Published August 18, 2022
| Version v1
Journal article
Open
A HYBRID CAPTURE BAIT SET FOR BEGONIA
Authors/Creators
- 1. Institute of Molecular Plant Sciences, University of Edinburgh, The King's Buildings, Edinburgh & Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK.
- 2. Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115201, Taiwan. & Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK. & Institute of Biodiversity Animal Health & Comparative Medicine, Glasgow University, Graham Kerr Building, Glasgow G12 8QQ, Scotland, UK.
- 3. Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115201, Taiwan.
Description
Michel, T., Tseng, Y.-H., Wilso, H. P., Chung, K.-F., Kidner, C. A. (2022): A HYBRID CAPTURE BAIT SET FOR BEGONIA. Edinburgh Journal of Botany 79 (409): 1-33, DOI: 10.24823/EJB.2022.409, URL: http://dx.doi.org/10.24823/ejb.2022.409
Files
source.pdf
Files
(4.3 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:0348f8e99ae07a1b927f66907fb6854f
|
4.3 MB | Preview Download |
Linked records
Additional details
Identifiers
- LSID
- urn:lsid:plazi.org:pub:0348FFE9FFE07A1B927FFF90FFB6854F
References
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology. 215(3):403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
- Andermann T, Cano A, Zizka A, Bacon C, Antonelli A. 2018. SECAPR - a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments. PeerJ. 6:e5175. https://doi.org/10.7717/peerj.5175
- Arbor Biosciences. 2018. myBaits: Hybridization Capture for Targeted NGS. Manual, version 4.01. Ann Arbor, Michigan: Arbor Biosciences. https://arborbiosci.com/wp-content/uploads/2019/08/myBaits- Manual-v4.pdf
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology. 19(5):455-477. https://doi.org/10.1089/cmb.2012.0021
- Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114-2120. https://doi.org/10.1093/bioinformatics/btu170
- Borowiec ML. 2016. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ. 4:e1660. https://doi.org/10.7717/peerj.1660
- Brennan AC, Bridgett S, Shaukat Ali M, Harrison N, Matthews A, Pellicer J, Twyford AD, Kidner CA. 2012. Genomic resources for evolutionary studies in the large, diverse, tropical genus, Begonia. Tropical Plant Biology. 5:261-276. https://doi.org/10.1007/s12042-012-9109-6
- Campos-Dominguez L. 2020. Does a dynamic genome drive speciation in a mega-diverse genus? Ph.D. thesis, University of Edinburgh.
- Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 25(15):1972-1973. https:// doi.org/10.1093/bioinformatics/btp348
- Carlsen MM, Fer T, Schmickl R, Leong-Skornickova 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. Molecular and Phylogenetic Evolution. 128:55-68. https:// doi.org/10.1016/j.ympev.2018.07.020
- Conesa A, Gotz S. 2008. Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics. 2008:619832. https://doi.org/10.1155/2008/619832
- Constantinides B, Robertson DL. 2017. Kindel: indel-aware consensus for nucleotide sequence alignments. Journal of Open Source Software. 2(15):282. https://doi.org/10.21105/joss.00282
- Couvreur TLP, Helmstetter AJ, Koenen EJM, Bethune K, Brandao RD, Little SA, Sauquet H, Erkens RHJ. 2018. Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes. Frontiers in Plant Science. 9:1941. https://doi.org/10.3389/fpls.2018.01941
- Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J. 2012. Targeted enrichment strategies for next-generation plant biology. American Journal of Botany. 99(2):291-311. https:// doi.org/10.3732/ajb.1100356
- Dodsworth S, Pokorny L, Johnson MG, Kim JT, Maurin O, Wickett NJ, Forest F, Baker WJ. 2019. Hyb-Seq for flowering plant systematics. Trends in Plant Science. 24(10):887-891. https:// doi.org/10.1016/j.tplants.2019.07.011
- Emelianova K. 2017. Using next generation sequencing to investigate the generation of diversity in the genus Begonia. Ph.D. thesis, University of Edinburgh.
- Emelianova K, Martinez Martinez A, Campos-Dominguez L, Kidner C. 2021. Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family. Scientific Reports. 11(1):17773. https://doi.org/10.1038/s41598-021-96854-y
- Fer T, Schmickl RE. 2018. HybPhyloMaker: target enrichment data analysis from raw reads to species trees. Evolutionary Bioinformatics Online. 14:1176934317742613. https:// doi.org/10.1177/1176934317742613
- Folk RA, Mandel JR, Freudenstein JV. 2015. A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae). Applications in Plant Sciences. 3(8):1500039. https://doi.org/10.3732/apps.1500039
- Forrest LL, Hart ML, Hughes M, Wilson HP, Chung KF, Tseng YH, Kidner CA. 2019. The limits of Hyb-Seq for herbarium specimens: impact of preservation techniques. Frontiers in Ecology and Evolution. https://doi.org/10.3389/fevo.2019.00439
- Frantz LAF, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, et al. 2016. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science. 352(6290):1228-1231. https://doi.org/10.1126/science.aaf3161
- Frodin DG. 2004. History and concepts of big plant genera. Taxon. 53(3):753-776. https:// doi.org/10.2307/4135449
- Gagnon E, Hilgenhof R, Orejuela A, McDonnell A, Sablok G, Aubriot X, Giacomin L, Gouvea Y, Bragionis T, Stehmann JR, Bohs L, Dodsworth S, Martine C, Poczai P, Knapp S, Sarkinen T. 2022. Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum. American Journal of Botany. 109(4):580-601. https://doi.org/10.1002/ajb2.1827
- Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. 2019. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience. 4(8):giz018. https://doi.org/10.1093/gigascience/giz018
- Goodall-Copestake WP, Perez-Espona S, Harris DJ, Hollingsworth PM. 2010. The early evolution of the mega-diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies. Biologial Journal of the Linnean Society, London. 101(2):243-250. https:// doi.org/10.1111/j.1095-8312.2010.01489.x
- Hale H, Gardner EM, Viruel J, Pokorny L, Johnson MG. 2020. Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. Applications in Plant Science. 8(4):e11337. https://doi.org/10.1002/aps3.11337
- Harris K. 2019. From a database of genomes to a forest of evolutionary trees. Nature Genetics. 51:1306-1307. https://doi.org/10.1038/s41588-019-0492-x
- Hart ML, Forrest LL, Nicholls JA, Kidner CA. 2016. Retrieval of hundreds of nuclear loci from herbarium specimens. Taxon. 65:1081-1092. https://doi.org/10.12705/655.9
- Helmstetter AJ, Kamga SM, Bethune K, Lautenschlager T, Zizka A, Bacon CD, Wieringa JJ, Stauffer F, Antonelli A, Sonke B, Couvreur TLP. 2020. Unraveling the phylogenomic relationships of the most diverse African palm genus Raphia (Calamoideae, Arecaceae). Plants. 9(4):549. https:// doi.org/10.3390/plants9040549
- Hendriks KP, Mandakova T, Hay NM, Ly E, Hooft van Huysduynen A, Tamrakar R, Thomas SK, Toro-Nunez O, Pires JC, Nikolov LA, Koch MA, Windham MD, Lysak MA, Forest F, Mummenhoff K, Baker WJ, Lens F, Bailey CD. 2021. The best of both worlds: combining lineage-specific and universal bait sets in target-enrichment hybridization reactions. Applications in Plant Science. 9(7). https://doi.org/10.1002/aps3.11438
- Hill CB, Wong D, Tibbits J, Forrest K, Hayden M, Zhang XQ, Westcott S, Angessa TT, Li C. 2019. Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley. Scientific Data. 6:12. https://doi.org/10.1038/s41597-019-0011-z
- Huerta-Cepas J, Serra F, Bork P. 2016. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Molecular Biology and Evolution. 33(6):1635-1638. https:// doi.org/10.1093/molbev/msw046
- Hughes M, Peng CI, Lin CW, Rubite RR, Blanc P, Chung KF. 2018. Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species. PLoS One. 13:e0194877. https:// doi.org/10.1371/journal.pone.0194877
- Johnson MG, Malley C, Goffinet B, Shaw AJ, Wickett NJ. 2016. A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). Molecular Phylogenetics and Evolution. 98:29-40. https://doi.org/10.1016/j.ympev.2016.01.008
- Johnson MG, Pokorny L, Dodsworth S, Botigue LR, Cowan RS, Devault A, Eiserhardt WL, Epitawalage N, Forest F, Kim JT, Leebens-Mack JH, Leitch IJ, Maurin O, Soltis DE, Soltis PS, Wong GKS, Baker WJ, Wickett NJ. 2019. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-Medoids clustering. Systematic Biology. 68(4):594-606. https:// doi.org/10.1093/sysbio/syy086
- Jombart T, Kendall M, Almagro-Garcia J, Colijn C. 2017. treespace: statistical exploration of landscapes of phylogenetic trees. Molecular Ecology Resources. 17(6):1385-1392. https:// doi.org/10.1111/1755-0998.12676
- Jones KE, Fer T, Schmickl RE, Dikow RB, Funk VA, Herrando-Moraira S, Johnston PR, Kilian N, Siniscalchi CM, Susanna A, Slovak 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. Applications in Plant Science. 7:e11295. https://doi.org/10.1002/aps3.11295
- Jonsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L. 2013. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 29(13):1682-1684. https://doi.org/10.1093/bioinformatics/btt193
- Kadlec M, Bellstedt DU, Le Maitre NC, Pirie MD. 2017. Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"? PeerJ. 5:e3569. https://doi.org/10.7717/peerj.3569
- Kates HR, Johnson MG, Gardner EM, Zerega NJC, Wickett NJ. 2018. Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus. American Journal of Botany. 105(3):404-416. https://doi.org/10.1002/ajb2.1068
- Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics. 9(4):286-298. https://doi.org/10.1093/bib/bbn013
- Kendall M, Colijn C. 2016. Mapping phylogenetic trees to reveal distinct patterns of evolution. Molecular Biology and Evolution. 33(10):2735-2743. https://doi.org/10.1093/molbev/msw124
- Koenen EJM, Ojeda DI, Steeves R, Migliore J, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Bruneau A, Hughes CE. 2020. Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies. New Phytologist. 225(3):1355-1369. https://doi.org/10.1111/nph.16290
- Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods. 9:357- 359. https://doi.org/10.1038/nmeth.1923
- Larridon I, Villaverde T, Zuntini AR, Pokorny L, Brewer GE, Epitawalage N, Fairlie I, Hahn M, Kim J, Maguilla E, Maurin O, Xanthos M, Hipp AL, Forest F, Baker WJ. 2020. Tackling rapid radiations with targeted sequencing. Frontiers in Plant Science. 10:1655. https://doi.org/10.3389/fpls.2019.01655
- Lee AK, Gilman IS, Srivastav M, Lerner AD, Donoghue MJ, Clement WL. 2021. Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights. American Journal of Botany. 108(7):1122-1142. https://doi.org/10.1002/ajb2.1695
- Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25:1754-1760. https://doi.org/10.1093/bioinformatics/btp324
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 25(16):2078-2079. https://doi.org/10.1093/bioinformatics/btp352
- Liu SH, Tseng YH, Zure D, Rubite RR, Balangcod TD, Peng CI, Chung KF. 2019a. Begonia balangcodiae sp. nov. from northern Luzon, the Philippines and its natural hybrid with B. crispipila, B. × kapangan nothosp. nov. Phytotaxa. 407(1):5-21. https://doi.org/10.11646/phytotaxa.407.1.3
- Liu Y, Johnson MG, Cox CJ, Medina R, Devos N, Vanderpoorten A, Hedenas L, Bell NE, Shevock JR, Aguero B, Quandt D, Wickett NJ, Shaw AJ, Goffinet B. 2019b. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature Communications. 10:1485.
- Mandel JR, Dikow RB, Funk VA. 2015. Using phylogenomics to resolve mega-families: an example from Compositae. Journal of Systematics and Evolution. 53(5):391-402. https://doi.org/10.1111/jse.12167
- McKain MR, Johnson MG, Uribe-Convers S, Eaton D, Yang Y. 2018. Practical considerations for plant phylogenomics. Applications in Plant Sciences. 6(3):e1038. https://doi.org/10.1002/aps3.1038
- Melicharkova A, Slenker M, Zozomova-Lihova J, Skokanova K, Singliarova B, Kacmarova T, Cabonova M, Kempa M, Sramkova G, Mandakova T, Lysak MA, Svitok M, Martonfiova L, Marhold K. 2020. So closely related and yet so different: strong contrasts between the evolutionary histories of species of the Cardamine pratensis polyploid complex in Central Europe. Frontiers in Plant Sciences. 11:588856. https://doi.org/10.3389/fpls.2020.588856
- Moonlight PW, Richardson JE, Tebbitt MC, Thomas DC, Hollands R, Peng CI, Hughes M. 2015. Continental-scale diversification patterns in a megadiverse genus: the biogeography of Neotropical Begonia. Journal of Biogeography. 42(6):1137-1149. https://doi.org/10.1111/jbi.12496
- Moonlight PW, Ardi WH, Padilla LA, Chung K-F, Fuller D, Girmansyah D, Hollands R, Jara-Munoz A, Kiew R, Leong W-C, Liu Y, Mahardika A, Marasinghe LDK, O'Connor M, Peng C-I, Perez AJ, Phutthai T, Pullan M, Rajbhandary S, Reynel C, Rubite RR, Sang J, Scherberich D, Shui Y-M, Tebbitt MC, Thomas DC, Wilson HP, Zaini NH, Hughes M. 2018. Dividing and conquering the fastest-growing genus: towards a natural sectional classification of the mega-diverse genus Begonia (Begoniaceae). Taxon 67(2):267-323. https://doi.org/10.12705/672.3
- Morales-Briones DF, Liston A, Tank DC. 2018. Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae). New Phytologist. 218(4):1668-1684. https://doi.org/10.1111/nph.15099
- Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA. 2015. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Frontiers in Plant Science. 6:710. https://doi.org/10.3389/fpls.2015.00710
- Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution. 32(1):268-274. https://doi.org/10.1093/molbev/msu300
- Pezzini FF. 2019. Phylogeny, taxonomy and biogeography of Ceiba Mill. (Malvaceae: Bombacoideae). Ph.D. thesis, University of Edinburgh.
- Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE. 5(3):e9490. https://doi.org/10.1371/journal.pone.0009490
- Schneider JV, Jungcurt T, Cardoso D, Amorim AM, Topel M, Andermann T, Poncy O, Berberich T, Zizka G. 2021. Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa. Taxon. 70(1):48-71. https://doi.org/10.1002/tax.12421
- Schubert M, Ermini L, Der Sarkissian C, Jonsson H, Ginolhac A, Schaefer R, Martin MD, Fernandez R, Kircher M, McCue M, Willerslev E, Orlando L. 2014. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nature Protocols. 9:1056-1082. https://doi.org/10.1038/nprot.2014.063
- Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, Orlando L. 2017. Zonkey: a simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. Journal of Archaeological Science. 78:147-157. https://doi.org/10.1016/j.jas.2016.12.005
- Shaukat Ali M. 2013. Genetic architecture of species level differences in Begonia section Gireoudia. Ph.D. thesis, University of Edinburgh.
- Shee ZQ, Frodin DG, Camara-Leret R, Pokorny L. 2020. Reconstructing the complex evolutionary history of the papuasian Schefflera radiation through herbariomics. Frontiers in Plant Science. 11:258. https://doi.org/10.3389/fpls.2020.00258
- Shen XX, Hittinger CT, Rokas A. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology and Evolution. 1:126. https:// doi.org/10.1038/s41559-017-0126
- Slater GSC, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 6:31. https://doi.org/10.1186/1471-2105-6-31
- Slenker M, Kantor A, Marhold K, Schmickl R, Mandakova T, Lysak MA, Perny M, Cabonova M, Slovak M, Zozomova-Lihova J. 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 Cardamine barbaraeoides. Fronteris in Plant Science. 12:659275. https://doi.org/10.3389/fpls.2021.659275
- Slimp M, Williams LD, Hale H, Johnson MG. 2021. On the potential of Angiosperms353 for population genomic studies. Applications in Plant Science. https://doi.org/10.1002/aps3.11419
- Smith SA, Moore MJ, Brown JW, Yang Y. 2015. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology. 15:150. https://doi.org/10.1186/s12862-015-0423-0
- Soto Gomez M, Pokorny L, Kantar MB, Forest F, Leitch IJ, Gravendeel B, Wilkin P, Graham SW, Viruel J. 2019. A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae). Applications in Plant Science. 7(6):e11254. https:// doi.org/10.1002/aps3.11254
- Thomas DC, Hughes M, Phutthai T, Ardi WH, Rajbhandary S, Rubite R, Twyford AD, Richardson JE. 2012. West to east dispersal and subsequent rapid diversification of the mega-diverse genus Begonia (Begoniaceae) in the Malesian archipelago. Journal of Biogeography. 39(1):98-113. https:// doi.org/10.1111/j.1365-2699.2011.02596.x
- Thomas AE, Igea J, Meudt HM, Albach DC, Lee WG, Tanentzap AJ. 2021. Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica. American Journal of Botany. 108(7):1289-1306. https://doi.org/10.1002/ajb2.1678
- Tomasello S, Karbstein K, Hodac L, Paetzold C, Horandl E. 2020. Phylogenomics unravels Quaternary vicariance and allopatric speciation patterns in temperate-montane plant species: a case study on the Ranunculus auricomus species complex. Molecular Ecology. 29:2031-2049. https:// doi.org/10.1111/mec.15458
- Tseng YH, Huang HY, Xu WB, Yang HA, Liu Y, Peng CI, Chung KF. 2017. Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae). Applications in Plant Science. 5(5):1700024. https://doi.org/10.3732/apps.1700024
- Tseng YH, Huang HY, Xu WB, Yang HA, Peng CI, Liu Y, Chung KF. 2019. Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure. Botanical Studies. 60(1):20. https://doi.org/10.1186/s40529-019-0267-9
- Twyford AD, Ennos RA, White CD, Ali MS, Kidner CA. 2014. The evolution of sex ratio differences and inflorescence architectures in Begonia (Begoniaceae). American Journal of Botany. 101(2):308-317. https://doi.org/10.3732/ajb.1300090
- Vallebueno-Estrada M, Rodriguez-Arevalo I, Rougon-Cardoso A, Martinez Gonzalez J, Garcia Cook A, Montiel R, Vielle-Calzada JP. 2016. The earliest maize from San Marcos Tehuacan is a partial domesticate with genomic evidence of inbreeding. Proceedings of the National Academy of Sciences of the United States of America. 113(49):14151-14156. https:// doi.org/10.1073/pnas.1609701113
- Van Andel T, Veltman MA, Bertin A, Maat H, Polime T, Hille Ris Lambers D, Tjoe Awie J, De Boer H, Manzanilla V. Hidden rice diversity in the Guianas. Frontiers in Plant Science. 2019. 10:1161. https:// doi.org/10.3389/fpls.2019.01161
- J, Riina R, Sanmartin I. 2018. Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. New Phytol. 220(2):636-650. https://doi.org/10.1111/nph.15312
- Weitemier K, Straub SCK, Cronn RC, Fishbein M, Schmickl R, McDonnell A, Liston A. 2014. Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics. Applications in Plant Science. 2(9):1400042. https://doi.org/10.3732/apps.1400042
- Wilson H. 2021. Megadiversity and the New Guinea orogeny. Ph.D. thesis, University of Glasgow.
- Yang L, Koo DH, Li Y, Zhang X, Luan F, Havey MJ, Jiang J, Weng Y. 2012. Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. The Plant Journal. 71(6):895-906. https://doi.org/10.1111/j.1365-313X.2012.05017.x
- 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. https:// doi.org/10.1186/s12859-018-2129-y