Phylogeny of the genus Pistacia as determined from analysis of the chloroplast genome

Abstract

Classification within the genus Pistacia has been based on leaf morphology and geographical distribution. Molecular genetic tools (PCR amplification followed by restriction analysis of a 3.2-kb region of variable chloroplast DNA, and restriction fragment length polymorphism analysis of the Pistacia cpDNA with tobacco chloroplast DNA probes) provided a new set of variables to study the phylogenetic relationships of 10 Pistacia species. Both parsimony and cluster analyses were used to divide the genus into two major groups. P. vera was determined to be the least derived species. P. weinmannifolia, an Asian species, is most closely related to P. texana and P. mexicana, New World species. These three species share a common origin, suggesting that a common ancestor of P. texana and P. mexicana originated in Asia. P. integerrima and P. chinensis were shown to be distinct whereas the pairs of species were monophyletic within each of two tertiary groups, P. vera:P. khinjuk and P. mexicana:P. texana. An evolutionary trend from large to small nuts and leaves with few, large leaflets to many, small leaflets was supported. The genus Pistacia was shown to have a low chloroplast DNA mutation rate: 0.05-0.16 times that expected of annual plants.

Figure 1

Pistacia polymorphic cpDNA restriction fragments from 3.2-kb amplified region in a 2% agarose gel. Lanes 1–18 with enzyme and restricted cpDNA, respectively: 100-bp molecular weight marker ladder, HinfI:P. vera, HinfI:P. weinmannifolia, HinfI:P. atlantica, PalI:P. vera, PalI:P. weinmannifolia, RsaI:P. vera, RsaI:P. weinmannifolia, StyI:P. weinmannifolia, StyI:P. lentiscus, StyI:P. vera, BstNI:P. lentiscus, BstNI:P. vera, ScrFI:P. lentiscus, ScrFI:P. vera, DdeI:P. weinmannifolia, DdeI:P. vera, and HindIII:λ DNA.

Figure 2

Improved resolution of <200-bp fragments in 5% FMC Metaphor agarose gel. Lanes 1–10, left to right, with restriction enzyme and restricted cpDNA, respectively: 100-bp molecular weight marker ladder, undigested:P. vera, HinfI:P. weinmannifolia, HinfI:P. atlantica, HinfI:P. vera, MboI:P. vera, MspI:P. vera, AluI:P. vera, AluI:P. weinmannifolia, and HindIII:λ DNA.

Figure 3

Map of restriction sites within Pistacia cpDNA 3.2-kb amplified region. (a) Location of all identified restriction sites in P. vera. (b) Location of mutations DdeI-1, DdeI-2, BstNI-4, StyI-5, StyI-6, RsaI-7, and PalI-8; +, site gain, −, site loss referenced to P. vera. Mutations HinfI-10 and HinfI-11 were not mapped. lent, P. lentiscus; wien, P. weinmannifolia; tex, P. texana; mex, P. mexicana.

Figure 4

Phylograms from (a) mixed Dollo parsimony, (b) unordered parsimony and 50% majority rule bootstrap consensus tree from unordered parsimony, and (c) 50% majority rule bootstrap consensus tree from mixed Dollo parsimony analyses of 10 Pistacia species and Schinus molle outgroup. Arm lengths represent relative extent of divergence from nodes with number of mutations/arm. Bootstrap confidence levels are shown in parentheses. Proposed sectional groupings are shown with dotted lines at Right.