Resolving relationships despite past hybridization in Aliciella subsection Subnuda (Polemoniaceae)
Resolving relationships despite past hybridization in Aliciella subsection Subnuda (Polemoniaceae)
Phylogenetics is crucial in the study of evolutionary processes and events transpiring in the course of species diversification. Phylogenetic studies within kingdom Plantae often reveal hybridization and introgression. Here, we study a subsection rife with historic hybridization and discuss the impacts of such processes on evolutionary trajectories. Aliciella subsection Subnuda comprises seven species of herbaceous plants occurring in Utah, the Navajo Nation, and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of nuclear ITS and chloroplast DNA regions and genome-wide RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from chloroplast and nuclear ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny and multispecies coalescent species tree robustly resolve relationships between six species-level clades. We use STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest that hybridization has occurred among all species in the subsection at some point in their history. Cytonuclear discordance reveals historic chloroplast capture, and we discuss potential causes of the observed discordance. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.
Aliciella / cytonuclear discordance / introgression / phylogenomics / RAD-seq
1 | J Abdelkrim, L Aznar-Cormano, B Buge, A Fedosov, Y Kantor, P Zaharias, N Puillandre. 2018. Delimiting species of marine gastropods (Turridae, Conoidea) using RAD sequencing in an integrative taxonomy framework. Molecular Ecology 27: 4591–4611. |
2 | C Blair, C Ané. 2019. Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data. Systematic Biology 69: 593–601. |
3 | PD Blischak, J Chifman, AD Wolfe, LS Kubatko. 2018. HyDe: A Python package for genome-scale hybridization detection. Systematic Biology 67: 821–829. |
4 | JR Bombonato, DT do Amaral, GAR Silva, G Khan, EM Moraes, SC da Silva Andrade, DA Eaton, DP Alonso, PEM Ribolla, N Taylor. 2020. The potential of genome-wide RAD sequences for resolving rapid radiations: A case study in Cactaceae. Molecular Phylogenetics and Evolution 151: 106896. |
5 | J Cavender-Bares, A Gonzalez-Rodriguez, DAR Eaton, AAL Hipp, A Beulke, PS Manos. 2015. Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): A genomic and population genetics approach. Molecular Ecology 24: 3668–3687. |
6 | MJ Clement, Q Snell, P Walker, D Posada, KA Crandall. 2002. TCS: Estimating gene genealogies. Proceedings 16th International Parallel and Distributed Processing Symposium. 184. |
7 | M Crotti, CD Barratt, SP Loader, DJ Gower, JW Streicher. 2019. Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus). Zoologica Scripta 48: 157–167. |
8 | KW Cullings. 1992. Design and testing of a plant-specific PCR primer for ecological and evolutionary studies. Molecular Ecology 1: 233–240. |
9 | M Currat, M Ruedi, RJ Petit, L Excoffier. 2008. The hidden side of invasions: Massive introgression by local genes. Evolution: International Journal of Organic Evolution 62: 1908–1920. |
10 | JW Davey, T Cezard, P Fuentes-Utrilla, C Eland, K Gharbi, ML Blaxter. 2013. Special features of RAD sequencing data: Implications for genotyping. Molecular Ecology 22: 3151–3164. |
11 | Z-Y Du, A Harris, Q-YJ Xiang,. 2020. Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous. Molecular Phylogenetics and Evolution 145: 106726. |
12 | EY Durand, N Patterson, D Reich, M Slatkin. 2011. Testing for ancient admixture between closely related populations. Molecular Biology and Evolution 28: 2239–2252. |
13 | DA Earl, BM Vonholdt. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361. |
14 | DA Eaton, EL Spriggs, B Park, MJ Donoghue. 2017. Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants. Systematic Biology 66: 399–412. |
15 | DAR Eaton, AL Hipp, A Gonzalez-Rodriguez, J Cavender-Bares. 2015. Historical introgression among the American live oaks and the comparative nature of tests for introgression. Evolution 69: 2587–2601. |
16 | DAR Eaton, RH Ree. 2013. Inferring phylogeny and introgression using RADseq data: An example from flowering plants (Pedicularis: Orobanchaceae). Systematic Biology 62: 689–706. |
17 | D Eaton, I Overcast. 2016. ipyrad: Interactive assembly and analysis of RADseq data sets [online]. Available from [accessed 17 October 2017]. |
18 | G Evanno, S Regnaut, J Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14: 2611–2620. |
19 | L Fishman, AL Sweigart. 2018. When two rights make a wrong: The evolutionary genetics of plant hybrid incompatibilities. Annual Review of Plant Biology 69: 707–731. |
20 | RA Folk, PS Soltis, DE Soltis, R Guralnick. 2018. New prospects in the detection and comparative analysis of hybridization in the tree of life. American Journal of Botany 105: 364–375. |
21 | DJ Funk, KE Omland. 2003. Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics 34: 397–423. |
22 | RC Garrick, IA Bonatelli, C Hyseni, A Morales, TA Pelletier, MF Perez, E Rice, JD Satler, RE Symula, MTC Thomé. 2015. The evolution of phylogeographic data sets. Molecular Ecology 24: 1164–1171. |
23 | V Grant. 1994. Historical development of ornithophily in the western North American flora. Proceedings of the National Academy of Sciences USA 91: 10407–10411. |
24 | RE Green, J Krause, AW Briggs, T Maricic, U Stenzel, M Kircher, N Patterson, H Li, W Zhai, MH-Y Fritz. 2010. A draft sequence of the Neandertal genome. Science 328: 710–722. |
25 | S Greiner, R Bock. 2013. Tuning a menage a trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants. Bioessays 35: 354–365. |
26 | S Guindon, J-F Dufayard, V Lefort, M Anisimova, W Hordijk, O Gascuel. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology 59: 307–321. |
27 | M Hamilton. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8: 521–523. |
28 | A Healey, A Furtado, T Cooper, RJ Henry. 2014. Protocol: A simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 10: 21. |
29 | DT Hoang, O Chernomor, A Von Haeseler, BQ Minh, LS Vinh. 2017. UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35: 518–522. |
30 | Y Hou, MD Nowak, V Mirré, CS Bjorå, C Brochmann, M Popp. 2015. Thousands of RAD-seq loci fully resolve the phylogeny of the highly disjunct arctic-alpine genus Diapensia (Diapensiaceae). PLoS One 10: e0140175. |
31 | HT Huang, LL Knowles. 2016. Unforeseen consequences of excluding missing data from next-generation sequences: Simulation study of RAD sequences. Systematic Biology 65: 357–365. |
32 | M Hughes, C-I Peng, C-W Lin, RR Rubite, P Blanc, K-F Chung. 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. |
33 | JK Janes, JM Miller, JR Dupuis, RM Malenfant, JC Gorrell, CI Cullingham, RL Andrew. 2017. The K = 2 conundrum. Molecular Ecology 26: 3594–3602. |
34 | LA Johnson, LM Chan, TL Weese, LD Busby, S McMurry. 2008. Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae). Molecular Phylogenetics and Evolution 48: 997–1012. |
35 | LA Johnson, JM Porter. 2017. Fates of angiosperm species following long-distance dispersal: Examples from American amphitropical Polemoniaceae. American Journal of Botany 104: 1729–1744. |
36 | ST Kalinowski. 2011. The computer program STRUCTURE does not reliably identify the main genetic clusters within species: Simulations and implications for human population structure. Heredity 106: 625. |
37 | S Kalyaanamoorthy, BQ Minh, TK Wong, A von Haeseler, LS Jermiin. 2017. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods 14: 587. |
38 | A Kawabe, H Nukii, HY Furihata. 2018. Exploring the history of chloroplast capture in arabis using whole chloroplast genome sequencing. International Journal of Molecular Sciences 19: 602. |
39 | SA Kelchner. 2000. The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden 87: 482–498. |
40 | CBA Lange, TP Hauser, V Deichmann, M Ørgaard. 2022. Hybridization and complex evolution of Barbarea vulgaris and related species (Brassicaceae). Molecular Phylogenetics and Evolution 169: 107425. |
41 | A Larsson. 2014. AliView: A fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30: 3276–3278. |
42 | AD Leaché, JR Oaks. 2017. The utility of single nucleotide polymorphism (SNP) data in phylogenetics. Annual Review of Ecology, Evolution, and Systematics 48: 69–84. |
43 | LA Lecaudey, UK Schliewen, AG Osinov, EB Taylor, L Bernatchez, SJ Weiss. 2018. Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing. Molecular Phylogenetics and Evolution 124: 82–99. |
44 | JA Lee-Yaw, CJ Grassa, S Joly, RL Andrew, LH Rieseberg. 2019. An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus). New Phytologist 221: 515–526. |
45 | GL Lenhart. 2004. 2004 survey results for odd Gilia. Project report prepared for the Bureau of Land Management Richfield Field Office, Richfield, UT. |
46 | HY Lin, YJ Hao, JH Li, CX Fu, PS Soltis, DE Soltis, YP Zhao. 2019. Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae). Molecular Phylogenetics and Evolution 135: 1–11. |
47 | AG Linan, PP Lowry, A Miller, GE Schatz, JC Sevathian, CE Edwards. 2020. RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees. Molecular Ecology 30: 4520–4537. |
48 | E Maguilla, M Escudero, AL Hipp, M Luceño. 2017. Allopatric speciation despite historical gene flow: Divergence and hybridization in Carex furva and C. lucennoiberica (Cyperaceae) inferred from plastid and nuclear RAD-seq data. Molecular Ecology 26: 5646–5662. |
49 | SL McMurry, LA Johnson, DJ Clark, R Etches, J Alonso. 2006. Chloroplast phylogeography of the Mussentuchit Gilia (Aliciella tenuis, Polemoniaceae). Botanical Society of America annual meetings, Chico, CA. |
50 | SM Mussmann, MR Douglas, DD Oakey, ME Douglas. 2020. Defining relictual biodiversity: Conservation units in speckled dace (Cyprinidae: Rhinichthys osculus) of the Greater Death Valley Ecosystem. Ecology and Evolution 10: 10798–10817. |
51 | EA Myers. 2021. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Molecular Phylogenetics and Evolution 165: 107313. |
52 | AG Nazareno, JB Bemmels, CW Dick, LG Lohmann. 2017. Minimum sample sizes for population genomics: An empirical study from an Amazonian plant species. Molecular Ecology Resources 17: 1136–1147. |
53 | L-T Nguyen, HA Schmidt, A von Haeseler, BQ Minh. 2014. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268–274. |
54 | C Paetzold, KR Wood, D Eaton, WL Wagner, MS Appelhans. 2019. Phylogeny of Hawaiian Melicope (Rutaceae): RAD-Seq resolves species relationships and reveals ancient introgression. Frontiers in Plant Science 10: 1074. |
55 | E Pante, J Abdelkrim, A Viricel, D Gey, S France, M-C Boisselier, S Samadi. 2015. Use of RAD sequencing for delimiting species. Heredity 114: 450. |
56 | AC Payton, AA Naranjo, W Judd, M Gitzendanner, PS Soltis, DE Soltis. 2019. Population genetics, speciation, and hybridization in Dicerandra (Lamiaceae), a North American Coastal Plain endemic, and implications for conservation. Conservation Genetics 20: 531–543. |
57 | M Piwczyński, P Trzeciak, MO Popa, M Pabijan, JM Corral, K Spalik, A Grzywacz. 2020. Using RAD seq for reconstructing phylogenies of highly diverged taxa: A test using the tribe Scandiceae (Apiaceae). Journal of Systematics and Evolution 59: 58–72. |
58 | JM Porter. 1993. Phylogeny of Gilia sect. Giliandra (Polemoniaceae). Ph.D. Dissertation. Tucson: University of Arizona. |
59 | JM Porter. 1998. Aliciella, a recircumscribed genus of Polemoniaceae. Aliso 17: 23–46. |
60 | JM Porter. 2011. Two new Aliciella species and a new subspecies in Ipomopsis (Polemoniaceae) from the western United States of America. Phytotaxa 15: 15–25. |
61 | JK Pritchard, M Stephens, P Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959. |
62 | J Pritchard, X Wen, D Falush. 2010. Documentation for STRUCTURE software, version 2.3. Chicago: University of Chicago. |
63 | ZC Qi, Y Yu, X Liu, A Pais, T Ranney, R Whetten, QY Xiang. 2015. Phylogenomics of polyploid Fothergilla (Hamamelidaceae) by RAD-tag based GBS—Insights into species origin and effects of software pipelines. Journal of Systematics and Evolution 53: 432–447. |
64 | AM Quattrini, T Wu, K Soong, MS Jeng, Y Benayahu, CS McFadden. 2019. A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals. BMC Evolutionary Biology 19: 19. |
65 | RK Ramasamy, S Ramasamy, BB Bindroo, VG Naik. 2014. STRUCTURE PLOT: A program for drawing elegant STRUCTURE bar plots in user friendly interface. SpringerPlus 3: 431. |
66 | A Rambaut. 2018. FigTree. Molecular evolution, phylogenetics and epidemiology. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh [online]. Available from [accessed 3 April 2019]. |
67 | PA Reeves, CL Bowker, CE Fettig, LR Tembrock, CM Richards. 2016. Effect of error and missing data on population structure inference using microsatellite data. bioRxiv 080630. [Preprint]. |
68 | LH Rieseberg, DE Soltis. 1991. Phylogenetic consequences of cytoplasmic gene flow in plants. Evolutionary Trends in Plants 5: 65–84. |
69 | JP Rose, CA Toledo, EM Lemmon, AR Lemmon, KJ Sytsma. 2021. Out of sight, out of mind: Widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal. Systematic Biology 70: 162–180. |
70 | BE Rubin, RH Ree, CS Moreau. 2012. Inferring phylogenies from RAD sequence data. Plos One 7: e33394 |
71 | JB Sambatti, JL Strasburg, D Ortiz-Barrientos, EJ Baack, LH Rieseberg. 2012. Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers. Evolution: International Journal of Organic Evolution 66: 1459–1473. |
72 | J Shaw, EB Lickey, JT Beck, SB Farmer, W Liu, J Miller, KC Siripun, CT Winder, EE Schilling, RL Small. 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142–166. |
73 | DB Sloan, JC Havird, J Sharbrough. 2017. The on-again, off-again relationship between mitochondrial genomes and species boundaries. Molecular Ecology 26: 2212–2236. |
74 | PS Soltis, DE Soltis. 2009. The role of hybridization in plant speciation. Annual review of plant biology. Annual Review of Plant Biology 60: 561–588. |
75 | DL Swofford. 2002. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sunderland: Sinauer Associates. |
76 | P Taberlet, L Gielly, G Pautou, J Bouvet. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105–1109. |
77 | DP Toews, A Brelsford. 2012. The biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology 21: 3907–3930. |
78 | EA Tripp, YHE Tsai, YB Zhuang, KG Dexter. 2017. RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia. Ecology and Evolution 7: 7920–7936. |
79 | A Tsitrone, M Kirkpatrick, DA Levin. 2003. A model for chloroplast capture. Evolution 57: 1776–1782. |
80 | OM Vargas, EM Ortiz, BB Simpson. 2017. Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium). New Phytologist 214: 1736–1750. |
81 | DLJ Vendrami, L Telesca, H Weigand, M Weiss, K Fawcett, K Lehman, MS Clark, F Leese, C McMinn, H Moore, JI Hoffman. 2017. RAD sequencing resolves fine-scale population structure in a benthic invertebrate: Implications for understanding phenotypic plasticity. Royal Society Open Science 4: 16. |
82 | XQ Wang, XY Ye, L Zhao, DZ Li, ZH Guo, HF Zhuang. 2017. Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae). Scientific Reports 7: 11. |
83 | SL Welsh, ND Atwood, S Goodrich, LC Higgins. 2015. A Utah Flora, 5th edition. Provo: Brigham Young University Print Services. |
84 | SL Welsh, R Kass. 2013. A distinctive new taxon: Gilia karenae (Polemonaceae). Western North American Naturalist 74: 138–141. |
85 | KD Whitney, JR Ahern, LG Campbell, LP Albert, MS King. 2010. Patterns of hybridization in plants. Perspectives in Plant Ecology Evolution and Systematics 12: 175–182. |
86 | EM Willing, C Dreyer, C van Oosterhout. 2012. Estimates of genetic differentiation measured by F-ST do not necessarily require large sample sizes when using many SNP markers. PLoS One 7: 7. |
87 | LL Xu, RM Yu, XR Lin, BW Zhang, N Li, K Lin, DY Zhang, WN Bai. 2021. Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts. New Phytologist 232: 388–403. |
88 | WB Zhou, X Ji, S Obata, A Pais, YB Dong, R Peet, QY Xiang. 2018. Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling. Molecular Phylogenetics and Evolution 126: 1–16. |
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