Balkans – a progress report.

Strid A. (1986). “

Suda J., Trávníček P. (2006a). Estimation of relative nuclear DNA content in dehydrated plant tissues by flow cytometry. PubMed DOI

Suda J., Trávníček P. (2006b). Reliable DNA ploidy determination in dehydrated tissues of vascular plants by DAPI flow cytometry–new prospects for plant research. PubMed DOI

Surina B., Pfanzelt S., Einzmann H. J. R., Albach D. C. (2014). Bridging the Alps and the Middle East: evolution, phylogeny and systematics of the genus DOI

Tan K. (2002). “

Tedder A., Helling M., Pannell J. R., Shimizu-Inatsugi R., Kawagoe T., van Campen J., et al. (2015). Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of PubMed DOI PMC

Temsch E. M., Greilhuber J., Krisai R. (2010). Genome size in liverworts.

Thompson J. D. (2020). DOI

Tillich M., Lehwark P., Pellizzer T., Ulbricht-Jones E. S., Fischer A., Bock R., et al. (2017). GeSeq – versatile and accurate annotation of organelle genomes. PubMed DOI PMC

Tkach N., Röser M., Suchan T., Cieślak E., Schönswetter P., Ronikier M. (2019). Contrasting evolutionary origins of two mountain endemics: PubMed DOI PMC

Tomasello S., Karbstein K., Hodač L., Paetzold C., Hörandl E. (2020). Phylogenomics unravels Quaternary vicariance and allopatric speciation patterns in temperate-montane plant species: a case study on the PubMed DOI

Tomović G., Lakušić D., Ranğelović V., Marhold K. (2009). DOI

Tomović G., Niketić M., Lakušić D., Ranğelović V., Stevanović V. (2014). Balkan endemic plants in Central Serbia and Kosovo regions: distribution patterns, ecological characteristics, and centres of diversity. DOI

Vargas O. M., Ortiz E. M., Simpson B. B. (2017). Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-andean diversification (Asteraceae: Astereae: PubMed DOI

Vatanparast M., Powell A., Doyle J. J., Egan A. N. (2018). Targeting legume loci: a comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. PubMed DOI PMC

Villaverde T., Pokorny L., Olsson S., Rincón-Barrado M., Johnson M. G., Gardner E. M., et al. (2018). Bridging the micro-and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. PubMed DOI

Walker J. F., Walker-Hale N., Vargas O. M., Larson D. A., Stull G. W. (2019). Characterizing gene tree conflict in plastome-inferred phylogenies. PubMed DOI PMC

Weitemier K., Straub S. C., Cronn R. C., Fishbein M., Schmickl R., McDonnell A., et al. (2014). Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics. PubMed DOI PMC

Weitemier K., Straub S. C. K., Fishbein M., Liston A. (2015). Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in PubMed DOI PMC

Wen D., Yu Y., Zhu J., Nakhleh L. (2018). Inferring phylogenetic networks using PhyloNet. PubMed DOI PMC

Zhang C., Rabiee M., Sayyari E., Mirarab S. (2018). ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. PubMed DOI PMC

Zozomová-Lihová J., Malánová-Krásná I., Vít P., Urfus T., Senko D., Svitok M., et al. (2015). Cytotype distribution patterns, ecological differentiation, and genetic structure in a diploid-tetraploid contact zone of PubMed DOI

Zozomová-Lihová J., Melichárková A., Svitok M., Španiel S. (2020). Pleistocene range disruption and postglacial expansion with secondary contacts explain the genetic and cytotype structure in the western Balkan endemic DOI

Multiple hybrid zones involving four Cardamine species and their triploid progeny: watching allopolyploid speciation in action?

Historical introgression as a driver of diversification of diploid Picris (Compositae) in the Mediterranean Basin

Bridging micro and macroevolution: insights from chromosomal dynamics in plants

A chromosome-level genome assembly for the amphibious plant Rorippa aquatica reveals its allotetraploid origin and mechanisms of heterophylly upon submergence

The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella

Evolution of hygrophytic plant species in the Anatolia-Caucasus region: insights from phylogenomic analyses of Cardamine perennials