A timescale for diatom evolution based on four molecular markers: reassessment of ghost lineages and major steps defining diatom evolution.

ABSTRACT. – Phylogenies and molecular clocks of the diatoms have largely been inferred from SSU rDNA sequences. A new phylogeny of diatoms was estimated using four gene markers SSU and LSU rDNA rbcL and psbA (total 4352 bp) with 42 diatom species. The four gene trees analysed with a maximum likelihood (ML) and Baysian (BI) analysis recovered a monophyletic origin of the new diatom classes with high bootstrap support, which has been controversial with single gene markers using single outgroups and alignments that do not take secondary structure of the SSU gene into account. The divergence time of the classes were calculated from a ML tree in the MultliDiv Time program using a Bayesian estimation allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. These divergence times are generally in agreement with those proposed by other clocks using single genes with the exception that the pennates appear much earlier and suggest a longer Cretaceous fossil record that has yet to be sampled. Ghost lineages (i.e. the discrepancy between first appearance (FA) and molecular clock age of origin from an extant taxon) were revealed in the pennate lineage, whereas those ghost lineages in the centric lineages previously reported by others are reviewed and referred to earlier literature.

A timescale for diatom evolution based on four molecular markers: reassessment of ghost lineages and major steps defining diatom evolution.

ABSTRACT. – Phylogenies and molecular clocks of the diatoms have largely been inferred from SSU rDNA sequences. A new phylogeny of diatoms was estimated using four gene markers SSU and LSU rDNA rbcL and psbA (total 4352 bp) with 42 diatom species. The four gene trees analysed with a maximum likelihood (ML) and Baysian (BI) analysis recovered a monophyletic origin of the new diatom classes with high bootstrap support, which has been controversial with single gene markers using single outgroups and alignments that do not take secondary structure of the SSU gene into account. The divergence time of the classes were calculated from a ML tree in the MultliDiv Time program using a Bayesian estimation allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. These divergence times are generally in agreement with those proposed by other clocks using single genes with the exception that the pennates appear much earlier and suggest a longer Cretaceous fossil record that has yet to be sampled. Ghost lineages (i.e. the discrepancy between first appearance (FA) and molecular clock age of origin from an extant taxon) were revealed in the pennate lineage, whereas those ghost lineages in the centric lineages previously reported by others are reviewed and referred to earlier literature.

Evolution of the Diatoms: VIII. Re-Examination of the SSU-Rrna Gene Using Multiple Outgroups and a Cladistic Analysis of Valve Features.

The resolution of the SSU rRNA gene for phylogenetic analysis in the diatoms has been evaluated by Theriot et al. who claimed that the SSU rRNA gene could not be used to resolve the monophyly of the three diatoms classes described by Medlin and Kaczmarska. Although they used both only bolidomonads and heterokonts as outgroups, they did not explore outgroups further away than the heterokonts. In this study, the use of the multiple outgroups inside and outside the heterokonts with the rRNA gene for recovering the three monophyletic clades at the class level is evaluated. Trees with multiple outgroups ranging from only bolidophytes to Bacteria and Archea were analyzed with Bayesian and Maximum Likelihood analyses and two data sets were recovered with the classes being monophyletic. Other data sets were analyzed with non-weighted and weighted maximum parsimony. The latter reduced the number of clades and lengthened branch lengths between the clades. One data set using a weighted analysis recovered the three classes as monophyletic. Taking only bolidophytes as the only outgroup never produced monophyletic clades. Multiple outgroups including many heterokonts and certain members of the crown group radiation recovered monophyletic clades. The three classes can be defined by clear morphological differences primarily based on auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. A cladistic analysis of some of these features is presented and recovers the three classes.