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New insights into the phylogeny and taxonomy of Chinese species of Gagea (Liliaceae)—speciation through hybridization

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Abstract

A new region of speciation for the genus Gagea (Liliaceae) was investigated (Bogda-Shan and Urumqi; northwestern Xinjiang, China). Two species were recorded as new for the region (G. rufidula, G. davlianidzeae); three species are described as new to science (G. angelae, G. jensii and G. huochengensis). The description of G. nigra is emendated. Sequence data (cpDNA: trnL-trnF IGS+psbA-trnH IGS, nrDNA: ITS), including representatives of all Gagea sections, were used to compare the new species with closely related taxa. A nuclear single copy gene region (pCOS At103) was analysed for representatives of the Sects. Minimae and Gagea. Network analysis of cpDNA and nDNA indicates hybridization and recent speciation in Xinjiang. ITS and pCOS At103 sequences reveal gene flow between G. davlianidzeae and G. nigra. A cpDNA haplotype network constructed from representatives of Sect. Gagea was highly informative phylogenetically. Gagea angelae and G. huochengensis, sharing gene flow, are related closely to a basal clade represented by G. ancestralis, G. xiphoidea and G. capusii, which may include the putative progenitor of all other taxa of the large Eurasian Sect. Gagea. Whereas speciation in Sect. Minimae seems to be driven mainly by hybridization, speciation in the Sect. Gagea may be influenced by both hybridization and geographical separation. We confirm the monophyly of Sects. Bulbiferae and Minimae.

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Acknowledgments

We are grateful for the logistical support of the group of Nurbay Abdusalih, Institute of Natural Resources and Environment, Xinjiang University. Anne Petzold and Gymeniaz Saidahmet helped with field work. Niels Thevs kindly provided the translation of the Chinese description of G. nigra. Petra Oswald (IPK Gatersleben) is gratefully acknowledged for cloning and sequencing At103. We are grateful to M. Zarrei for providing Gagea material from Iran. Morphological research was supported by the Russian Foundation of Basic Research (grant 08-04-00670 to I.G.L.). We also thank three anonymous reviewers for very detailed and helpful comments.

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Correspondence to Martin Schnittler.

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Appendix 1

Appendix 1

Sources of the studied material and EMBL/NCBI accession numbers. Taxon (sample code)a: origin: voucher: (number of collection site)b: trnL-trnF IGS, psbA–trnH IGS, ITS region: ITS1 + 5.8SrDNA+ITS2, pCOS At103 region (#sequences taken from EMBL/NCBI)

Gagea afghanica A. Terracc.: Iran, Province Khorasan: 52/04DNALevichev (LE)/ HAL101785: (Zarrei & Ajani 830): AJ890373, AJ973160, AM087953, -. G. aipetriensis Levichev: Ukraine, Crimea: 15/04DNALevichev (LE), HAL01801: AJ970178, AM049259, AM087955, -. G. altaica Schischk. & Sumnev.: Kazakhstan: 51/04DNALevichev (LE), HAL101786: AJ890374, AJ973159, AM162670, -. G. ancestralis Levichev: Russia, Republic Altai: 144/10DNA Levichev (LE): FR690249, FR690844, FR691052, -. G. artemczukii Krasnova: Ukraine, Crimea: 19/04DNALevichev (LE), HAL101481: AM180470, AM409339, AM409331, -. G. angelae Levichev et Schnittler sp. nov.: (1B): China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N, 88°06′59″E, 1,980 m: LE 00002135: (200913): FR690259, FR691028, FR690104, -. (1 C-I): China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N, 88°06′59″E, 1,980 m: HAL108470: (200913, generative sample): FR690260, FR691029, FR690105, -. (1 C-II): China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N,88°06′59″E, 1,980 m: HAL108470: (200913, vegetative sample): FR690261, FR691030, FR690106, -. (2 C): China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N, 88°10′15″E, 2,250 m: HAL108477: (200914): FR690262, FR691031, FR690107, -. (3 G): China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108476: (200915): FR690263, FR691032, FR690108, -. (3 M): China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108475: (200915): FR690264, FR691033, FR690109, FR691334-FR691339 (3P) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108474: (200915): FR690265, FR691034, FR690110, -. (3Q) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108473: (200915): FR690266, FR691035, FR690111, -. (3R) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108472: (200915): FR690267, FR691036, FR690112, -. (3S) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2173 m: HAL108471: (200915): FR690268, FR691037, FR690113, FR691328-FR691333. G. bulbifera (Pall.) Salisb.: (1A) China, Xinjiang, Urumqi, Yamalik Hill Forest Park, 43°48′00″N, 87°34′51″E, 942 m: HAL107953: (200930): FR690234, FR690829, FR689753, -. (1 C) China, Xinjiang, Urumqi, Yamalik Hill Forest Park, 43°48′00″N, 87°34′51″E, 942 m: HAL107952: (200930): FR690235, FR690830, FR689754, -. (2) Russia, District Astrakhan: 2/04DNALevichev (LE), HAL101840: AJ969119, M049260, AM162669, -. (3)# Iran: Zarrei & al. TUH-E BOT.EXP. 35713 (TUH)(Kew 23140): -, -, EU912027, -. (4)# Iran: Zarrei & al. TUH-E BOT.EXP. 35709 (TUH)(Kew 23166): -, -, EU912028, -. G. capusii A. Terracc.: Uzbekistan: 24/04DNALevichev (LE), HAL101839: AJ969123, AM085143, AM422455, -. G. chlorantha (Bieb.) Schult. et Schult. f. #: -: -: -, EU939231, -, -. G. circumplexa Vved.: Uzbekistan: 30/04DNALevichev (LE), HAL101795: AJ969122, AJ973172, AM265529, -. G. confusa A. Terracc.: (1) Iran, Tehran: 13/04DNALevichev (LE), HAL101803: AJ890369, AJ973173, AM087949, -. (2)#Iran: Zarrei & Zarrei 35266 (TUH)(Kew 23137): -, -, EU912040, -. (3)#Iran: TUH-E BOT.EXP. 35712 (TUH)(Kew 23169): -, -, EU912041, -. G. davlianidzeae Levichev: (1A) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′52″N, 88°08′08″E, 1,928 m: HAL107948: (200925): FR690236, FR690831, FR689755, FR691346-FR691351 (2A) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N, 88°10′15″E, 2,250 m: HAL107946: (200926): FR690237, FR690832, FR689756, FR691352- FR691357 (2B-I) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N, 88°10′15″E, 2,250 m: HAL107945: (200926): FR690238, FR690833, FR689757, -. (2B-II) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N, 88°10′15″E, 2,250 m: HAL107945: (200926): FR690239, FR690834, FR689758, FR691358-FR691363 (3B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′51″N, 88°07′51″E, 1,928 m: HAL107943: (200927): FR690240, FR690835, FR689759, FR691364- FR691369. (4 C) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°54′44″N, 88°07′00″E, -: HAL107941: (200928): FR690241, FR690836, FR689760, -. (5B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°54′15″N, 88°06′51″E, -: HAL107939: (200929): FR690242, FR690837, FR689761, -. G. dschungarica Regel: Kyrgyzstan: 14/04DNALevichev (LE), HAL101802: AJ970175, AJ973164, AM087952,-. G. elegans Wall. ex D. Don in Royle: India, Punjab, Bashar State, Simla District: 2889 (LE): FR690255, -. -, -. G. erubescens (Besser) Besser: Ukraine, near Charkow: 25/04DNALevichev, G-103 (LE), HAL103861: AM180469, AM238516, AM493953, -. G. filiformis (Ledeb.) Kar. et Kir.: (1) Kazakhstan: 12/04DNALevichev (LE), HAL101804: AM084904, AM161459, AM180457, -. (2) Western Tian-Shan, 1550 m: 72/09DNALevichev (LE): FR690250, FR690845, FR689768, -. G. graeca (L.) Irmisch.: Greece, Crete, Ori Thriptis, HAL105185: AM939645, AM939648, AM939649, -. G. graminifolia Vved.: Kyrgyzstan, 114/09DNALevichev (LE): FR690251, FR690846, FR689769, -. G. granulosa Turcz.: (1) 11a/04DNALevichev (LE), HAL101805: AM180462, AM238518, AM265533, -. (2) Kazakhstan: 11b/04DNALevichev (LE), HAL101836: AM180463, AM238517, AM287278, -. (3) Ukraine, Poltava: 100/09DNALevichev (LE): FR690252, FR690847, -, -. (4) Russia, Sibiria, near Tomsk: 141/09DNALevichev(LE): FR690253, FR690848, -, -. G. helenae Grossh: Russia, Dagestan: 22/04DNALevichev (LE), HAL101798: AJ969120, AM161461, AM265531, -. G. huochengensis Levichev sp. nov.: (1 G) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N, 88°06′59″E, 1,980 m: HAL108466: (200922): FR690269, FR691038, FR690114, -. (1H) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N, 88°06′59″E, 1,980 m: HAL108465: (200922): FR690270, FR691039, FR690115, FR691322-FR691327. (2B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N, 88°10′15″E, 2,250 m: HAL108467: (200923): FR690271, FR691040, FR690116, -. (2 C) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N, 88°10′15″, 2,250 m: HAL108469: (200923): FR690273, FR691043, FR690119, -. (3H) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108468: (200924): FR690272, FR691041, FR690117, -. (4) Kazakhstan, 1,550 m: 132/09DNALevichev (LE), HAL107949: FR690274, FR691042, FR690118, -. G. jensii Levichev et Schnittler sp. nov.: (1B): China, Xinjiang, Urumqi, hills near cemetery, 43°43′53″N, 87°35′46″E, 987 m: HAL108482: (200917): FR690256, FR691025, FR690101, -. (1E): China, Xinjiang, Urumqi, hills near cemetery, 43°43′53″N, 87°35′46″E, 987 m: HAL108483: (200917): FR690257, FR691026, FR690102, -. (2) China, Xinjiang, Urumqi, Yamalik Hill Forest Park, 43°47′26″N, 87°34′21″E, 1,027 m: HAL108480: (200918): FR690258, FR691027, FR690103, -. G. liotardii (Sternberg) Schult. et Schult f. (=G. fragifera (Vill.) Ehr. Bayer & G. López González): (1A) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′54″N/ 88°09′47″E, 2,146 m: HAL107898: (200919): FN868226, FN868198, FN868162, -. (2A) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N/ 88°10′15″E, 2,250 m: HAL107896: (200920): FN868227, FN868199, FN868163, -. (3A) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°58′10″N/ 88°05′28″E, 2,350 m: HAL107894: (200921): FN868228, FN868200, FN868164, -. (4) Bulgaria, Pirin Mountains: HAL070407: AJ890368, AJ973158, AM162677, -. (5) Kazakhstan: 29b/04DNALevichev (LE), HAL101796: AM161467, AM238521, AM180455, -. (6) Ukraine, Crimea: 29a/04DNALevichev (LE), HAL101797: AM161466, AM238522, AM265532, -. (7) Switzerland, Canton Graubuenden: ZT10726: AJ890375, AM238531, -, -. G. lutea Ker Gawl.: Germany, Saxony-Anhalt: -: AJ419165, AJ416368, AJ427544, -. G. minima (L.) Ker Gawl.: (1) Italy, Calabria (Pollino Massif), 1,860 m: CLU 12698: AM283109, AM282996, AM287273, -. (2) Ukraine, Carpathians: 9/04DNALevichev (LE), HAL101808: AM238539, AM238524, AM087948, -. (3) Russia, Republic Tatarstan, Nizhnyaya Kama: 10/04DNALevichev (LE), HAL101806: AM180471, AM238519, AM180459, -. (4) Germany, Saxony-Anhalt: -: AJ419164, AJ416374, AJ427546, -. G. nakaiana Kitag.: Russia, Khabarovsk Territory: 17/04DNALevichev/55 (LE), HAL101799: AM110256, AM161457, AM180454, -. G. neopopovii Golosk.: Eastern Kazakhstan, Za-Iliskii Altai:120/09DNALevichev (LE): FR690254, FR690849, FR689770, -. G. nigra L.Z. Shue, emend. Schnittler: (1B): China, Xinjiang, Urumqi, 43°43′53″N, 87°35′46″E, 987 m: HAL108464: (200904): FR690123, FR691010, FR690081, FR691056-FR691061. (2A) China, Xinjiang, Urumqi, 43°38′50″N, 87°39′04″E: HAL108462: (200905): FR690124, FR691011, FR690082, -. (3A) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′27″N, 88°06′46″E: HAL108459: (200906): FR690125, FR691012, FR690083, -. (3B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′27″N, 88°06′46″E: HAL108458: (200906): -, -, FR690084, -. (3 C) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′27″N, 88°06′46″E: HAL108181: (200906): FR690126, FR691013, FR690085, -. (3 F) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′27″N, 88°06′46″E: HAL108182: (200906): FR690127, FR691014, FR690086, -. (4B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 88°06′02″E, 2,173 m: HAL108461: (200931) -, -, FR690087, -, (4D) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 88°06′02″E, 2,173 m: HAL108460: (200931): FR690128, FR691015, FR690088, FR691062-FR691067. (5B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°52′35″N, 88°07′41″E, 1,950 m: HAL108456: (200907): FR690129, FR691016, FR690089, -. (5 C) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°52′35″N, 88°07′41″E, 1,950 m: HAL108455: (200907): FR690130, FR691017, FR690090, -. (6 C): China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°50′17″N, 88°10′15″E, 2,250 m: HAL108183: (200908): FR690131, FR691018, FR690091, -. (7D) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′51″N, 88°08′23″E, 1,900 m: HAL108457: (200909): FR690132, FR691019, FR690092, -. (8B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N, 88°06′59″E, 1,980 m: DNAAP8B 2010Levichev (LE): (200910): FR690133, FR691020, FR690093, -. (8D) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N, 88°06′59″E, 1,980 m: HAL108184: (200910): FR690134, FR691021, FR690094, -. (9B) China, Xinjiang, Urumqi, Yamalik Hill Forest Park, 43°47′47″N, 87°34′38″E, 941 m: HAL108452: (200911): FR690135, FR691022, FR690095, -. (9 C) China, Xinjiang, Urumqi, Yamalik Hill Forest Park, 43°47′47″N, 87°34′38″E, 941 m: HAL108451: (200911): FR690136, FR691023, FR690096, -. (10) China, Xinjiang, Urumqi, (N9714, Sichuan Univ., Chengdu / 134/10DNALevichev, LE): FR690137, FR691024, -, -. Gagea ova Stapf: (1A) China, Xinjiang, Urumqi, Yamalik Hill Forest Park, 43°47′44″N,87°34′29″E, 938 m: HAL107951: (200912): FR690243, FR690838, FR689762, -. (1 C) China, Xinjiang, Urumqi, Yamalik Hill Forest Park, 43°47′44″N,87°34′29″E, 938 m: HAL 107950: (200912): FR690244, FR690839, FR689763, -. (2) Iran, Province Golestan: 39b/04DNALevichev (LE)/ HAL10183: (Zarrei 899): AM180466, AM265588, AM287277, -. (3) Iran, Province Khorasan: 39a/04DNALevichev (LE), HAL101834: AM180465, AM238526, AM287276, -. G. paczoskii (Zapal.) Grossh.: Italy: HAL104323: AM903072, AM903061, AM903051, -. G. pauciflora Turcz. ex Ledeb.: (1) Mongolia, Ulan Bator: HAL070423: AJ890372, AJ973168, AM409330, -. (2) Russia, District Krasnoyarsk: 1/04DNALevichev (LE), HAL103857: AM161468, AM287266, AM493952, -. G. podolica Schult. et Schult. f.: Ukraine: 21/04DNALevichev (LE), HAL101832: AM084903, AM238525, AM409334, -. G. pomeranica Ruthe: Germany: Saxony-Anhalt HAL095842: AJ419167, AJ416375, AJ427543,-. G. pratensis (Pers.) Dumort.: Germany, Saxony-Anhalt: HAL095847: AJ419162, AJ416372, AJ427542,-. G. pusilla (F.W. Schmidt) Sweet: cultivated: 18/04DNALevichev (LE): HAL101831: AM180464, AM161458, AM422453, -. G. reticulata (Pall.) Schult. et Schult.: (1) Israel, Central Negev: Z34650: -, -, AM087954, -. (2) Armenia, near Erivan: 35b/04DNALevichev (LE), HAL103856: AM238532, AM238528, -, -. G. rubicunda Meinsh. emend. Levichev: Estonia: 26/04DNALevichev (LE), HAL103855: AM238541, AM409338, AM493954, -. G. rufidula Levichev: (1D) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′38″N,88°07′02″E, 1,950 m: HAL107929: (200901): FR690245, FR690840, FR689764, -. (2 G) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 88°06′02″E, 2,173 m: HAL107924: (200902): FR690246, FR690841, FR689765, -. (3B) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°54′27″N, 88°06′46″E: HAL107922: (200903): FR690247, FR690842, FR689766, -. (4) Kyrgyzstan: 149/09DNALevichev (LE): FR690248, FR690843, FR689767, -. G. shmakoviana Levichev: Russia, Altai: 23/04DNALevichev (LE), HAL101830: AM265520, AM287265, AM422454, -. G. serotina (L.) Ker Gawl. (=L. serotina): Kazakhstan: 45a/04DNALevichev (LE), HAL101789: AJ890376, AM238530, AM087956, -. G. spathacea (Hayne) Salisb.: Germany, Saxony-Anhalt: HAL095844: AJ419166, AJ416369, AJ427541, -. G. stipitata Merckl. ex Bunge: Iran, Province Khorasan: 49/04DNALevichev (LE)/ HAL101828: (Zarrei & Ajani 816): AM265519, AM265594, AM409336, -. G. terraccianoana Pascher: Russia: 55/04DNALevichev (LE), HAL103853: AM287280, AM287268, AM493955, -. G. tisoniana Peruzzi, Bartolucci, Frignani & Minutillo: Italy CLU14920: AM409358, AM409349, AM422466, -. G. transversalis Steven: Ukraine, Crimea: 56/04DNALevichev, 365 (LE), HAL101783: AJ890370, AJ973167, AM162671,-. G. uliginosa Siehe & Pascher: #Iran: Zarrei et al. TUH-E BOT.EXP. 35304, (TUH)(Kew 23153): -, -, EU912089, -. G. vegeta Vved.: Uzbekistan: 32/04DNALevichev, 339a (LE), HAL103691:-, -,AM287275,-. G. villosa (Bieb.) Sweet: Germany, Saxony-Anhalt: -: AJ419163, AJ416373, AJ427545, -. G. xiphoidea Levichev (1) cultivated in (LE): Russia, Republic Altai, district Kosch-Agaczensis, 1,620 m: 71/09DNALevichev (LE): (G271-topotypus): FR690138, FR691044, FR690097, -. (2) Russia, Republic Altai, district Kosch-Agaczensis, 1,620 m: 102/09DNALevichev (LE): FR690139, FR691045, FR690098, -. G . cf. xiphoidea (3I) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108479: (200916): FR690140, FR691046, FR690099, FR691340-FR691345 (3 K) China, Xinjiang, Tian-Shan, Bogda-Shan, Tianchi Lake, 43°53′31″N, 86°06′02″E, 2,173 m: HAL108478: (200916): FR690141, FR691047, FR690100, -. Lilium candidum L.: -: -: -, AJ431692, -, -. Tulipa clusiana D.C.:-: HAL101864: - AM085140,-,-. T. cretica Boiss. & Heldr.: Greece, Crete: HAL099934: AJ810118, AM049257, AM180461,-.

aSample codes were used only if more than one individual was studied for a species (see explanation under Materials and methods)

bNumber of collection sites are given for all species collected by us in Xinjiang

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Peterson, A., Levichev, I.G., Peterson, J. et al. New insights into the phylogeny and taxonomy of Chinese species of Gagea (Liliaceae)—speciation through hybridization. Org Divers Evol 11, 387–407 (2011). https://doi.org/10.1007/s13127-011-0059-x

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