HybPhyloMaker

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Bash scripts for analysis of Hyb-Seq data (from raw reads to species trees/networks)

HybPhyloMaker 최신버젼 다운로드

최종 버전 다운로드 (.zip)

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# HybPhyloMaker
   
> Fér T. & Schmickl R. (2018): [HybPhyloMaker: target enrichment data analysis from raw reads to species trees.](http://journals.sagepub.com/doi/10.1177/1176934317742613) *Evolutionary Bioinformatics* 14: 1176934317742613. doi: 10.1177/1176934317742613  
   
**Set of bash scripts for analysis of HybSeq data (from raw reads to species trees).** Consists of several steps:

**0:**  Prepare FASTQ files to folder (optionally download files from Illumina BaseSpace storage or SRA/ENA archives)  
**1:**  Processing raw reads (PhiX removal, adaptor removal, quality filtering, summary statistics)  
**2:**  Mapping reads to reference (using Bowtie2/BWA), create consensus sequence  
**3:**  Recognize sequences matching probes (generate PSLX files using BLAT)  
**4:**  Create alignments for all genes (+ optionally correct reading frame and/or select low heterozygosity loci)  
**5:**  Treat missing data, select best genes  
**6:**  Generate FastTree or RAxML gene trees + calculate/plot trees-alignment properties  
**7:**  Root gene trees with outgroup, combine gene trees into a single file  
**8:**  Estimate species tree  and other methods... (ASTRAL-III, ASTRAL-IV, ASTRID, MRL, BUCKy, concatenation FastTree/ExaML, NeighbourNetwork, Dsuite, SuperQ network, quartet sampling, SNaQ, PhyloNet, SNP heatmap)  
**9:**  Subselect suitable genes (and repeat steps 7+8)  
**10:** Subselect trees based on samples presence, collapse unsupported branches  
**11:** Calculate PhyParts  
**12:** Subselect samples based on exclude list  
**13:** DiscoVista  
**14:** treePL divergence dating of a species tree (ASTRAL-IV, FastTree, or ExaML), date all selected gene trees and annotate species tree with 95% HPD intervals  
**15:** combine bootstrap support values from multiple species trees
  
Uses many additional software that must be installed and put in the PATH prior to run scripts (see [Table](docs/HybPhyloMaker_software.pdf) located in the docs folder and consider to run [install_software.sh](install_software.sh)).  
Also utilizes many scripts developed by others (located in [HybSeqSource folder](HybSeqSource)). PLEASE CITE APPROPRIATELY THOSE SCRIPTS WHEN USING HybPhyloMaker!

Read [manual](docs/HybPhyloMaker_manual1.8.4.pdf) located in the docs folder before running HybPhyloMaker.

# HybPhyloMaker workflow
![HybPhyloMaker workflow](https://github.com/tomas-fer/HybPhyloMaker/blob/master/docs/HybPhyloMaker_workflow.png)

# Papers citing HybPhyloMaker
1. Carlsen MM, Fér T, Schmickl R, Leong-Škorničková J, Newman M, Kress WJ. 2018. [Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data](https://www.sciencedirect.com/science/article/pii/S1055790317309296). Molecular Phylogenetics and Evolution 128:55-68. doi: 10.1016/j.ympev.2018.07.020  
2. Herrando-Moraira S, Cardueae Radiations Group. 2018. [Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae)](https://www.sciencedirect.com/science/article/pii/S1055790318302501). Molecular Phylogenetics and Evolution 128:69-87. doi: 10.1016/j.ympev.2018.07.012  
3. Villaverde T, Pokorny L, Olsson S, Rincón-Barrado M, Johnson MG, Gardner EM, Wickett NJ, Molero J, Riina R, Sanmartín I. 2018. [Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above](https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15312). New Phytologist 220:636-650. doi: 10.1111/nph.15312  
4. Jones KE, Fér T, Schmickl RE, Dikow RB, Funk VA, Herrando-Moraira S, Siniscalchi CM, Susanna A, Slovák M, Thapa R, Watson LE, Mandel JR. 2019. [An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae](https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11295). Applications in Plant Sciences 7(10):e11295. doi: 10.1002/aps3.11295  
5. Karimi N, Grover CE, Galagher JP, Wendel JF, Ané C, Baum DA. 2020. [Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (_Adansonia_; Bombacoideae; Malvaceae)](https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz073/5613901). Systematic Biology 69:462-478. doi: 10.1093/sysbio/syz073  
6. Mao Y, Hou S, Shi J, Economo EP. 2020. [TREEasy: an automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data](https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13149). Molecular Ecology Resources 20:832-840. doi: 10.1111/1755‐0998.13149  
7. 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 _Ranunculus auricomus_ species complex](https://doi.org/10.1111/mec.15458). Molecular Ecology 29:2031-2049. doi: 10.1111/mec.15458  
8. Karbstein K, Tomasello S, Hodač L, Dunkel FG, Daubert M, Hörandl E. 2020. [Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic _Ranunculus auricomus_ complex (Ranunculaceae)](https://onlinelibrary.wiley.com/doi/full/10.1002/tax.12365). Taxon 69:1191-1220. doi: 10.1002/tax.12365  
9. Knyshov A, Gordon ERL, Christiane Weirauch C. 2021. [New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics](https://peerj.com/articles/11019/). PeerJ 9:e11019. doi: 10.7717/peerj.11019  
10. Rejlová L, Böhmová A, Chumová Z, Hořčicová Š, Josefiová J, Schmidt PA, Trávníček P, Urfus T, Vít P, Chrtek J. 2021. [Disparity between morphology and genetics in _Urtica dioica_ (Urticaceae)](https://academic.oup.com/botlinnean/article-abstract/195/4/606/5903206). Botanical Journal of the Linnean Society 195:606-621. doi: 10.1093/botlinnean/boaa076  
11. McLay TGB, Birch JL, Gunn BF, Ning W, Tate JA, Nauheimer L, Joyce EM, Simpson L, Schmidt-Lebuhn AN, Baker WJ, Forest F, Jackson CJ. 2021. [New targets acquired: Improving locus recovery from the Angiosperms353 probe set](https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11420). Applications in Plant Sciences 9(7): e11420. doi: 10.1002/aps3.11420  
12. Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K. 2021. [HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets](https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11441). Applications in Plant Sciences 9(7):e11441. doi:10.1002/aps3.11441  
13. Ufimov R, Zeisek V, Píšová S, Baker WJ, Fér T, van Loo M, Dobeš Ch, Schmickl R. 2021. [Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae](https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11442). Applications in Plant Sciences 9(7):e11442. doi:10.1002/aps3.11442  
14. Montero-Mendieta S, De la Riva I, Irisarri I, Leonard JA, Webster MT, Vilà C. 2021. [Phylogenomics and evolutionary history of _Oreobates_ (Anura: Craugastoridae) Neotropical frogs along elevational gradients](https://www.sciencedirect.com/science/article/pii/S1055790321001007). Molecular Phylogenetics and Evolution 161:107167. doi: 10.1016/j.ympev.2021.107167  
15. Chumová Z, Záveská E, Hloušková P, Ponert J, Schmidt PA, Čertner M, Mandáková T, Trávníček P. 2021 [Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids](https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.15306). The Plant Journal 107:511-524. doi: 10.1111/tpj.15306  
16. Reichelt N, Wen J, Pätzold C, Appelhans MS. 2021. [Target enrichment improves phylogenetic resolution in the genus _Zanthoxylum_ (Rutaceae) and indicates both incomplete lineage sorting and hybridization events](https://academic.oup.com/aob/article/128/4/497/6319059). Annals of Botany 128:497-510. doi: 10.1093/aob/mcab092  
17. Nesi N, Tsagkogeorga G, Tsang SM, Nicolas V, Lalis A, Scanlon AT, Riesle-Sbarbaro SA, Wiantoro S, Hitch AT, Juste J, Pinzari CA, Bonaccorso FJ,  Todd CM, Lim BK,  Simmons NB, McGowen MR, Rossiter SJ. 2021. [Interrogating phylogenetic discordance resolves deep splits in the rapid radiation of Old World fruit bats (Chiroptera: Pteropodidae)](https://academic.oup.com/sysbio/article/70/6/1077/6161783). Systematic Biology 70:1077-1089. doi: 10.1093/sysbio/syab013  
18. Lara-Cabrera SI, Perez-Garcia ML, Maya-Lastra CA, Montero-Castro JC, Godden GT, Cibrian-Jaramillo A, Fisher AE, Porter JM. 2021. [Phylogenomics of _Salvia_ L. subgenus _Calosphace_ (Lamiaceae)](https://www.frontiersin.org/articles/10.3389/fpls.2021.725900/full). Frontiers in Plant Science 12:725900. doi: 10.3389/fpls.2021.725900  
19. Sangvirotjanapat S, Fér T, Denduangboripant J,  Newman MF. 2022. [Phylogeny of _Globba_ section _Nudae_ and taxonomic revision of the new _Globba_ subsection _Pelecantherae_](https://link.springer.com/article/10.1007%2Fs00606-021-01789-6). Plant Systematics and Evolution 308:5. doi: 10.1007/s00606-021-01789-6  
20. Kandziora M, Sklenář P, Kolář F, Schmickl R. 2022. [How to tackle phylogenetic discordance in recent and rapidly radiating groups? Developing a workflow using _Loricaria_ (Asteraceae) as an example](https://www.frontiersin.org/articles/10.3389/fpls.2021.765719/full). Frontiers in Plant Science 12:765719. doi: 10.3389/fpls.2021.765719
21. Gizaw A, Gorospe JM, Kandziora M, Chala D, Gustafsson L, Zinaw A, Salomón L, Eilu G, Brochmann C, Kolář F, Schmickl R. 2022. [Afro-alpine fagships revisited II: elucidating the evolutionary relationships and species boundaries in the giant senecios (_Dendrosenecio_, Asteraceae)](https://link.springer.com/article/10.1007/s00035-021-00268-5). Alpine Botany 132:89-105. doi: 10.1007/s00035-021-00268-5  
22. Hatami E, Jones KE, Kilian N. 2022. [New insights into the relationships within subtribe Scorzonerinae (Cichorieae, Asteraceae) using hybrid capture phylogenomics (Hyb-Seq)](https://www.frontiersin.org/articles/10.3389/fpls.2022.851716/full). Frontiers in Plant Science 13:851716. doi: 10.3389/fpls.2022.851716  
23. Karbstein K, Tomasello S, Hodač L, Wagner N, Marinček P, Barke BH, Pätzold C, Hörandl E. 2022. [Untying Gordian knots: Unraveling reticulate polyploid plant evolution by genomic data using the large _Ranunculus auricomus_ species complex](https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18284). New Phytologist 235:2081-2098. doi: 10.1111/nph.18284  
24. Michel T, Tseng YH, Wilson H, Chung KF, Kidner C. 2022. [A hybrid capture bait set for _Begonia_](https://journals.rbge.org.uk/ejb/article/view/409). Edinburgh Journal of Botany 79:409. doi: 10.24823/ejb.2022.409  
25. Ufimov R, Gorospe JM, Fér T, Kandziora M, Salomon L, van Loo M, Schmickl R. 2022. [Utilizing paralogs for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13684). Molecular Ecology Resources 22:3018-3034. doi: 10.1111/1755-0998.13684  
26. Méndez-Urbano F, Sierra-Giraldo JA, Carlsen MM, Rodríguez-Rey GT, Castaño-Rubiano N. 2022. [_Anthurium caldasii_: a new species of Araceae from Colombia and its phylogenetic relationships with other black-spathed _Anthurium_ species](https://link.springer.com/article/10.1007/s12228-022-09722-y). Brittonia 74:419-435. doi: 10.1007/s12228-022-09722-y  
27. Woudstra Y, Quatela A-S, Kidner C, Viruel J, Zuntini A, Martin MD, Michel T, Grace OM. 2022. Chapter 14. Target capture. In: [de Boer H, Rydmark MO, Verstraete B, Gravendeel B (Eds) Molecular identification of plants: from sequence to species](https://ab.pensoft.net/book/98875). Advanced Books. doi: 10.3897/ab.e98875  
28. Hlavatá K, Leong-Škorničková J, Záveská E, Šída O, Newman M, Mandáková T, Lysak MA, Marhold K, Fér T. 2023: [Phylogenomics and genome size evolution in _Amomum_ s. s. (Zingiberaceae): comparison of traditional and modern sequencing methods](https://www.sciencedirect.com/science/article/pii/S1055790322002792). Molecular Phylogenetics and Evolution 178:107666. doi: 10.1016/j.ympev.2022.107666  
29. Böhmová A, Leong-Škorničková J, Šída O, Poulsen AD, Newman MF, Fér T. 2023. [Next-generation sequencing data show rapid radiation and several long-distance dispersal events in early Costaceae](https://www.sciencedirect.com/science/article/abs/pii/S1055790322002779). Molecular Phylogenetics and Evolution 179:107664. doi: 10.1016/j.ympev.2022.107664  
30. Blanco-Gavaldà C, Galbany-Casals M, Susanna A, Andrés-Sánchez S, Bayer RJ, Brochmann C, Cron GV, Bergh NG, Garcia-Jacas N, Gizaw A, Kandziora M, Kolář F, López-Alvarado J, Leliaert F, Letsara R, Moreyra LD, Razafimandimbison SG, Schmickl R, Roquet C. 2023. [Repeatedly northwards and upwards: southern African grasslands fuel the colonization of the African sky islands in _Helichrysum_ (Compositae)](https://www.mdpi.com/2223-7747/12/11/2213). Plants 12:2213. doi: 10.3390/plants12112213  
31. Scheunert A, Lautenschlager U, Ott T, Oberprieler C. 2023. [Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads](https://onlinelibrary.wiley.com/doi/10.1002/ece3.10190). Ecology and Evolution 13:e10190. doi: 10.1002/ece3.10190  
32. Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. 2023. [Target capture and genome skimming for plant diversity studies](https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11537). Applications in Plant Sciences 11:e11537. doi: 10.1002/aps3.11537  
33. Moreyra LD, Garcia-Jacas N, Roquet C, Ackerfield JR, Arabacı T, Blanco-Gavaldà C, Brochmann C, Calleja JA, Dirmenci T, Fujikawa K, Galbany-Casals M, Gao T, Gizaw A, López-Alvarado J, Mehregan I, Vilatersana R, Yıldız B, Leliaert F, Seregin AP, Susanna A. 2023. [African mountain thistles: three new genera in the _Carduus_-_Cirsium_ Group](https://www.mdpi.com/2223-7747/12/17/3083). Plants 12:3083. doi: 10.3390/plants12173083  
34. Bradican JP, Tomasello S, Boscutti F, Karbstein K, Hörandl E. 2023. [Phylogenomics of southern European taxa in the _Ranunculus auricomus_ species complex: the apple doesn't fall far from the tree](https://www.mdpi.com/2223-7747/12/21/3664). Plants 12:3664. doi: 10.3390/plants12213664  
35. Xie P, Guo Y, Teng Y, Zhou W,  Yu Y. 2024. [GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13924). Molecular Ecology Resources 24:e13924. doi:10.1111/1755-0998.13924  
36. Skopalíková J, Leong-Škorničková J, Šída O, Newman M, Chumová Z, Fér T, Záveská E. 2024. [Ancient hybridization in _Curcuma_ (Zingiberaceae) – Accelerator or brake in lineage diversification?](https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.16408). The Plant Journal 116:773-785. doi: 10.1111/tpj.16408  
37. Hlavatá K, Záveská E, Leong-Škorničková J, Pouch M, Poulsen AD, Šída O, Khadka B, Mandáková T & Fér T. 2024. [Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus _Amomum_ (Zingiberaceae)](https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1324358). Frontiers in Plant Science 15:1324358. doi: 10.3389/fpls.2024.1324358  
38. Ning W, Meudt HM & Tate JA. 2024. [A roadmap of phylogenomic methods for studying polyploid plant genera](https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11580). Applications in Plant Sciences 12:e11580. doi: 10.1002/aps3.11580  
39. Bradican JP, Tomasello S, Vollmer J & Hörandl E. 2024. [Converging forms: an examination of sub-Arctic, circumarctic, and Central Asian _Ranunculus auricomus_ agg. populations](https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1415059/full). Frontiers in Plant Science 15:1415059. doi: 10.3389/fpls.2024.1415059  
40. Poulsen AD, Fér T, Kumarage Marasinghe LD, Sabu M, Hughes M, Valderrama E & Leong-Škorničková J. 2024. [The cardamom conundrum resolved: Recircumscription and placement of _Elettaria_ in the only pantropically distributed ginger lineage](https://doi.org/10.1002/tax.13242). Taxon 73:1187-1213. doi: 10.1002/tax.13242  
41. Manzo E, Nillies S, Gutiérrez DG, Panero JL, Bräuchler C & Tomasello S. 2024. [Species delimitation in _Xanthium_ sect. _Acanthoxanthium_ (Heliantheae, Asteraceae) and the neglected species _Xanthium argenteum_](https://onlinelibrary.wiley.com/doi/10.1002/tax.13245). Taxon 73:1251-1271. doi: 10.1002/tax.13245  
42. Blanco-Gavaldà C, Roquet C, Puig-Surroca G, Andrés-Sánchez S, Razafimandimbison SG, Letsara R, Bergh N, Cron GV, Moreyra LD, Calleja JA, Castillo O, Bayer RJ, Leliaert F, Susanna A & Galbany-Casals M. 2025. [Biome conservatism prevailed in repeated long-distance colonization of Madagascar’s mountains by _Helichrysum_ (Compositae, Gnaphalieae)](https://www.sciencedirect.com/science/article/pii/S1055790324002756). Molecular Phylogenetics and Evolution 204:108283. doi: 10.1016/j.ympev.2024.108283
43. Moreyra LD, Susanna A, Calleja JA, Ackerfield JR, Arabacı T, Blanco-Gavaldà C, Brochmann C, Dirmenci T, Fujikawa K, Galbany-Casals M, Gao T, Gizaw A, Mehregan I, Vilatersana R, Viruel J, Yıldız B, Leliaert F, Seregin AP & Roquet C. 2025. [A thorny tale: The origin and diversification of _Cirsium_ (Compositae)](https://www.sciencedirect.com/science/article/pii/S1055790325000028). Molecular Phylogenetics and Evolution 204:108285. doi: 10.1016/j.ympev.2024.108285  
44. Xu L, Song Z, Li T, Jin Z, Zhang B, Du S, Liao S, Zhong X & Chen Y. 2025. [New insights into the phylogeny and infrageneric taxonomy of _Saussurea_ based on hybrid capture phylogenomics (Hyb-Seq)](https://www.sciencedirect.com/science/article/pii/S2468265924001689). Plant Diversity 47:21-23. doi: 10.1016/j.pld.2024.10.003
45. Galatius A, Kinze CC, Olsen MT, Tougaard J, Gotzek D & McGowen MR. 2025. [Phylogenomic, morphological and acoustic data support a revised taxonomy of the lissodelphinine dolphin subfamily](https://www.sciencedirect.com/science/article/pii/S1055790325000168). Molecular Phylogenetics and Evolution 205:108299. doi: 10.1016/j.ympev.2025.108299  
46. Ang L-P, Brambach F, Tomasello S, Wen J & Appelhans MS. 2025. [Hybrid capture resolves the phylogeny of _Tetradium_ (Rutaceae) and supports the inclusion of a species from Sulawesi](https://doi.org/10.1111/jse.13127). Journal of Systematics and Evolution 63:416-430. doi: 10.1111/jse.13127
47. Manzo E & Tomasello S. 2025. [Recent long-distance-dispersal explains the range disjunction of the Old-Word cockleburs (_Xanthium strumarium_)](https://onlinelibrary.wiley.com/doi/10.1111/jbi.15104). Journal of Biogeography 52:e15104. doi: 10.1111/jbi.15104  
48. Joyce EM, Schmidt-Lebuhn AN, Orel HK, Nge FJ, Anderson BM, Hammer TA & McLay TGB. 2025. [Navigating phylogenetic conflict and evolutionary inference in plants with target capture data](https://www.publish.csiro.au/SB/SB24011). Australian Systematic Botany 38:SB24011. doi: 10.1071/SB24011
49. Gorospe JM, Záveská E, Chala D, Gizaw A, Tusiime FM, Gustafsson ALS, Piálek L, Kolář F, Brochmann C & Schmickl R. 2025. [Ecological speciation with gene flow followed initial large-scale geographic speciation in the enigmatic afroalpine giant senecios (_Dendrosenecio_)](https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.20432). New Phytologist 246:2307-2323. doi: 10.1111/nph.20432
50. Salomón L, Gorospe JM, Fér T, Kolář F, Sklenář P & Schmickl R. 2025. [So young, so rich: habitat shifts combined with trait evolution promoted species radiation in _Senecio_ in the Andes](https://onlinelibrary.wiley.com/doi/10.1111/jbi.15161). Journal of Biogeography 52:e15161. doi: 10.1111/jbi.15161  
51. Trávníček P, Ponert J, Dantas-Queiroz MV & Chumová Z. 2025. [Integrating genome-wide traits and multi-loci phylogeny to investigate orchid evolution—A case study on Pleurothallidinae](https://onlinelibrary.wiley.com/doi/10.1111/tpj.70281). The Plant Journal 122:e70281. doi: 10.1111/tpj.70281  
52.  Blanco-Gavaldà C, Onstein RE, Valente L, Janzen T, Andrés-Sánchez S, Bergh N, Calleja JA, Carnicero P, Castillo Ò, Cron GV, Leliaert F, Moreyra LD, Puig-Surroca G, Razafimandimbison SG, Susanna A, Roquet C, Galbany-Casals M. 2025. [Climatic oscillations, dispersibility and adaptability behind worldwide mountain radiations of the _Helichrysum-Anaphalis-Pseudognaphalium_ (HAP) clade (Compositae)](https://academic.oup.com/aob/advance-article/doi/10.1093/aob/mcaf110/8154208). Annals of Botany. doi: 10.1093/aob/mcaf110  
53. Ang L-P, Tomasello S, Wen J & Appelhans MS. 2025. [Phylogeny of the species-rich pantropical genus _Zanthoxylum_ (Rutaceae) based on hybrid capture](https://www.sciencedirect.com/science/article/pii/S1055790325001150). Molecular Phylogenetics and Evolution 211:108398. doi: 10.1016/j.ympev.2025.108398  
54. Gorospe JM, Salomón L, Armijos-Barros J, Kantor A, Kolář F, Arnelas I, Sklenář P & Schmickl R. 2025. [Are we witnessing a speciation continuum? Evidence from current and past gene flow in the genus _Oritrophium_ s.s. (Asteraceae) from the tropical high Andes](https://onlinelibrary.wiley.com/doi/10.1111/mec.70095). Molecular Ecology 34:e70095. doi: 10.1111/mec.70095  
55. Gorospe JM, Fér T, Rurik I, Vďačný P, Kučera J, Dönmez AA, Yüzbaşıoğlu İS, Aydın ZU, Lučanová M, Schmickl RE, Slovák M. 2025. [Historical introgression as a driver of diploid plant diversity of _Picris_ (Compositae) in the Mediterranean Basin](https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.70565). The Plant Journal 124:e70565. doi: 10.1111/tpj.70565  
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57. Dantas-Queiroz MV, Khadka B, Vásquez D, Chumová Z, Trávníček P, Zeisek V, Šída O, Leong-Škorničková J, Suksathan P, Trần Hữu Đ, Mamiyil S, Mandáková T, Poulsen A, Fér T, Záveská E. 2026. [The origin and diversification of turmerics (_Curcuma_ L.: Zingiberaceae) in paleotropical biodiversity hotspots: the role of ancient hybridization and historical climate change](https://onlinelibrary.wiley.com/doi/10.1111/geb.70244). Global Ecology and Biogeography 35:e70244. doi: 10.1111/geb.70244
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