Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists.

The Chromalveolata "supergroup" is a massive assemblage of single-celled and multicellular protists such as ciliates and kelps that remains to be substantiated in molecular trees. Recent multigene analyses place chromalveolates into two major clades, the SAR (Stramenopiles, Alveolata, and Rhizaria) and the Cryptophyta+Haptophyta. Here we determined 69 new sequences from different chromalveolates to study the interrelationships of its constituent phyla. We included in our trees, the novel groups Telonemia and Katablepharidophyta that have previously been described as chromalvoleate allies. The best phylogenetic resolution resulted from a 6-protein (actin, alpha-tubulin, beta-tubulin, cytosolic HSP70, BIP HSP70, HSP90) and a 5-protein (lacking HSP90) alignment that validated the SAR and cryptophyte+haptophyte clades with the inclusion of telonemids in the former and katablepharids in the latter. We assessed the Plastidophila hypothesis that is based on EF2 data and suggest this grouping may be explained by horizontal gene transfers involving the EF2 gene rather than indicating host relationships.

Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium.

Transposable elements contribute significantly to plant genome evolution in myriad ways, ranging from local insertional mutations to global effects exerted on genome size through accumulation. Differential accumulation and deletion of transposable elements may profoundly affect genome size, even among members of the same genus. One example is that of Gossypium (cotton), where much of the 3-fold genome size variation is due to differential accumulation of one gypsy-like LTR retrotransposon, Gorge3. Copia and non-LTR LINE retrotransposons are also major components of the Gossypium genome, but unlike Gorge3, their extant copy numbers do not correlate with genome size. In the present study, we describe the nature and timing of transposition for copia and LINE retrotransposons in Gossypium. Our findings indicate that copia retrotransposons have been active in each lineage since divergence from a common ancestor, and that they have proliferated in a punctuated manner. However, the evolutionary history of LINEs contrasts markedly with that of the copia retrotransposons. Although LINEs have also been active in each lineage, they have accumulated in a stochastically regular manner, and phylogenetic analysis suggests that extant LINE populations in Gossypium are dominated by ancient insertions. Interestingly, the magnitude of transpositional bursts in each lineage corresponds directly with extant estimated copy number.

Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea.

The study of recently formed species is important because it can help us to better understand organismal divergence and the speciation process. However, these species often present difficult challenges in the field of molecular phylogenetics because the processes that drive molecular divergence can lag behind phenotypic divergence. In the current study we show that species of the recently diverged North American endemic genus of purple coneflower, Echinacea, have low levels of molecular divergence. Data from three nuclear loci and two plastid loci provide neither resolved topologies nor congruent hypotheses about species-level relationships. This lack of phylogenetic resolution is likely due to the combined effects of incomplete lineage sorting, hybridization, and backcrossing following secondary contact. The poor resolution provided by molecular markers contrasts previous studies that found well-resolved and taxonomically supported relationships from metabolic and morphological data. These results suggest that phenotypic canalization, resulting in identifiable morphological species, has occurred rapidly within Echinacea. Conversely, molecular signals have been distorted by gene flow and incomplete lineage sorting. Here we explore the impact of natural history on the genetic organization and phylogenetic relationships of Echinacea.