Incorrect handling of calibration information in divergence time inference: an example from volcanic islands

Divergence time studies rely on calibration information from several sources. The age of volcanic islands is one of the standard references to obtain chronological data to estimate the absolute times of lineage diversifications. This strategy assumes that cladogenesis is necessarily associated with island formation, and punctual calibrations are commonly used to date the splits of endemic island species. Here, we re-examined three studies that inferred divergence times for different Hawaiian lineages assuming fixed calibration points. We show that, by permitting probabilistic calibrations, some divergences are estimated to be significantly younger or older than the age of the island formation, thus yielding distinct ecological scenarios for the speciation process. The results highlight the importance of using calibration information correctly, as well as the possibility of incorporating volcanic island studies into a formal, biogeographical hypothesis-testing framework.     

A new recent genus and species of three‐toed jerboas (Rodentia: Dipodinae) from China: A living fossil?

The new recent genus and species of three‐toed jerboas (Rodentia: Dipodinae), from southern Ningxia, China, is described. This form demonstrated a unique mixture of external, cranial, and dental characters that individually are typical for one or another of all known genera of Dipodinae. Based on morphological characters, it is recovered as the part of Dipodinae tree, distinct from all other members due to its unique combination of morphological characters, and appears to be a nearly ideal living ancestor of all other dipodines. In contrast to morphology, the molecular data indicate a relatively young age for this lineage and consistently place it as the sister group to Stylodipus. The results of the molecular clock analysis suggest that the separation of the two lineages dates back to the Early Pliocene or the Pliocene/Miocene boundary. The estimated geographic range of the new form seems extremely small. The conservational status of the new species remains to be determined; however, the available information suggests that it requires protection.     

Who is the closest extant cousin of humans? Total‐evidence approach to hominid phylogenetics via simultaneous optimization

J. R. Grehan & J. H. Schwartz (Journal of Biogeography, 2009, 36 , 1823–1844) argued that humans (Homo) are more closely related to orangutans (Pongo) than to chimpanzees (Pan), and used this scenario to draw biogeographical conclusions about human origins. They discussed a contradiction between phenotypical and molecular results that has led to a debate about the reliability of genetic versus phenotypic data. The main aim of our study is to test the conflicting phylogenetic hypotheses by a total‐evidence analysis based on simultaneous optimization of extensive phenotypic and molecular data sets. Our results supported the human–chimpanzee clade, without any phenotypical–molecular data conflict, as the same phylogeny emerged both from the total analysis and when the molecular and phenotypic data were analysed separately. Sensitivity analyses showed that the result was not dependent on the parameters chosen for character weighting.     

Supplementary ultraviolet-B irradiation reveals differences in stress responses between Arabidopsis thaliana ecotypes

Irradiation of Arabidopsis thaliana ecotypes C24, Wassilewskija (Ws) and Columbia-0 (Col-0) with supplementary ultraviolet-A+B (UV-A+B) radiation revealed ecotype-specific differences in expression of the gene for the pathogenesis-related protein PR-5. C24 showed an increased expression level of PR-5 (5- and 20-fold higher compared with Col-0 and Ws, respectively). Expression of other molecular markers such as CHS (encoding chalcone synthase), MEB5.2 [encoding a gene strongly up-regulated by ultraviolet-B (UV-B)] and PYROA [encoding a pyridoxine (Vitamin B6) biosynthesis enzyme] only showed slight differences between ecotypes. Oxidative stress during UVA+B exposure was monitored by staining for H2O2. This analysis also revealed important ecotype-specific differences. 'H2O2 hot spots' were found in C24, whereas an even distribution of H2O2 was found in Ws and Col-0. Necrotic lesions also appeared on C24 leaves after prolonged UV-B exposure. There was a reverse correlation between the H2O2 steady-state concentration and the PR-5 gene expression; Ws showed the highest level of H2O2 accumulation but the lowest expression level of the PR-5 gene. Furthermore, application of paraquat on the rosettes led to similar PR-5 expression and H2O2 accumulation patterns as were found after UV-A+B irradiation. The observed ecotypic differences were also reflected in a statistically significant UV-B-dependent decrease in biomass, rosette size and leaf area for Ws, but not for C24 and Col-0. Our results show that a significant ecotype-specific genetic variability in general UV-B responses in Arabidopsis exists. Moreover, the signal transduction or gene regulation pathway for PR-5 differs from the other molecular markers used in this study.