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Dated phylogeny and biogeography of the Eurasian Allium section Rhizirideum (Amaryllidaceae)

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Abstract

Allium section Rhizirideum constitutes a group of approximately 24 species, distributed mostly in steppe areas of the Eurasian temperate zone. Its phylogenetic relationships are therefore relevant for understanding of the evolutionary and biogeographical patterns of the Eurasian steppes. Based upon DNA sequences from two plastid regions (trnQ-rps16 and trnL-rpl32) and the internal transcribed spacer region of nuclear ribosomal DNA, the phylogenetic relationships in Allium section Rhizirideum are investigated by using maximum parsimony and Bayesian inference. Dated phylogenies revealed (1) that diversification started in the upper Pliocene and further speciation events occurred during the Pleistocene and (2) a clear division of the section Rhizirideum into an “Asiatic” and “European” geographical group. Nomenclature, distribution maps and identification key for all species are provided. Origin and diversification within this section thus reflect the development and history of the modern Eurasian steppe.

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References

  • Agapova ND, Arkharova KB, Vakhtina LI, Zemskova EA, Tarvis LV (1990) Numeri chromosomatum magnoliophytorum florae URSS: Aceraceae—Menyanthaceae. Nauka, Sectio Leninopolitana, St Petersburg

    Google Scholar 

  • Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge

    Google Scholar 

  • Bardy KE, Albach DC, Schneeweiss GM, Fischer MA, Schönswetter P (2010) Disentangling phylogeography, polyploid evolution and taxonomy of a woodland herb (Veronica chamaedrys group, Plantaginaceae s.l.) in southeastern Europe. Molec Phylogen Evol 57:771–786

    Article  Google Scholar 

  • Barkalov VY (1987) Sem. 143. Lukovye – Alliaceae J. Agardh. In: Charkevicz SS (ed) Plantae vasculares Orientis Extremi Sovietici, Tomus 2. Nauka, Leningrad, pp 376–393

    Google Scholar 

  • Blattner FR (1999) Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR. Biotechniques 27:1180–1186

    CAS  PubMed  Google Scholar 

  • Bolkhovskikh ZV, Grif VG, Zakhar’eva OI, Matveyeva TS (1969) Khromosomnye chisla tsvetkovych rastenii. Nauka, Leningrad

    Google Scholar 

  • Cheremushkina VA (2004) Biologiia lukov Evrazii, Novosibirsk

  • Choi HJ (2015) Portrayal of Allium spurium G. Don (Amaryllidaceae) from the border area of China and North Korea: a putative unrecorded species in the Korean Peninsula. Botanica. Pacifica 4:1–3. doi:10.17581/bp.2015.04202

    Google Scholar 

  • Choi HJ, Oh BU (2010) A new species and a new combination of Allium sect. Rhizirideum (Alliaceae) from northeastern China and Korea. Brittonia 62:199–205

    Article  Google Scholar 

  • Delplancke M, Alvarez N, Benoit L, Espindola A, Joly HI, Neuenschwander S, Arrigo N (2013) Evolutionary history of almond tree domestication in the Mediterranean basin. Molec Ecol 22:1092–1104

    Article  CAS  Google Scholar 

  • Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214

    Article  PubMed  PubMed Central  Google Scholar 

  • Ehrendorfer F (1980) Chapter 3 polyploidy and distribution. In: Lewis WH (ed) Polyploidy, biological relevance. Plenum Press, New York, pp 45–60

    Chapter  Google Scholar 

  • Favarger C (1961) Sur l’emploides nombres de chromosomes en géographie botanique historique. Ber Geobot Inst ETH Stiftung Rübel 32:119–146

    Google Scholar 

  • Favarger C (1984) Cytogeography and biosystematics. In: Grant WF (ed) Plant biosystematics. Academic Press, Vancouver, pp 453–476

    Chapter  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Franzke A, Hurka H, Janssen D, Neuffer B, Friesen N, Markov M (2004) Molecular signals for late Tertiary/Early Quarternary range splits of an Eurasian steppe plant: Clausia aprica (Brassicaceae). Molec Ecol 13:2789–2795

    Article  CAS  Google Scholar 

  • Friesen N (1987) Rod Allium L. In: Malyshev LI, Peshkova GA (eds) Flora Sibiri. Araceae-Orchidaceae, Novosibirsk, pp 55–96

    Google Scholar 

  • Friesen N (1988) Lukovye Sibiri: sistematika, kariologiia, khorologiia. Nauka-Sibirskoe otd, Novosibirsk

    Google Scholar 

  • Friesen N (1992) Systematics of the Siberian polyploid complex in subgenus Rhizirideum (Allium). In: Hanelt P, Hammer K, Knupffer H (eds) The genus Allium: taxonomic problems and genetic resources, proceedings of an international symposium held at Gatersleben. Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, pp 55–66

    Google Scholar 

  • Friesen N (1995) The genus Allium L. in the flora of Mongolia. Feddes Repert 106:59–81

    Article  Google Scholar 

  • Friesen N, Hermann N (1998) Taxonomy, chorology and evolution of Allium lusitanicum: the European “A. senescens”. Linzer Biol Beitr 30:815–830

    Google Scholar 

  • Friesen N, Bolognini G, Nimis PL (1993) Quantitative phytogeography of the genus Allium in Siberia and Mongolia. Nordic J Bot 5:295–307

    Article  Google Scholar 

  • Friesen N, Fritsch RM, Blattner FR (2006) Phylogeny and intrageneric classification of Allium L. (Alliaceae) based on nuclear ribosomal DNA ITS. Aliso 22:372–395

    Google Scholar 

  • Friesen N, German DA, Hurka H, Herden T, Oyuntsetseg B, Neuffer B (2015) Dated phylogenies and historical biogeography of Dontostemon and Clausia (Brassicaceae) mirror the palaegeographical history of the Eurasian steppe. J Biogeogr. doi:10.1111/jbi.12658

    Google Scholar 

  • Fritsch RM (2001) Taxonomy of the genus Allium: contributions from IPK Gatersleben. Herbertia 56:19–50

    Google Scholar 

  • Fritsch RM, Friesen N (2002) Evolution, domestication, and taxonomy. In: Rabinovich HD, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Wallingford, pp 5–30

    Chapter  Google Scholar 

  • Herden T, Hanelt P, Friesen N (2016) Phylogeny of Allium L. subgenus Anguinum (G. Don. ex W. D. J. Koch) N. Friesen (Amaryllidaceae). Molec Phylogen Evol 95:79–93

    Article  Google Scholar 

  • Hermy M, Honnay O, Firbank L, Grasof-Bokdam C, Lawesson JE (1999) An ecological comparison between ancient and other forest plant species of Europe, and the implications for forest conservation. Biol Conservation 91:9–22

    Article  Google Scholar 

  • Hewitt GM (2001) Speciation, hybrid zones and phylogeography: or seeing genes in space and time. Molec Ecol 10(3):537–549

    Article  CAS  Google Scholar 

  • Huang C-C, Hung K-H, Wang W-K, Ho C-W, Huang C-L, Hsu T-W, Osada N et al (2012) Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae). Gene 499:194–201

    Article  CAS  PubMed  Google Scholar 

  • Hurka H, Friesen N, German DA, Franzke A, Neuffer B (2012) ‘Missing link’ species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae). Molec Ecol 21:1223–1238

    Article  Google Scholar 

  • Huson DH, Scornavacca C (2010) A survey of combinatorial methods for phylogenetic networks. Genome Biol Evol 3:23–35. doi:10.1093/gbe/evq077

    Article  PubMed  PubMed Central  Google Scholar 

  • Huson DH, Scornavacca C (2012) Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 61:1061–1067. doi:10.1093/sysbio/sys062

    Article  PubMed  Google Scholar 

  • IPCN (1979–2016) Index to plant chromosome numbers. Goldblatt P, Johnson DE (eds) Missouri Botanical Garden, St. Louis. http://mobot.mobot.org/W3T/Search/ipcn.html. Accessed 15 Jan 2016

  • Jeanmogin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403–405

    Article  Google Scholar 

  • Kamelin RV (2004) Lektsii po sistematike rastenii. Glavy teoreticheskoi sistematiki rastenii, Izdatel’stvo “AzBuka”, Barnaul

  • Kay K, Whittall J, Hodges S (2006) A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evol Biol 6:36

    Article  Google Scholar 

  • Kirschner J, Kirschnerova L, Stĕpánek J (2007) Generally accepted plant names based on material from the Czech Republic and published in 1753–1820. Preslia 79:323–365

    Google Scholar 

  • Koldaeva MN (2015) On the infraspecific diversity of Allium spirale Willd. ex Schlecht. (Alliaceae) in the Russian Far East. Turczaninowia 18:5–10

    Article  Google Scholar 

  • Krogulevich RE, Rostovtseva TS (1984) Khromosomnye chisla tsvetkovykh rastenii Sibiri i Dal’nego Vostoka. Nauka, Sibirskoe Otdelenie, Novosibirsk

    Google Scholar 

  • Li QQ, Zhou DZ, He XH, Xu Y, Zhang YC, Wei XQ (2010) Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Ann Bot (Oxford) 106:709–733

    Article  CAS  Google Scholar 

  • Nürk NM, Uribe-Convers S, Gehrke B, Tank DC, Blattner FR (2015) Oligocene niche shift, Miocene diversification: cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae). BMC Evol Biol 15:80. doi:10.1186/s12862-015-0359-4

    Article  PubMed  PubMed Central  Google Scholar 

  • Parisod C, Holderegger R, Brochmann C (2010) Evolutionary consequences of autopolyploidy. New Phytol 186:5–17

    Article  CAS  PubMed  Google Scholar 

  • Pastor J (1982) Karyology of Allium species from the Iberian Peninsula. Phyton (Horn) 22:171–200

    Google Scholar 

  • Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818

    Article  CAS  PubMed  Google Scholar 

  • Ronquist R, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  CAS  PubMed  Google Scholar 

  • Schmitt T (2007) Molecular biogeography of Europe: pleistocene cycles and postglacial trends. Front Zool 4:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Seregin AP, Anaćkov G, Friesen N (2015) Molecular and morphological revision of the Allium saxatile group (Amaryllidaceae): geographical isolation as the driving force of underestimated speciation. Bot J Linn Soc 178:67–101. doi:10.1111/boj.12269

    Article  Google Scholar 

  • Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequence to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Amer J Bot 94:275–288

    Article  CAS  Google Scholar 

  • Sinitsyna TA, Friesen N (2008) Phylogeny of the Allium L. section Rhizirideum G. Don ex W. D. J. Koch based on molecular-genetic data: In: Proceedings of 7th international scientific-practical conference on problems of botany of South Siberia and Mongolia. (Barnaul, 21–24 Oktober 2008): 323–326

  • Stehlik I, Blattner FR, Holderegger R, Bachmann K (2002) Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages. Molec Ecol 11:2027–2036

    Article  CAS  Google Scholar 

  • Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (* and other methods), vers. 4.0. Sinauer Associates, Inc., Sunderland

  • Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl Molec Biol 17:1105–1109

    Article  CAS  Google Scholar 

  • Taberlet P, Fumagalli L, Wust-Saucy A-G, Cosson J-F (1998) Comparative phylogeography and postglacial colonization routes in Europe. Molec Ecol 7:453–464

    Article  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molec Biol Evol 28(10):2731–2739. doi:10.1093/molbev/msr121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vvedensky AI (1935) Rod 267. Luk: Allium L. In: Komarov VL (ed) Flora URSS IV, Izdatel’stvo AN SSSR, Leningrad, pp 112–280

  • Xu JM, Kamelin RV (2000) Allium L. In: Wu ZY, Raven PH (eds) Flora of China. Science Press and Missouri Botanical Garden Press, Beijing and St. Louis

    Google Scholar 

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Acknowledgments

Curators and managers of the visited herbaria are greatly acknowledged for help and providing leaf material. We thank Herbert Hurka and Reinhard Fritsch for helpful comments on the manuscript and Lucille Schmieding for correcting the English. We want to give special thanks to the reviewers, for their valuable comments and suggestions on this manuscript. For financial support, we are grateful to DAAD for a Grant (PKZ A/07/90071) to the first author as well as to DFG for supporting the collecting of Allium specimen in Siberia and Mongolia for N. Friesen and to RSF (Russian Science Foundation, Project 14-14-00472) for T. Sinitsyna.

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Authors and Affiliations

  1. Altai State University, Lenina Pr. 61, Barnaul, Russia, 656049

    Tatiana A. Sinitsyna

  2. Botanical Garden of the Osnabrueck University, Albrechtstr. 29, 49076, Osnabrüeck, Germany

    Tobias Herden & Nikolai Friesen

Authors
  1. Tatiana A. Sinitsyna
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  2. Tobias Herden
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  3. Nikolai Friesen
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Correspondence to Nikolai Friesen.

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We confirm that this work is original and has not been published elsewhere nor is it currently under consideration for publication elsewhere. We the authors declare that the manuscript “Dater phylogeny and biogeography of the eurasian section rhizirideum G.Don ex W.D.J.Koch (Allium L., Amaryllidaceae)” (PLSY-D-16-00066) complies with all the requirements of “the ethical responsibilities of the authors” part in the “instruction for authors” guideline (Cope guidlines).

Additional information

Handling editor: Livia Wanntorp.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Online resources ESM1

Sources of geographical information. (PDF 371 kb)

Online resources ESM2

Chromosome numbers of Allium sect. Rhizirideum species and sources of information. (PDF 298 kb)

Online resources ESM3

ITS Alignment of all accessions of section Rhizirideum. (PDF 451 kb)

Online resources ESM4

ITS Alignment with only diploid species of section Rhizirideum. (PDF 418 kb)

Online resources ESM5

Plastid Alignment. (PDF 376 kb)

Online resources ESM6

Hybridogenic Network, based on ITS and plastid trees. (PDF 721 kb)

Online resources ESM7

Estimated mean ages. (PDF 375 kb)

Information on Electronic Supplementary Material

Information on Electronic Supplementary Material

Online resource 1. Sources of geographical information.

Online resource 2. Chromosome numbers of Allium sect. Rhizirideum species and sources of information.

Online resource 3. ITS Alignment of all accessions of section Rhizirideum.

Online resource 4. ITS Alignment with only diploid species of section Rhizirideum.

Online resource 5. Plastid Alignment.

Online resource 6. Hybridogenic Network, based on ITS and plastid trees.

Online resource 7. Estimated mean ages.

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Sinitsyna, T.A., Herden, T. & Friesen, N. Dated phylogeny and biogeography of the Eurasian Allium section Rhizirideum (Amaryllidaceae). Plant Syst Evol 302, 1311–1328 (2016). https://doi.org/10.1007/s00606-016-1333-3

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  • DOI: https://doi.org/10.1007/s00606-016-1333-3

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