RAD-seq data provide new insights into biogeography, diversity anomaly, and species delimitation in eastern Asian–North American disjunct clade Benthamidia of Cornus (Cornaceae)

Abstract

The big-bracted dogwood clade Benthamidia of Cornus is a typical example of the well-known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than in NA. The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective. We generated RAD-seq data, conducted phylogenomic and biogeographic analyses for the clade with sampling of all species (9) and subspecies (10) currently recognized in floras. We also assessed species delineation and calculated phylogenetic diversity to evaluate the diversity unevenness between EA and NA. Finally, we examined variation of diversification rates and ecological niches on the phylogeny to explore potential causes underlying the observed diversity pattern. Our results revealed phylogenetic relationships congruent with previous studies and suggested a trans-Beringian ancestral distribution of the clade Benthamidia in the mid-Oligocene, dispersal from Mexico to eastern United States in the mid-Miocene, and early diversification of the EA clade in SW China. Our results also confirmed greater phylogenetic diversity and diversification rate of the EA clade. Species delimitation analysis suggested 17 species in the clade Benthamidia, including all recognized subspecies. By integrating the results of molecular data with morphology, we proposed to retain the subspecies without changing their ranks. Our data suggested increased diversification rate in EA as an intrinsic factor explaining the greater species diversity in the region driven mainly by biogeographic isolation and partially by niche divergence.

Keywords

Benthamidia clade / biogeography / Cornus / niche similarity / phylogenomics

References

1	J Adams. 2009. Species richness: Patterns in the diversity of life. Chichester, UK: Praxis Publishing.
2	ME Alfaro, F Santini, C Brock, H Alamillo, A Dornburg, DL Rabosky, G Carnevale, LJ Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences 106: 13410–13414.
3	BA Atkinson, RA Stockey, GW Rothwell. 2016. Cretaceous origin of dogwoods: An anatomically preserved Cornus (Cornaceae) fruit from the Campanian of Vancouver Island. Peer J 4: e2808.
4	DI Axelrod, I Al-Shehbaz, PH Raven. 1996. History of the modern flora of China. In: Zhang A, Wu S eds. Floristic characteristics and diversity of East Asia plants. Beijing: China Higher Education Press. 43–55.
5	JF Bain, KE Denford. 1979. The herbaceous members of the genus Cornus in NW North America. Botaniska Notiser 132: 121–129.
6	AJ Barley, JM Brown, RC Thomson. 2018. Impact of model violations on the inference of species boundaries under the multispecies coalescent. Systematic Biology 67: 269–284.
7	SP Blomberg, T Garland Jr., AR Ives. 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57: 717–745.
8	DE Boufford, SA Spongberg. 1983. Eastern Asian-eastern North American phytogeographical relationships: A history from the time of Linnaeus to the twentieth century. Annals of the Missouri Botanical Garden 70: 423–439.
9	PD Cantino, K de Queiroz. 2020. International code of phylogenetic nomenclature (PhyloCode): Version 6. Boca Raton: CRC Press.
10	EA Chambers, DM Hillis. 2020. The multispecies coalescent over-splits species in the case of geographically widespread taxa. Systematic Biology 69: 184–193.
11	D Darriba, GL Taboada, R Doallo, D Posada. 2012. jModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9: 772.
12	W-N Ding, RH Ree, RA Spicer, Y-W Xing. 2020. Ancient orogenic and monsoon-driven assembly of the world's richest temperate alpine flora. Science 369: 578–581.
13	MJ Donoghue, SA Smith. 2004. Patterns in the assembly of temperate forests around the Northern Hemisphere. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359: 1633–1644.
14	J Doyle. 1991. DNA protocols for plants—CTAB total DNA isolation. In: Hewitt GM, Johnston A eds. Molecular techniques in taxonomy. Berlin: Springer. 283–293.
15	AJ Drummond, MA Suchard, D Xie, A Rambaut. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969–1973.
16	ZY Du, A Harris, Q-Y 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.
17	ZY Du, QY Xiang, J Cheng, W Zhou, QF Wang, DE Soltis, PS Soltis. 2023. An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data. American Journal of Botany 110: e16116.
18	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.
19	DAR Eaton, I Overcast. 2018. ipyrad: Interactive assembly and analysis of RADseq data sets [online]. Available from [accessed 10 June 2018].
20	AM Ellison, CC Davis, PJ Calie, RF Naczi. 2014. Pitcher Plants (Sarracenia) provide a 21st-century perspective on infraspecific ranks and interspecific hybrids: A modest proposal for appropriate recognition and usage. Systematic Botany 39: 939–949.
21	JT Eronen, M Fortelius, A Micheels, F Portmann, K Puolamäki, CM Janis. 2012. Neogene aridification of the Northern Hemisphere. Geology 40: 823–826.
22	RH Eyde. 1988. Comprehending Cornus: Puzzles and progress in the systematics of the dogwoods. The Botanical Review 54: 233–351.
23	WP Fang. 1953. Notes on Dendrobenthamia. Acta Phytotaxonomica Sinica 2: 89–114.
24	SE Fick, RJ Hijmans. 2017. WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37: 4302–4315.
25	CN Fu, ZQ Mo, JB Yang, XJ Ge, DZ Li, QJ Xiang, LM Gao. 2019. Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous. Molecular Phylogenetics and Evolution 140: 106601.
26	Q Guo. 1999. Ecological comparisons between eastern Asia and North America: Historical and geographical perspectives. Journal of Biogeography 26: 199–206.
27	LJ Harmon, JT Weir, CD Brock, RE Glor, W Challenger. 2008. GEIGER: Investigating evolutionary radiations. Bioinformatics 24: 129–131.
28	AJ Harris, J Wen, QY Xiang. 2013. Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA approach. Journal of Systematics and Evolution 51: 117–133.
29	D-Y Hong, S Blackmore. 2015. Plants of China: A companion to the flora of China. New York: Cambridge University Press.
30	DH Huson, D Bryant. 2014. Estimating phylogenetic trees and networks using SplitsTree4 [online]. Available from [accessed 12 July 2022].
31	H Hu, J Ye, B Liu, L Mao, SA Smith, RL Barrett, PS Soltis, DE Soltis, Z Chen, L Lu. 2022. Temporal and spatial comparisons of angiosperm diversity between eastern Asia and North America. National Science Review 9: nwab199.
32	W Hu, T Soong, Z Song. 1990. Cornaceae. In: Flora Reipublicae Popularis Sinicae. Beijing: Science Press. 56: 1–106.
33	NJ Isaac, J Mallet, GM Mace. 2004. Taxonomic inflation: Its influence on macroecology and conservation. Trends in Ecology and Evolution 19: 464–469.
34	SW Kembel, PD Cowan, MR Helmus, WK Cornwell, H Morlon, DD Ackerly, SP Blomberg, CO Webb. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26: 1463–1464.
35	NM Kopelman, J Mayzel, M Jakobsson, NA Rosenberg, I Mayrose. 2015. Clumpak: A program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15: 1179–1191.
36	RE Latham, RE Ricklefs. 1993. Continental comparisons of temperate-zone tree species diversity. In: Ricklefs RE, Schluter D eds. Species diversity in ecological communities: Historical and geographical perspectives. Chicago: University of Chicago Press. 294–314.
37	AD Leaché, T Zhu, B Rannala, Z Yang. 2019. The spectre of too many species. Systematic Biology 68: 168–181.
38	H-L Li. 1952. Floristic relationships between eastern Asia and eastern North America. Transactions of the American Philosophical Society 42: 371–429.
39	K Lindelof, JA Lindo, W Zhou, X Ji, QY Xiang. 2020. Phylogenomics, biogeography, and evolution of the blue-or white-fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation. Journal of Systematics and Evolution 58: 604–645.
40	A Luo, C Ling, SY Ho, C-D Zhu. 2018. Comparison of methods for molecular species delimitation across a range of speciation scenarios. Systematic Biology 67: 830–846.
41	Z-Y Lv, X-H Huang, X Zhang, Z Yusupov, H-C Wang, K Tojibaev, T Deng, Z-M Li. 2019. Cornus sunhangii (Cornaceae), a new species from Tibet (China). Phytotaxa 409: 273–282.
42	DH Mai, H Walther. 1978. Die fossilen Floren der Haselbacher Serie im Weisselster-Becken (Bezirk Leipzig, DDR). Abhandlungen des Staatlichen Museums für Mineralogie und Geologie zu Dresden 28: 1–200.
43	NJ Matzke. 2013. BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis in R Scripts [online]. Available from: [accessed 10 June 2018].
44	AE Melton, MH Clinton, DN Wasoff, L Lu, H Hu, Z Chen, K Ma, DE Soltis, PS Soltis. 2022. Climatic niche comparisons of eastern North American and eastern Asian disjunct plant genera. Global Ecology and Biogeography 31: 1290–1302.
45	ZE Murrell. 1993. Phylogenetic relationships in Cornus (Cornaceae). Systematic Botany 18: 469–495.
46	ZE Murrell, DB Poindexter. 2016. Cornaceae. In: Flora of North America Editorial Committee ed. Flora of North America north of Mexico. New York: Oxford University Press. 12: 443–457.
47	M Pagel. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877–884.
48	BK Peterson, JN Weber, EH Kay, HS Fisher, HE Hoekstra. 2012. Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS one 7: e37135.
49	JK Pritchard, X Wen, D Falush. 2010. Documentation for structure software: Version 2.3. Chicago: University of Chicago.
50	H Qian, RE Ricklefs. 1999. A comparison of vascular plant taxonomic richness in China and the United States. American Naturalist 154: 160–181.
51	H Qian, RE Ricklefs. 2000. Large-scale processes and the Asian bias in temperate plant species diversity. Nature 407: 180–182.
52	H Qian, Y Jin, RE Ricklefs. 2017. Phylogenetic diversity anomaly in angiosperms between eastern Asia and eastern North America. Proceedings of the National Academy of Sciences 114: 11452–11457.
53	A Rambaut. 2014. FigTree v1.4.3 software [online]. Available from [accessed 9 May 2019].
54	A Rambaut, AJ Drummond, D Xie, G Baele, MA Suchard. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67: 901–904.
55	B Rannala, Z Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645–1656.
56	B Rannala, Z Yang. 2017. Efficient Bayesian species tree inference under the multispecies coalescent. Systematic Biology 66: 823–842.
57	RH Ree, SA Smith. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 4–14.
58	LJ Revell. 2012. phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3: 217–223.
59	RE Ricklefs, F He. 2016. Region effects influence local tree species diversity. Proceedings of the National Academy of Sciences 113: 674–679.
60	F Ronquist, M Teslenko, P Van Der Mark, DL Ayres, A Darling, S Höhna, B Larget, L Liu, MA Suchard, JP Huelsenbeck. 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542.
61	K Shearer, TG Ranney. 2013. Ploidy levels and relative genome sizes of species, hybrids, and cultivars of dogwood (Cornus spp.). HortScience 48: 825–830.
62	A Stamatakis. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313.
63	T Su, RA Spicer, S-H Li, H Xu, J Huang, S Sherlock, Y-J Huang, S-F Li, L Wang, L-B Jia. 2019. Uplift, climate and biotic changes at the Eocene-Oligocene transition in south-eastern Tibet. National Science Review 6: 495–504.
64	MA Suchard, P Lemey, G Baele, DL Ayres, AJ Drummond, A Rambaut. 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution 4: vey016.
65	J Sukumaran, LL Knowles. 2017. Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences 114: 1607–1612.
66	SK Thomas, X Liu, ZY Du, Y Dong, A Cummings, L Pokorny, QY Xiang, JH Leebens-Mack. 2021. Comprehending Cornales: Phylogenetic reconstruction of the order using the Angiosperms353 probe set. American Journal of Botany 108: 1112–1121.
67	BH Tiffney. 1985. The Eocene North Atlantic land bridge: Its importance in tertiary and modern phytogeography of the Northern Hemisphere. Journal of the Arnold Arboretum 66: 243–273.
68	DL Warren, NJ Matzke, M Cardillo, JB Baumgartner, LJ Beaumont, M Turelli, RE Glor, NA Huron, M Simões, TL Iglesias. 2021. ENMTools 1.0: An R package for comparative ecological biogeography. Ecography 44: 504–511.
69	J Wen. 1999. Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Annual Review of Ecology and Systematics 30: 421–455.
70	J Wen, S Ickert-Bond, Z-L Nie, R Li. 2010. Timing and modes of evolution of eastern Asian-North American biogeographic disjunctions in seed plants. In: Darwin's heritage today: Proceedings of the Darwin 2010 Beijing International Conference. Beijing: Higher Education Press. 252–269.
71	J Wen, ZL Nie, MS Ickert-Bond. 2016. Intercontinental disjunctions between eastern Asia and western North America in vascular plants highlight the biogeographic importance of the Bering land bridge from late Cretaceous to Neogene. Journal of Systematics and Evolution 54: 469–490.
72	J Wen, J Zhang, Z-L Nie, Y Zhong, H Sun. 2014. Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau. Frontiers in Genetics 5: 4.
73	QD Wheeler, R Meier. 2000. Species concepts and phylogenetic theory: A debate. New York: Columbia University Press.
74	ZY Wu. 1983. On the significance of Pacific intercontinental discontinuity. Annals of the Missouri Botanical Garden 70: 577–590.
75	Q-Y Xiang. 1987. System and synopsis of Cornus subgen. Syncarpea (Nakai) QY Xiang (Cornaceae). Bulletin of Botanical. Research 7: 33–52.
76	Q-Y Xiang, DE Boufford. 2005. Cornaceae, Mastixiaceae, Toricelliaceae, Helwingiacaee, Aucubaceae. In: Wu ZY, Raven PH, Hong DY eds. Flora of China. Beijing: Science Press; St. Louis: Missouri Botanical Garden Press. 14: 206–234.
77	Q-Y Xiang, SJ Brunsfeld, DE Soltis, PS Soltis. 1996. Phylogenetic relationships in Cornus based on chloroplast DNA restriction sites: Implications for biogeography and character evolution. Systematic Botany 21: 515–534.
78	Q-Y Xiang, DE Soltis. 2001. Dispersal-vicariance analyses of intercontinental disjuncts: Historical biogeographical implications for angiosperms in the Northern Hemisphere. International Journal of Plant Sciences 162: S29–S39.
79	Q-Y Xiang, DE Soltis, DR Morgan, PS Soltis. 1993. Phylogenetic relationships of Cornus L. sensu lato and putative relatives inferred from rbcL sequence data. Annals of the Missouri Botanical Garden 80: 723–734.
80	QY Xiang, DE Soltis, PS Soltis. 1998. Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences. American Journal of Botany 85: 285–297.
81	Q-Y Xiang, DT Thomas, QP Xiang. 2011. Resolving and dating the phylogeny of Cornales--Effects of taxon sampling, data partitions, and fossil calibrations. Molecular Phylogenetics and Evolution 59: 123–138.
82	Q-Y Xiang, DT Thomas, W Zhang, SR Manchester, Z Murrell. 2006. Species level phylogeny of the genus Cornus (Cornaceae) based on molecular and morphological evidence—Implications for taxonomy and Tertiary intercontinental migration. Taxon 55: 9–30.
83	Q-Y Xiang, JL Thorne, TK Seo, W Zhang, DT Thomas, RE Ricklefs. 2008. Rates of nucleotide substitution in Cornaceae (Cornales)—Pattern of variation and underlying causal factors. Molecular Phylogenetics and Evolution 49: 327–342.
84	Q-Y Xiang, WH Zhang, RE Ricklefs, H Qian, ZD Chen, J Wen, JH Li. 2004. Regional differences in rates of plant speciation and molecular evolution: A comparison between eastern Asia and eastern North America. Evolution 58: 2175–2184.
85	HF Yan, CY Zhang, AA Anderberg, G Hao, XJ Ge, JJ Wiens. 2018. What explains high plant richness in east Asia? Time and diversification in the tribe Lysimachieae (Primulaceae). New Phytologist 219: 436–448.
86	Z Yang. 2015. The BPP program for species tree estimation and species delimitation. Current Zoology 61: 854–865.
87	Z Yang, B Rannala. 2014. Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution 31: 3125–3135.
88	Y Yu, C Blair, X He. 2020. RASP 4: Ancestral state reconstruction tool for multiple genes and characters. Molecular Biology and Evolution 37: 604–606.
89	FE Zachos, S Lovari. 2013. Taxonomic inflation and the poverty of the phylogenetic species concept—A reply to Gippoliti and Groves. Hystrix 24: 142–144.
90	XX Zhang, JF Ye, SW Laffan, BD Mishler, AH Thornhill, LM Lu, LF Mao, B Liu, YH Chen, AM Lu. 2022. Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation. Journal of Integrative Plant Biology 64: 105–117.
91	W Zhou, X Ji, S Obata, A Pais, Y Dong, R Peet, Q-YJ 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.
92	W Zhou, Q-Y Xiang, J Wen. 2020. Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae). Journal of Systematics and Evolution 58: 571–603.
93	W Zhou, Q-Y Xiang. 2022. Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel)–Choosing between RAD-seq and Hyb-Seq approaches. Molecular Phylogenetics and Evolution 176: 107592.
94	W Zhou, A Harris, Q-Y Xiang. 2022. Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq. Journal of Systematics and Evolution 60: 1241–1262.