To date, most molecular phylogenetic studies of Apocynaceae have been based on plastid DNA regions or nuclear ribosomal DNA. In this study, we used part of the PHYA (phytochrome A) exon, a low-copy nuclear gene, and combined it with the trnL-F region (intron and spacer) to investigate placement of Periplocoideae, intergeneric relationships of Asclepiadoideae and relationships within Rauvolfioideae. We included 112 taxa representing most major clades of Apocynaceae. The study confirms that both subfamilies Apocynoideae and Rauvolfioideae are paraphyletic and that Periplocoideae are nested within Apocynoideae. The APSA clade (Apocynoideae, Periplocoideae, Secamonoideae and Asclepiadoideae) is strongly supported here, but the crown clade of Apocynaceae (comprised of subfamilies Asclepiadoideae, Secamonoideae, Periplocoideae and Echiteae, Mesechiteae, Odontadenieae and Apocyneae of Apocynoideae) has only moderate support. The present study places Periplocoideae as part of the sister group to the rest of the crown clade. This contrasts with results from the previous only PHYA and plastid marker–based studies in which periplocoids appeared as sister to a clade comprising Baisseeae (Apocynoideae) plus Secamonoideae and Asclepiadoideae. Old World Cynanchinae form a well-supported clade with the New World MOG (Metastelmatinae, Oxypetalinae and Gonolobinae) tribes rather than with the largely Old World. Asclepiadinae and Tylophorinae, as suggested by earlier studies. In our combined analyses, resolution among most groups is improved as compared to previous plastid-only analyses.
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