A chloroplast DNA phylogeny of easternPhlox(Polemoniaceae): implications of congruence and incongruence with the ITS phylogeny

Abstract

The comparison of independent phylogenies is a valuable approach to the study of evolutionary pattern and process. Available data on eastern North American Phlox, including our recent ITS phylogeny, suggest that relationships are complicated in the group and that hybridization may have been a contributing factor. We used restriction site data from the chloroplast genome to develop a second phylogeny for eastern Phlox. Sampling was the same as that for the ITS study and consisted of 79 samples (including all 22 eastern Phlox species and most eastern subspecies, as well as multiple populations of many taxa). The resulting cpDNA phylogeny agrees with the ITS phylogeny in many respects, strengthening earlier conclusions. Nevertheless, incongruence between the trees is noteworthy: many samples, particularly of members of the P. pilosa and P. glaberrima complexes, are placed in different clades. A variety of tests were carried out to assess congruence in terms of topological patterns, character congruence, and homogeneity of data sets. Significant conflict between the phylogenies is discussed in light of the hypothesis that hybridization has affected relationships in this genus.

Evolution of a RNA Polymerase Gene Family in Silene (Caryophyllaceae)—Incomplete Concerted Evolution and Topological Congruence Among Paralogues

“…As noted by Goldman et al (2000), the selection of a ML topology a posteriori (in our case, the deviating data ML topology) obscures the statistical interpretation of the obtained probability value. First, the test must obviously be one-sided, because the ML topology has higher likelihood than any other tree.…”

“…These differences in likelihood score indicate deviations from the model including the topology parameter and/or other model parameter values (ML estimates from the combined data set) supplied as input to PLATO (Grassly and Holmes, 1997 inferred from the deviating regions (i.e., ITS, RPA2, and RPB2, respectively) discovered with PLATO are different from the ML topologies inferred from the rest of the combined data (excluding, in turn, ITS, RPA2,ar\d RPB2) at some level of significance. Typically, different implementations of parametric bootstrapping (Huelsenbeck and Bull, 1996) are formulated to test whether the maximum likelihood topology or an alternative topology is true (Goldman et al, 2000). However, because we are interested in whether the ML topology differs significantly from an alternative topology, this is not the appropriate question to ask in our case.…”

“…This, however, severely reduces the power of the test. Parametric tests, such as those devised by Goldman et al (2000), are much more sensitive, but also much more dependent on adequate models. Therefore, we refrain from making strict probabilistic conclusions from our tests, but rather use them to evaluate tlie relative topological incongruence from the data sets identified by PLATO as favoring significantly different models.…”

“…Due to the predominant maternal inheritance of chloroplasts, the evolutionary history of CpDNA may differ substantially trom that of the main part of the nuclear genome (Cronn et al, 2002;Ferguson and Jansen, 2002), and the transfer of DNA regions from the plastid to the nucleus (Martin and Herrmann, 1998;Rujan and Martin, 2001) may further complicate the picture.…”

Sequence analyses of the ITS regions and the matK gene for determining phylogenetic relationships of Diospyros kaki (persimmon) with other wild Diospyros (Ebenaceae) species

“…The position of D. glandulosa to D. oleifera and D. kaki is especially intriguing. A lack of congruence between nuclear and organellar data sets has often been attributed to hybridization, particularly in plants (Soltis et al 1991(Soltis et al , 1996Soltis and Kuzoff 1995;Wendel et al 1995;Sang et al 1997;Hardig et al 2000;Ferguson and Jansen 2002). Phylogenies based on gene sequences from a maternally inherited, clonal lineage (i.e., mitochondrial or chloroplast genes) reflect the evolutionary history of that lineage and will only indicate the organismal phylogeny in the absence of introgression (Hardig et al 2000).…”