Primarily known only by the edible fruits of Citrus, Rutaceae comprise a large (c. 160 genera and 1900 species), morphologically diverse, cosmopolitan family. Of its extraordinary array of secondary chemical compounds, many have medicinal, antimicrobial, insecticidal, or herbicidal properties. To assist with the much-needed suprageneric reclassification and with studies of evolution of chemical compounds and biogeographic history of the family, here we included sequence data (from two noncoding regions of the chloroplast genome-rps16 intron and trnL-trnF region) from 65 species in 59 genera (more than one third of those in the family) that represented all subfamilies and tribes and more genera of Toddalioideae and of neotropical groups than previous studies. Results confirmed that Cneorum, Ptaeroxylon, Spathelia, and Dictyoloma form a clade sister to the remaining Rutaceae, none of the subfamilies with more than one genus (except Aurantioideae) is monophyletic, and characters of the ovary and fruit are not reliable for circumscription of subfamilies. Furthermore, clades are better correlated with geographic distributions of the genera than with ovary and fruit characters. Circumscriptions of subfamilies and tribes (and some subtribes of Rutoideae) must be reevaluated. Results are discussed in light of geographic distributions, caryology, chemotaxonomy, and other molecular studies.

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Sequence data for plastid rbcL and atpB from members of Anacardiaceae, Burseraceae, Cneoraceae, Meliaceae, Ptaeroxylaceae, Rutaceae, and Simaroubaceae were analyzed cladistically to evaluate the familial and subfamilial circumscriptions of Rutaceae. Taxa representing all subfamilies and tribes were sampled. The analysis shows that Rutaceae are paraphyletic, with Spathelia and Dictyoloma (Rutaceae), Harrisonia (Simaroubaceae), Cneorum (Cneoraceae), and Ptaeroxylon (Ptaeroxylaceae) forming a clade sister to all other Rutaceae. Circumscription of Rutaceae to include all of these taxa is recommended. This analysis indicates that Simaroubaceae and Meliaceae are the outgroups closest to Rutaceae. Correlation of the molecular phylogenies with biochemical data indicates that chemotaxonomic information is more reliable than fruit type as an indicator of familial and subfamilial circumscriptions. The subfamilial classification needs revision; none of the subfamilies of more than one genus is monophyletic.

Rutaceae is a family of angiosperms well known for the economically important genus Citrus. The division of Rutaceae into subfamilies is still inadequate and provisional. Previous phylogenetic studies at the family level are characterized by a limited sampling of genera and lack several crucial taxa. Here, we present a phylogenetic study based on six nuclear and plastid markers including 87.7% of the currently accepted genera, which is more than twice as many as in previous studies. Seven genera are included in a phylogenetic analysis for the first time. Most clades are resolved with high support, and we propose a new subfamily classification for Rutaceae that comprises the subfamilies Amyridoideae, Aurantioideae, Cneoroideae, Haplophylloideae, Rutoideae and Zanthoxyloideae. Aurantioideae is the only traditional subfamily that is resolved as monophyletic. We tested whether 13 morphological and karyological characters are taxonomically informative in Rutaceae. Chromosome numbers are clearly different in the two main clades of Rutaceae, but fruit characteristics, which have been used to define subfamilies in the past, do not distinguish between the main lineages of the family.

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