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Peaches and almonds: phylogeny of Prunus subg. Amygdalus (Rosaceae) based on DNA sequences and morphology

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Abstract

Almonds and peaches are among the most economically important fruit crops in subtropical and temperate regions. Questions regarding the origin and domestication of the crop species, interspecific relationships, and evolutionary patterns of fruits have remained unanswered due to the lack of phylogenetic data of Prunus subgenus Amygdalus, in which both almond and peach are classified. Twenty-two species of subg. Amygdalus were included in phylogenetic analyses of plastid ndhF-rpl32, rpL16, trnH-psbA, trnL-trnF, trnQ-5′rps16, and trnS-trnG and nuclear s6pdh genes to investigate the circumscription of subg. Amygdalus, phylogenetic relationships among the species, and implication for mesocarp and endocarp evolution. Prunus subg. Amygdalus is best circumscribed to include both almonds and peaches, comprising two sections, Amygdalus and Persica. Species traditionally placed close to almonds, such as P. tenella, P. petunnikowii, P. triloba, and P. pedunculata, should be excluded from subg. Amygdalus. Characteristics used to diagnose subg. Amygdalus, such as dry, splitting mesocarp and the ornamentation of endocarp evolved multiple times in Prunus; thus classification based solely on these morphological characters produces a taxonomic scheme that might not represent common ancestry. A dry, splitting mesocarp is likely to be ancestral for the common ancestor of subg. Amygdalus, and the fleshy, non-splitting mesocarp found in peaches was derived from the dry, splitting mesocarp, presumably by domestication and selection for a fleshy fruit in China. Very low genetic divergence among cultivated almond and its close relatives might be associated with gene flow and/or rapid speciation within the group.

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Acknowledgments

The authors thank Ali Donmez for his help in providing collections from Turkey and Iran. They are grateful to Daniela Potter and an anonymous reviewer for their helpful comments. The first author thanks Jerold Davis, Maria A. Gandolfo, Kevin Nixon and Dennis Stevenson for their helpful comments. This work was supported by an NSF Doctoral Dissertation Improvement Grant (DEB-0709971) to Kevin Nixon and M.Y.

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Authors and Affiliations

  1. L. H. Bailey Hortorium, Department of Plant Biology, 412 Mann Library, Cornell University, Ithaca, NY, 14853, USA

    M. Yazbek

  2. Department of Landscape Design and Ecosystem Management, American University of Beirut, Beirut, Lebanon

    M. Yazbek

  3. Nature Conservation Center, American University of Beirut, Beirut, Lebanon

    M. Yazbek

  4. Department of Biology, 7417 Basic Sciences Building, Daejeon University, Daejeon, 300-716, South Korea

    S.-H. Oh

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  1. M. Yazbek
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Correspondence to S.-H. Oh.

Appendix 1: List of voucher specimens used in this study

Appendix 1: List of voucher specimens used in this study

DPRU accessions from the USDA National Clonal Germplasm Repository, Davis. An asterisk indicates that DNA was isolated from an herbarium specimen. Classification scheme follows Mason (1913) and Rehder (1940).

Prunus subg. Amygdalus

Sect. Amygdalus

P. arabica (Oliv.) Meikle var. arabica, Yazbek 23

P. arabica var. scoparia (1) Donmez 14114 (2) Donmez 14114b (3) DPRU 2224.1

P. argentea (Lam.) Rehder (1) Donmez 4379 (2) Donmez 12606 (3) Yazbek 09

P. balansae, Donmez 12609

P. bucharica (Korsh.) B. Fedtsch. ex Rehder, Al-Shehbaz & Hisoriev 601

P. carduchorum (Bornm.) Meikle, Donmez 10761

P. discolor S. K. Schneid., Donmez 4299

P. dulcis (Mill.) D. A. Webb. (1) Donmez 12603 (2) Donmez 12462 (3) Yazbek 05 (4) Yazbek 11

P. eburnea Aitch., DPRU 2226.8

P. erioclada Bornm. (1) Donmez 14161 (2) Donmez 14169

P. fenzliana Fritsch (1) Fayvush 509 (2) Al-Shehbaz & Hisoriev 654 (3) Donmez 5145

P. haussknechtii S. K. Schneid. (1) Donmez 14117 (2) Rechinger 47822*

P. kotschyi (Boiss. & Hohen. ex Spach) Meikle (1) Iranshahr & Terme 12677e* (2) Rechinger 49085*

P. kuramica (Korsh.) Kitam., DPRU 1467.4

P. lycioides (Spach.) S. K. Schneid. (1) Donmez 5085 (2) Donmez 14125

P. spinosissima (Bunge) Franch. (1) Donmez 14104 (2) Donmez 14104b (3) Donmez 14106 (4) Donmez 14125

P. trichamygdalus Hand.-Mazz., Donmez 12378

P. webbii (Spach) Fritsch (1) Donmez 3145 (2) Donmez 12164 (3) Donmez 12614

Sect. Persica

P. davidiana (Carrière) Franch. (1) DPRU 2325.3 (3) DPRU 2494.1 (3) Yazbek & Wang 15

P. kansuensis Rehder (1) DPRU 0582 (2) Yazbek & Wang 25

P. mira Koehne (1) DPRU 2232 (2) DPRU 2583.2 (3) Yazbek & Wang 50

P. mongolica Maxim. (1) Yazbek & Wang 01 (2) Yazbek & Wang 02

P. persica (L.) Batsch (1) DPRU 1586 (2) Yazbek 61 (3) DPRU 2595.1

P. tangutica (Bataline) Koehne (1) Yazbek & Wang 28 (2) Yazbek & Wang 30

Sect. Chamaeamygdalus

P. tenella Batsch (1) Barta 2005-237 (2) Barta 2005-239* (3) DPRU 2225.7 (4) Vitek s.n.

P. petunnikowii Rehder, no voucher

Prunus subg. Emplectocladus

P. eremophila Prigge, Donmez 10219

P. fasciculata (Torr.) A. Gray, Potter 752

Prunus subg. Prunus

Sect. Louiseania

P. triloba Lindley (1) Yazbek 65 (2) Yazbek & Wang 04

P. pedunculata (Pall.) Maxim., DPRU 2328.4

Sect. Penarmeniaca

P. fremontii S. Watson (1) DPRU 2097 (2) Potter 754

P. andersonii A. Gray, no voucher

P. havardii (W. Wight) S. C. Mason, Spelleberg et al. 9685

Sect. Armeniaca

P. armeniaca L., no voucher

P. mume (Siebold) Siebold & Zucc., Yazbek 49

P. sibirica L., Yazbek & Wang 56

Sect. Prunus

P. domestica L., no voucher

P. spinosa L., DPRU 0473

Sect. Piloprunus

P. texana Dietr., JSH924

P. maritima Marshall, JSH877

P. hortulana L. H. Bailey, JSH821-017

P. angustifolia Marsh., JSH785

P. nigra Aiton, JSH979

P. umbellata Elliott, JSH774

Outgroups

P. virginiana L., JSH871

Physocarpus amurensis (Maxim.) Maxim., JSH1015

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Yazbek, M., Oh, SH. Peaches and almonds: phylogeny of Prunus subg. Amygdalus (Rosaceae) based on DNA sequences and morphology. Plant Syst Evol 299, 1403–1418 (2013). https://doi.org/10.1007/s00606-013-0802-1

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