Recent and rapid speciation with limited morphological disparity in the genus Rattus.

Recent and rapid radiations provide rich material to examine the factors that drive speciation. Most recent and rapid radiations that have been well-characterized involve species that exhibit overt ecomorphological differences associated with clear partitioning of ecological niches in sympatry. The most diverse genus of rodents, Rattus (66 species), evolved fairly recently, but without overt ecomorphological divergence among species. We used multilocus molecular phylogenetic data and five fossil calibrations to estimate the tempo of diversification in Rattus, and their radiation on Australia and New Guinea (Sahul, 24 species). Based on our analyses, the genus Rattus originated at a date centered on the Pliocene-Pleistocene boundary (1.84-3.17 Ma) with a subsequent colonization of Sahul in the middle Pleistocene (0.85-1.28 Ma). Given these dates, the per lineage diversification rates in Rattus and Sahulian Rattus are among the highest reported for vertebrates (1.1-1.9 and 1.6-3.0 species per lineage per million years, respectively). Despite their rapid diversification, Rattus display little ecomorphological divergence among species and do not fit clearly into current models of adaptive radiations. Lineage through time plots and ancestral state reconstruction of ecological characters suggest that diversification of Sahulian Rattus was most rapid early on as they expanded into novel ecological conditions. However, rapid lineage accumulation occurred even when morphological disparity within lineages was low suggesting that future studies consider other phenotypes in the diversification of Rattus.

Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs.

Divergent paralogs can create both obstacles and opportunities for phylogenetic reconstruction. Phylogenetic relationships among eucalypt genera have been incongruent among datasets in previous studies, where morphological characters supported monophyly of the genus Corymbia, while intergenic spacers of the nuclear ribosomes (ITS) and chloroplast loci (trnL, trnH, psbA) showed Corymbia as either equivocal or paraphyletic. Ribosomal DNA occurs in multiple copies in a genome. We cloned and sequenced the nrITS to investigate if gene duplication was the cause of incongruence among trees in the eucalypts. Three ITS riboforms, two of them widespread, were recovered within some genomes. One of the ITS riboforms recovered a robust phylogeny showing Corymbia as a monophyletic genus, corroborating the evidence from morphology, fossil data, a recent ITS/ETS dataset and microsatellites (SSRs). Compelling evidence suggested that this divergent riboform is a pseudogene, i.e., non-functional paralog: comparatively lower GC content suggesting lower structural stability, deamination-like mutations at potential methylation sites, lack of conserved helices and hairpins and conspicuously lower thermodynamic stability in secondary structures. Phylogenies from the apparently functional riboform retained Corymbia as paraphyletic. We show here that pseudogenes can recover a well-corroborated phylogeny whereas their functional paralogs show misleading hypotheses. We explain that phylogenetic signals may be obscured when functional constraints in ITS necessitate compensatory mutations in the secondary structure helices involved in RNA transcription, whereas pseudogenes mutate under neutrality.

Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae)

The utility of microsatellites (SSRs) in reconstructing phylogenies is largely confined to studies below the genus level, due to the potential of homoplasy resulting from allele size range constraints and poor SSR transferability among divergent taxa. The eucalypt genus Corymbia has been shown to be monophyletic using morphological characters, however, analyses of intergenic spacer sequences have resulted in contradictory hypotheses- showing the genus as either equivocal or paraphyletic. To assess SSR utility in higher order phylogeny in the family Myrtaceae, phylogenetic relationships of the bloodwood eucalypts Corymbia and related genera were investigated using eight polymorphic SSRs. Repeat size variation using the average square and Nei's distance were congruent and showed Corymbia to be a monophyletic group, supporting morphological characters and a recent combination of the internal and external transcribed spacers dataset. SSRs are selectively neutral and provide data at multiple genomic regions, thus may explain why SSRs retained informative phylogenetic signals despite deep divergences. We show that where the problems of size-range constraints, high mutation rates and size homoplasy are addressed, SSRs might resolve problematic phylogenies of taxa that have diverged for as long as three million generations or 30 million years.