Discussion of Phylogenetic Relationships
The monophyly of Polemoniaceae is strongly supported by cladistic analyses of DNA sequence data. The branch uniting Polemoniaceae shows a high level of character support in chloroplast matK (Johnson et al., 1996), chloroplast ndhF (Prather et al., 2000) and nuclear rDNA 18S (Johnson et al., 1999) sequence analyses. Although a cladistic analysis to assess the monophyly of the phlox family has not been conducted with morphology, monophyly can be inferred by a unique combination of morphological features that center on floral and reproductive characters (see discussion above and in Johnson et al., 1999). Historically, there has been little questioning of the limits of this family although Cobaea has sometimes been segregated into its own family, Cobaeaceae, based on its vining habit, septicidal capsules, and other distinctive morphological features (Hutchinson, 1959). Cladistic analyses, all currently DNA-sequence based, strongly indicate a derived position for Cobaea within Polemoniaceae, rather than a sister relationship to all other genera (see also Prather, 1999).
Phylogenetic reconstruction within the phlox family is a work in progress. Early cladistic analyses of nuclear rDNA ITS sequences (Porter, 1996) and chloroplast matK (Johnson et al., 1996) and ndhF (Prather et al., 2000) sequences generally agree in recognizing six major groups of Polemoniaceae that have been recognized taxonomically at either the tribal or subfamily level (Porter and Johnson, 2000). Separate and combined analyses of several chloroplast DNA regions and the nuclear rDNA ITS regions for 84 species representing the 26 genera recognized by Porter and Johnson (2000) further support these higher-level groups (Johnson et al., 2008). Support for relationships within and among these lineages varies, and additional work is needed to resolve the relationships among these major groups. Furthermore, while the clades ranked as tribes and subfamilies by Porter and Johnson (2000), particularly in subfamily Polemonioideae (all genera except Acanthogilia, Bonplandia, Cobaea, and Cantua), are supported to greater or lesser degrees by molecular data, well-defined morphological synapomorphies exclusive to these groups are lacking in many cases. Taxon descriptions for super-generic groups include ranges of morphological variation that are rarely unique to a single, higher-level taxon. Consequently, meaningful taxonomic diagnoses are difficult to construct, and terminal taxa for the phylogenetic hypothesis presented above are genera (or species when genera are monotypic) rather than tribes or subfamilies. In general, polytomies in this phylogenetic hypothesis indicate relationships that are weakly supported in all data sets.
Prather et al. (2000) summarize disagreement among molecular studies in the placement of Acanthogilia gloriosa. Based on ndhF sequences, these authors favor a sister relationship between Acanthogilia and Bonplandia+Cantua+Cobaea. However, this relationship is only weakly supported, and is in disagreement with other published analyses that, similarly, disagree with each other. Combined analyses of five chloroplast regions and these regions plus nrDNA ITS sequences do not resolve the position of this species (Johnson et al., 2008). Acanthogilia represents an important lineage in the early diversification of Polemoniaceae and is either sister to all other Polemoniaceae, to just Bonplandia+Cantua+Cobaea, or to all other Polemoniaceae except these three genera.
Bonplandia+Cantua+Cobaea form a monophyletic group. In cpDNA studies, Bonplandia is sister to Cobaea, and these two genera combined are sister to Cantua; nrITS sequences place Cobaea and Cantua as sisters. Neither alternative is strongly supported.
The remaining genera of Polemoniaceae, are well supported as a monophyletic group composed of four principal groups: Polemonieae (Polemonium and Polemoniopollis); Gilieae (Saltugilia, Gilia, Collomia, Navarretia, Allophyllum and Lathrocasis); Phlocideae (Linanthus, Gymnosteris, Leptosiphon, Phlox, and Microsteris); and Loeselieae (Aliciella, Dayia, Loeselia, Giliastrum, Bryantiella, Ipomopsis, Microgilia, Eriastrum, Langloisia, and Loeseliastrum). Relationships among these groups are not strongly supported. Polemonieae is consistently resolved as sister to Phlocideae in both nrITS and a matrix of five cpDNA regions (Johnson et al., 2008). This same study resolves Loeselieae and Gilieae as sister to each other. Bayesian posterior probabilities for these relationships are high, but parsimony bootstrap values are week.
Polemonieae contains the single extant genus Polemonium. Fossil Polemonium-like pollen grains from Pliocene deposits in Europe have been described as Polemonipollis majewskii (Krutzsch, 1966; Muller, 1981). This taxon is inferred from the scanty morphological evidence available to be allied with Polemonium.
Within Gilieae, Saltugilia is strongly supported as sister to the remainder of the tribe, and Lathrocasis may be sister to the remaing genera. DNA sequence data suggest Lathrocasis is sister to Gilia, Collomia+Navarretia+Allophyllum, or both of these groups combined (Johnson and Weese, 2000; Johnson et al., 2008). Though the seed coat of Lathrocasis is unique, Gilia shares a seed coat morphology with Collomia, Allophyllum, and Navarretia (Johnson et al., 2004). Gilisenium, a fossil genus, has an inferred relationship near Gilia based on readily apparent morphological similarities (Lott et al. 1998), but has not been directly included in cladistic analyses. It could also belong in Loeselieae. Allophyllum, Collomia, and Navarretia form a very well support clade.
Within Phlocideae, relationships among genera are largely resolved with molecular data. Linanthus shows some indications, mostly surrounding the taxon Linanthus inyoensis, of being paraphyletic with respect to the rest of the tribe, and support for monophyly of Linanthus is the weakest among genera in this tribe (Bell and Patterson, 2000). Additional morphological and molecular analyses are needed to resolve relationships with robustness at the base of this tribe. Microsteris, which has been treated within Phlox by various authors, remains supported as sister to Phlox in published analyses (Ferguson and Jansen, 2002).
Among major lineages, tribe Loeselieae has the weakest support for monophyly in the family, but this clade is consistently recovered in molecular analyses. The radiation of lineages appears to have occurred rapidly relative to rates of molecular evolution in sampled genes, giving little resolution among many of the genera in this clade. Although several genera are well-supported as monophyletic, such as Aliciella, Giliastrum, and Eriastrum, others are questionable at present. Additional work by J. M. Porter (Rancho Santa Ana Botanic Garden, unpublished), indicates Bryantiella may not be monophyletic. These same data show that Ipomopsis as presently circumscribed also contains lineages that lack most recent common ancestry with the bulk of this genus. Further morphological and molecular work focused on Loeseliastrum is also warranted to resolve the affinities and evolutionary history of L. depressum, a species recently transferred to this genus but with discordant affinities in ITS versus chloroplast sequence data.
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