Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes

The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.     

Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations

Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the "reduced-bias" mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of non-historical signal, such as from compositional non-stationarity. [Base composition; combined data; marsupial; mitochondrial genome; phylogeny.].     

The specificity enigma: from mechanics to poems.

Biological specificity is usually described in terms of the lock-and-key metaphor. However, this metaphor is to a certain extent misleading and does not grasp the complexity underlying biological specificity. The failure of the lock-and-key metaphor makes it difficult to understand immune recognition. This is the reason why immune specificity has been described as the "Specificity Enigma." In this article, I point at three important differences between biological specificity and mechanical specificity, and suggest an alternative lens through which immune specificity can be considered.     

Calcium leak from intracellular stores--the enigma of calcium signalling

Wherever you travel through the cytoplasm of the cells you will find organelles with internal [Ca(2+)] levels higher than in the surrounding cytosol. This is particularly true of the endoplasmic reticulum (ER) (or sarcoplasmic reticulum (SR) in muscle cells); such organelles serve as the main sources of releasable Ca(2+) for cytosolic cellular signalling. Calcium pumps of the SERCA family (sarcoplasmic and endoplasmic reticulum calcium ATP-ases) import calcium into the organelle lumen. The other mechanism that is responsible for the steady state calcium level within the lumen of ER or SR is a calcium leak that balances the influx created by the pumps. The leak remains the most enigmatic of the processes involved in calcium regulation. The molecular nature of the leak mechanism is not known. The basal leak is a relatively slow process, which is difficult to investigate and which is easily outmatched (both in the amplitude of calcium responses and in attractiveness to experimenters) by substantially faster second messenger-induced release. Nevertheless, information on the properties of the calcium leak, although thinly scattered through the pages of PubMed, has been slowly accumulating. In this review we will discuss the properties of the calcium leak and speculate about possible mechanisms, which could mediate this process.     

Chloride and calcium in Photosystem II: from effects to enigma*

This minireview focuses on the early evidence for roles of chloride and calcium ions in reactions of photosynthetic electron transport and on the reluctance with which an essential function of these inorganic ions in the process of water oxidation was accepted. For example, Daniel Arnon's group initially refuted the conclusion of Otto Warburg, the discoverer of a ‘chloride effect,’ that chloride was a ‘coenzyme.’ Their reasoning was that chloride had not been shown to be an essential mineral nutrient of plants. In the case of calcium, the problem was that the first ‘calcium effects’ had been seen with preparations from cyanobacteria rather than from green plants. While today the status of calcium and chloride as essential participants in the process of water oxidation is rarely disputed, the nature of their involvement still eludes all experimental inquiries. Substantial progress in this respect may come from recent refinements of the application of Fourier-transform infrared spectroscopy to the study of photosynthetic water oxidation. I dedicate this minireview to the memory of George Cheniae (1928–2001), my college for almost 40 years, whose excellance as a scientist and fairness have been an inspiration, whose critical mind I admired, whose wit I enjoyed, and whose friendship I cherished. This revised version was published online in June 2006 with corrections to the Cover Date.     

Molecular clocks and explosive radiations

Molecular data are ideal for exploring evolutionary history because of its universality, stochasticity, and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), potentially within a statistical framework that allows testing of evolutionary hypotheses. However, the discrepancy between molecular and paleontological dates for three key "explosive" radiations inferred from the fossil record--the Cambrian explosion of animal phyla and the post-KT radiations of modern orders of mammals and birds--have led to a reexamination of the assumptions on which molecular dates are based. Could variation in the rate of molecular evolution, perhaps associated with "explosive" radiations, cause overestimation of diversification dates? Here I examine four hypothetical causes of fast molecular rates in explosive radiations--body size, morphological rate, speciation rate, and ecological diversification--using available empirical evidence on patterns of variation in rate of molecular evolution.     

Temporal trends in childhood leukaemia incidence following exposure to radioactive fallout from atmospheric nuclear weapons testing

Notably raised rates of childhood leukaemia incidence have been found near some nuclear installations, in particular Sellafield and Dounreay in the United Kingdom, but risk assessments have concluded that the radiation doses estimated to have been received by children or in utero as a result of operations at these installations are much too small to account for the reported increases in incidence. This has led to speculation that the risk of childhood leukaemia arising from internal exposure to radiation following the intake of radioactive material released from nuclear facilities has been substantially underestimated. The radionuclides discharged from many nuclear installations are similar to those released into the global environment by atmospheric nuclear weapons testing, which was at its height in the late-1950s and early-1960s. Measurements of anthropogenic radionuclides in members of the general public resident in the vicinity of Sellafield and Dounreay have found levels that do not differ greatly from those in persons living remote from nuclear installations that are due to ubiquitous exposure to the radioactive debris of nuclear weapons testing. Therefore, if the leukaemia risk to children resulting from deposition within the body of radioactive material discharged from nuclear facilities has been grossly underestimated, then a pronounced excess of childhood leukaemia would have been expected as a consequence of the short period of intense atmospheric weapons testing. We have examined childhood leukaemia incidence in 11 large-scale cancer registries in three continents for which data were available at least as early as 1962. We found no evidence of a wave of excess cases corresponding to the peak of radioactive fallout from atmospheric weapons testing. The absence of a discernible increase in the incidence of childhood leukaemia following the period of maximum exposure to the radioactive debris of this testing weighs heavily against the suggestion that conventional methods are seriously in error when assessing the risk of childhood leukaemia from exposure to man-made radionuclides released from nuclear installations.     

Clusia: Holy Grail and enigma

Clusia is the only genus with bona fide dicotyledonous trees performing Crassulacean acid metabolism (CAM). Clusia minor L. is extraordinarily flexible, being C(3)/CAM intermediate and expressing the photosynthetic modes C(3), CAM, CAM-cycling, and CAM-idling. C(3) photosynthesis and CAM can be observed simultaneously in two opposite leaves on a node and possibly even within the same leaf in the interveinal lamina and the major vein tissue, respectively. The relative activity of photosystem II (PhiPSII) indicating photosynthetic energy use, is larger under photorespiratory than under non-photorespiratory conditions due to the particular energy demand of photorespiration. The heterogeneity of PhiPSII over the leaves as visualized by chlorophyll fluorescence imaging in the C(3) mode is larger under non-photorespiratory conditions than under photorespiratory conditions. These observations indicate that photorespiration, presumably by its particular energy demand, synchronizes photosynthetic activity over the leaves. In the CAM mode, the heterogeneity of PhiPSII is more dependent on the transitions between CAM phases. Free-running circadian oscillations of photosynthesis are strongly dampened in both the C(3) and the CAM mode. Photorespiration is under circadian clock control in both the C(3) and the CAM mode. PhiPSII and the heterogeneity of PhiPSII oscillate in phase with CO(2) uptake and photorespiration only under non-photorespiratory conditions. Under photorespiratory conditions, PhiPSII does not oscillate and there is no heterogeneity, again indicating the stabilizing function of photorespiration. Plants acclimatized to perform CAM switch to C(3) photosynthesis during free-running oscillations while subjected to constant illumination.     

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

The Alpine lake whitefish (Coregonus lavaretus) species complex is a classic example of a recent radiation, associated with colonization of the Alpine lakes following the glacial retreat (less than 15 kyr BP). They have formed a unique array of endemic lake flocks, each with one to six described sympatric species differing in morphology, diet and reproductive ecology. Here, we present a genomic investigation of the relationships between and within the lake flocks. Comparing the signal between over 1000 AFLP loci and mitochondrial control region sequence data, we use phylogenetic tree-based and population genetic methods to reconstruct the phylogenetic history of the group and to delineate the principal centres of genetic diversity within the radiation. We find significant cytonuclear discordance showing that the genomically monophyletic Alpine whitefish clade arose from a hybrid swarm of at least two glacial refugial lineages. Within this radiation, we find seven extant genetic clusters centred on seven lake systems. Most interestingly, we find evidence of sympatric speciation within and parallel evolution of equivalent phenotypes among these lake systems. However, we also find the genetic signature of human-mediated gene flow and diversity loss within many lakes, highlighting the fragility of recent radiations.