Intraspecific diversity and distribution of the cosmopolitan species Pseudo‐nitzschia pungens (Bacillariophyceae): morphology,genetics, and ecophysiology of the three clades

Three clades of Pseudo‐nitzschia pungens, determined by the internal transcribed space (ITS) region, are distributed throughout the world. We studied 15 P. pungens clones from various geographical locations and confirmed the existence of the three clades within P. pungens, based on ITS sequencing and described the three subgroups (IIIaa, IIIab, and IIIb) of clade III. Clade III (clade IIIaa) populations were reported for the first time in Korean coastal waters and the East China Sea. In morphometric analysis, we found the ultrastructural differences in the number of fibulae, striae, and poroids that separate the three clades. We carried out physiological tests on nine clones belonging to the three clades growing under various culture conditions. In temperature tests, only clade III clones could not grow at lower temperatures (10°C and 15°C), although clade I and II clones grew well. The estimated optimal growth range of clade I clones was wider than that of clades II and III. Clade II clones were considered to be adapted to lower temperatures and clade III to higher temperatures. In salinity tests, clade II and III clones did not grow well at a salinity of 40. Clade I clones were regarded as euryhaline and clade II and III clones were stenohaline. This supports the hypothesis that P. pungens clades have different ecophysiological characteristics based on their habitats. Our data show that physiological and morphological features are correlated with genetic intraspecific differentiation in P. pungens.     

Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from Culture Isolations,Clone Libraries,and Flow Cytometry

The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world’s oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance.     

Symbiodinium clade C dominates zooxanthellate corals (Scleractinia) in the temperate region of Japan

Endosymbiotic algae of the genus Symbiodinium have been divided into nine clades (A-I) following genetic classification; some clades are known to have physiological properties that enable the coral hosts to adapt to different environmental conditions. To understand the relationships of coral-alga symbioses, we focused on Symbiodinium diversity in zooxanthellate corals living under the severe environmental conditions of the temperate region (30°-35°N) of Japan. We investigated Symbiodinium clades in 346 colonies belonging to 58 coral species from six locations. We then selected three coral species-Acropora hyacinthus, Acropora japonica, and Cyphastrea chalcidicum-to investigate whether Symbiodinium clades changed during winter or summer over the course of year (May 2009-Apr 2010) in Tanabe Bay, Japan. Three Symbiodinium clades (C, D, and F) were detected in corals in the temperate region. Notably, 56 coral species contained Symbiodinium clade C. Oulastrea crispata predominantly contained clade D, but traces of clade C were also detected in all samples. The temperate-specific species Alveopora japonica contained clades C and F simultaneously. Seasonal change of symbiont clades did not occur in the three coral species during the investigation period where SSTs range on 12.5-29.2°C. However, we found Acropora (2 spp.) and Cyphastrea (1 sp.) contained different subcladal types of clade C. These results reveal that most coral species harbored Symbiodinium clade C stably throughout the year, suggesting that Symbiodinium clade C shows low-temperature tolerance, and that two hypothetical possibilities; genetic differences of subcladal types generating physiological differences or wide physiological flexibility in the clade C.     

Specificity is rarely absolute in coral-algal symbiosis: implications for coral response to climate change

Some reef-building corals have been shown to respond to environmental change by shifting the composition of their algal symbiont (genus Symbiodinium) communities. These shifts have been proposed as a potential mechanism by which corals might survive climate stressors, such as increased temperatures. Conventional molecular methods suggest this adaptive capacity may not be widespread because few (～25%) coral species have been found to associate with multiple Symbiodinium clades. However, these methods can fail to detect low abundance symbionts (typically less than 10-20% of the total algal symbiont community). To determine whether additional Symbiodinium clades are present, but are not detected using conventional techniques, we applied a high-resolution, real-time PCR assay to survey Symbiodinium (in clades A-D) from 39 species of phylogenetically and geographically diverse scleractinian corals. This survey included 26 coral species thought to be restricted to hosting a single Symbiodinium clade ('symbiotic specialists'). We detected at least two Symbiodinium clades (C and D) in at least one sample of all 39 coral species tested; all four Symbiodinium clades were detected in over half (54%) of the 26 symbiotic specialist coral species. Furthermore, on average, 68 per cent of all sampled colonies within a given coral species hosted two or more symbiont clades. We conclude that the ability to associate with multiple symbiont clades is common in scleractinian (stony) corals, and that, in coral-algal symbiosis, 'specificity' and 'flexibility' are relative terms: specificity is rarely absolute. The potential for reef corals to adapt or acclimatize to environmental change via symbiont community shifts may therefore be more phylogenetically widespread than has previously been assumed.     

Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms

Theory predicts the emergence of generalists in variable environments and antagonistic pleiotropy to favour specialists in constant environments, but empirical data seldom support such generalist–specialist trade‐offs. We selected for generalists and specialists in the dung fly Sepsis punctum (Diptera: Sepsidae) under conditions that we predicted would reveal antagonistic pleiotropy and multivariate trade‐offs underlying thermal reaction norms for juvenile development. We performed replicated laboratory evolution using four treatments: adaptation at a hot (31 °C) or a cold (15 °C) temperature, or under regimes fluctuating between these temperatures, either within or between generations. After 20 generations, we assessed parental effects and genetic responses of thermal reaction norms for three correlated life‐history traits: size at maturity, juvenile growth rate and juvenile survival. We find evidence for antagonistic pleiotropy for performance at hot and cold temperatures, and a temperature‐mediated trade‐off between juvenile survival and size at maturity, suggesting that trade‐offs associated with environmental tolerance can arise via intensified evolutionary compromises between genetically correlated traits. However, despite this antagonistic pleiotropy, we found no support for the evolution of increased thermal tolerance breadth at the expense of reduced maximal performance, suggesting low genetic variance in the generalist–specialist dimension.     

Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean

Although the SAR11 clade of the Alphaproteobacteria represents the most abundant and ubiquitous bacterioplankton in the ocean, very few laboratories have successfully cultured SAR11 cells. All of the SAR11 strains isolated thus far have been retrieved from the Oregon coast and the Sargasso Sea. In this study, a modified dilution-to-extinction culturing with prolonged incubation at low temperature was applied in an effort to cultivate major bacterioplankton lineages in the East Sea, Western Pacific Ocean. Five to 10 cells were inoculated into each well of 48-well plates, followed by the incubation of the plates at 10 °C for 4, 8, 20, and 24 weeks. Among a total of 35 isolated strains, 18 strains assigned to the SAR11 clade were isolated after 8, 20, and 24 weeks of incubation, whereas no SAR11 cells were detected in the samples after 4 weeks of incubation. The SAR11 isolates, noticeably, comprised 64–82% of the total isolates from the plates incubated for 20 and 24 weeks. Extinction cultures belonging to the Roseobacter , OM43, and SAR92 clades were also cultivated. The results of this study suggest that long-term incubation at low temperatures might prove an alternative for the efficient cultivation of new variants of the members of the SAR11 clade.     

Thermal properties of polysaccharides at low moisture: 1—An endothermic melting process and water-carbohydrate interactions

The thermal properties of a broad range of polysaccharides containing 5–25% w/w water have been studied by differential scanning calorimetry and dynamic mechanical thermal analysis (DMTA). Following room temperature conditioning, an endothermic event accompanied by material softening is observed at 45–80°C for all samples except those above their glass transition temperature. The temperature of the event is determined by thermal history and is apparently independent of polymer type or moisture content. The associated enthalpy increases with water content. Variable frequency DMTA analysis suggests a structural melting event rather than a relaxation process. The endothermic event is recovered over the days timescale after heating, and can be annealed to higher temperatures with increasing holding temperature.

Results are interpreted in terms of a dynamic hydration model in which specific energetic water-carbohydrate interactions occur but with a lifetime defined by their local effective microviscosity. The observation of the endotherm below glass transition temperatures suggests that in aqueous polysaccharide glasses, enthalpic structures involving the solvent can be made and broken.     

Thermal ecology and physiology of an elongate and semi-fossorial arthropod,the bark centipede

Organismal performance is strongly linked to temperature because of the fundamental thermal dependence of chemical reaction rates. However, the relationship between the environment and body temperature can be altered by morphology and ecology. In particular, body size and body shape can impact thermal inertia, as high surface area to volume ratios will possess low thermal mass. Habitat type can also influence thermal physiology by altering the opportunity for thermoregulation. We studied the thermal ecology and physiology of an elongate invertebrate, the bark centipede (Scolopocryptops sexspinosus). We characterized field body temperature and environmental temperature distributions, measured thermal tolerance limits, and constructed thermal performance curves for a population in southern Georgia. We found evidence that bark centipedes behaviorally thermoregulate, despite living in sheltered microhabitats, and that performance was maintained over a broad range of temperatures (over 20 °C). However, both the thermal optimum for performance and upper thermal tolerance were much higher than mean body temperature in the field. Together, these results suggest that centipedes can thermoregulate and maintain performance over a broad range of temperatures but are sensitive to extreme temperatures. More broadly, our results suggest that wide performance breadth could be an adaptation to thermal heterogeneity in space and time for a species with low thermal inertia.     

Decreased thermal niche breadth as a trade-off of antibiotic resistance

Evolutionary theory predicts that adaptations, including antibiotic resistance, should come with associated fitness costs; yet, many resistance mutations seemingly contradict this prediction by inducing no growth rate deficit. However, most growth assays comparing sensitive and resistant strains have been performed under a narrow range of environmental conditions, which do not reflect the variety of contexts that a pathogenic bacterium might encounter when causing infection. We hypothesized that reduced niche breadth, defined as diminished growth across a diversity of environments, can be a cost of antibiotic resistance. Specifically, we test whether chloramphenicol-resistant Escherichia coli incur disproportionate growth deficits in novel thermal conditions. Here we show that chloramphenicol-resistant bacteria have greater fitness costs at novel temperatures than their antibiotic-sensitive ancestors. In several cases, we observed no resistance cost in growth rate at the historic temperature but saw diminished growth at warmer and colder temperatures. These results were consistent across various genetic mechanisms of resistance. Thus, we propose that decreased thermal niche breadth is an under-documented fitness cost of antibiotic resistance. Furthermore, these results demonstrate that the cost of antibiotic resistance shifts rapidly as the environment changes; these context-dependent resistance costs should select for the rapid gain and loss of resistance as an evolutionary strategy.Subject terms: Bacterial evolution, Microbial ecology, Antibiotics     

Clade age and species richness are decoupled across the eukaryotic tree of life

Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.     

Bats, clocks, and rocks: diversification patterns in Chiroptera

Identifying nonrandom clade diversification is a critical first step toward understanding the evolutionary processes underlying any radiation and how best to preserve future phylogenetic diversity. However, differences in diversification rates have not been quantitatively assessed for the majority of groups because of the lack of necessary analytical tools (e.g., complete species-level phylogenies, estimates of divergence times, and robust statistics which incorporate phylogenetic uncertainty and test appropriate null models of clade growth). Here, for the first time, we investigate diversification rate heterogeneity in one of the largest groups studied thus far, the bats (Mammalia: Chiroptera). We use a recent, robust statistical approach (whole-tree likelihood-based relative rate tests) on complete dated species-level supertree phylogenies. As has been demonstrated previously for most other groups, among-lineage diversification rate within bats has not been constant. However, we show that bat diversification is more heterogeneous than in other mammalian clades thus far studied. The whole-tree likelihood-based relative rates tests suggest that clades within the families Phyllostomidae and Molossidae underwent a number of significant changes in relative diversification rate. There is also some evidence for rate shifts within Pteropodidae, Emballonuridae, Rhinolophidae, Hipposideridae, and Vespertilionidae, but the significance of these shifts depends on polytomy resolution within each family. Diversification rate in bats has also not been constant, with the largest diversification rate shifts occurring 30-50 million years ago, a time overlapping with the greatest number of shifts in flowering plant diversification rates.     

Geographical divergence in the Japanese land snail Euhadra herklotsi inferred from its molecular phylogeny and genital characters

We studied genetic variation within the Japanese land snail Euhadra herklotsi, which occurs on Kyushu and the surrounding islands, using partial sequences of the mitochondrial COI gene and nuclear ITS2 genes. The phylogenetic analysis revealed the existence of two major clades: clade N in the north and clade S in the south. These clades were parapatric and overlapped in southern Kyushu. Genetic divergence was high in clade N, whereas it was much lower in clade S. In addition, isolation-by-distance within each clade was implied. Since no current geographical barriers separate these clades, the genetic structure of clade S might have been influenced by historical events, such as volcanic activity, and a resulting population bottleneck followed by range expansion. The genital characteristics of clade-S snails were distinct from those of clade-N snails, and snails in both clades were sympatric at one locality. The shells of clade-N snails were generally larger than those of clade-S snails, but the shell-size variation within each clade could not be explained simply by environmental variables. Our study suggests that E. herklotsi likely consists of two sibling species. The taxonomic status of the previously proposed subspecies of E. herklotsi and related species requires reassessment.     

Phylogeny,niche conservatism and the latitudinal diversity gradient in mammals

Biologists have long searched for mechanisms responsible for the increase in species richness with decreasing latitude. The strong correlation between species richness and climate is frequently interpreted as reflecting a causal link via processes linked to energy or evolutionary rates. Here, we investigate how the aggregation of clades, as dictated by phylogeny, can give rise to significant climate–richness gradients without gradients in diversification or environmental carrying capacity. The relationship between climate and species richness varies considerably between clades, regions and time periods in a global-scale phylogenetically informed analysis of all terrestrial mammal species. Many young clades show negative richness–temperature slopes (more species at cooler temperatures), with the ages of these clades coinciding with the expansion of temperate climate zones in the late Eocene. In carnivores, we find steeply positive richness–temperature slopes in clades with restricted distributions and tropical origins (e.g. cat clade), whereas widespread, temperate clades exhibit shallow, negative slopes (e.g. dog–bear clade). We show that the slope of the global climate–richness gradient in mammals is driven by aggregating Chiroptera (bats) with their Eutherian sister group. Our findings indicate that the evolutionary history should be accounted for as part of any search for causal links between environment and species richness.     

Biotic interactions and macroevolution: extensions and mismatches across scales and levels

Clade dynamics in the fossil record broadly fit expectations from the operation of competition, predation, and mutualism, but data from both modern and ancient systems suggest mismatches across scales and levels. Indirect effects, as when antagonistic or mutualistic interactions restrict geographic range and thereby elevate extinction risk, are probably widespread and may flow in both directions, as when species- or organismic-level factors increase extinction risk or speciation probabilities. Apparent contradictions across scales and levels have been neglected, including (1) the individualistic geographic shifts of species on centennial and millennial timescales versus evidence for fine-tuned coevolutionary relationships; (2) the extensive and dynamic networks of interactions faced by most species versus the evolution of costly enemy-specific defenses and finely attuned mutualisms; and (3) the macroevolutionary lags often seen between the origin and the diversification of a clade or an evolutionary novelty versus the rapid microevolution of advantageous phenotypes and the invasibility of most communities. Resolution of these and other cross-level tensions presumably hinges on how organismic interactions impinge on genetic population structures, geographic ranges, and the persistence of incipient species, but generalizations are not yet possible. Paleontological and neontological data are both incomplete and so the most powerful response to these problems will require novel integrative approaches. Promising research areas include more realistic approaches to modeling and empirical analysis of large-scale diversity dynamics of ostensibly competing clades; spatial and phylogenetic dissections of clades involved in escalatory dynamics (where prey respond evolutionarily to a broad and shifting array of enemies); analyses of the short- versus long-term consequences of mutualistic symbioses; and fuller use of abundant natural experiments on the evolutionary impacts of ecosystem engineers.     

Geographic variation and acclimation effects on thermoregulation behavior in the widespread lizard Liolaemus pictus

Populations at the warm range margins of the species distribution may be at the greatest risks of extinction from global warming unless they can tolerate extreme environmental conditions. Yet, some studies suggest that the thermal behavior of some lizard species is evolutionarily rigid. During two successive years, we compared the thermal biology of two populations of Liolaemus pictus living at the northern (warmer) and one population living at the southern (colder) range limits, thus spanning an 800 km latitudinal distance. Populations at the two range margins belong to two deeply divergent evolutionary clades. We quantified field body temperatures (T_b), laboratory preferred body temperatures (PBT), and used operative temperature data (T_e) to calculate the effectiveness of thermoregulation (E). During one year in all populations, we further exposed half of the lizards to a cold or a hot acclimation treatment to test for plasticity in the thermal behavior. The environment at the southern range limit was characterized by cooler weather and lower T_e. Despite that, females had higher T_b and both males and females had higher PBT in the southernmost population (or clade) than in the northernmost populations. Acclimation to cold conditions led to higher PBT in all populations suggesting that plastic responses to thermal conditions, instead of evolutionary history, may contribute to geographic variation. Lizards regulated moderately well their body temperature (E≈0.7): they avoided warm microhabitats in the northern range but capitalized on warm microhabitats in the southern range. We review literature data to show that Liolaemus species increase their thermoregulation efficiency in thermally challenging environments. Altogether, this indicates that habitats of low thermal quality generally select against thermoconformity in these lizards.     

The dynamics of preferential host switching: Host phylogeny as a key predictor of parasite distribution*

Parasites often jump to and become established in a new host species. There is much evidence that the probability of such host shifts decreases with increasing phylogenetic distance between donor and recipient hosts, but the consequences of such preferential host switching remain little explored. We develop a computational model to investigate the dynamics of parasite host shifts in the presence of this phylogenetic distance effect. In this model, a clade of parasites evolves on an evolving clade of host species where parasites can cospeciate with their hosts, switch to new hosts, speciate within hosts or become extinct. Our model predicts that host phylogenies are major determinants of parasite distributions across trees. In particular, we predict that trees consisting of few large clades of host species and those with fast species turnover should harbor more parasites than trees with many small clades and those that diversify more slowly. Within trees, large clades are predicted to exhibit a higher fraction of infected species than small clades. We discuss our results in the light of recent cophylogenetic studies in a wide range of host–parasite systems.     

Ecological Genomics of Marine Picocyanobacteria

Summary: Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.     

Oak-insect herbivore interactions along a temperature and precipitation gradient

The interactions between herbivorous insects and their host plants are expected to be influenced by changing climates. Modern oaks provide an excellent system to examine this assumption because their interactions with herbivores occur over broad climatic and spatial scales, they vary in their defensive and nutritional investment in leaves by being deciduous or evergreen, and their insect herbivores range from generalists to highly specialized feeders. In this study, we surveyed leaf-litter samples of four oak species along an elevation gradient, from coastal northern California, USA, to the upper montane woodlands of the Sierra Nevada, to examine the relationship between climatic factors (mean annual temperature and precipitation) and oak herbivory levels at multiple scales; across all oak species pooled, between evergreen and deciduous species and within species.Overall, temperature and precipitation did not appear to have a significant effect on most measures of total herbivore damage (percent leaves damaged per tree, percent leaf area removed and average number of feeding damage marks per leaf) and the strongest predictor of herbivore damage overall was the identity of the host species. However, increases in precipitation were correlated with an increase in the actual leaf area removed, and specialized insects, such as those that make leaf mines and galls, were the most sensitive to differences in precipitation levels. This suggests that the effects of changing climate on some plant–insect interactions is less likely to result in broad scale increases in damage with increasing temperatures or changing precipitation levels, but is rather more likely to be dependent on the type of herbivore (specialist vs. generalist) and the scale (species vs. community) over which the effect is examined.     

Spatial extinction or persistence: landscape‐temperature interactions perturb predator–prey dynamics

Recognising that species interact across a range of spatial scales, we explore how landscape structure interacts with temperature to influence persistence. Specifically, we recognise that few studies indicate thermal shifts as the proximal cause of species extinctions; rather, species interactions exacerbated by temperature result in extinctions. Using microcosm‐based experiments, as models of larger landscape processes, we test hypotheses that would be problematic to address through field work. A text‐book predator–prey system (the ciliates Didinium and Paramecium) was used to compare three landscapes: an unfragmented landscape subjected to uniform temperatures (10, 20, 30°C); a fragmented landscape (potentially hosting metapopulations) subjected to these three temperatures; and a fragmented landscape subjected to a spatial temperature gradient (～ 10 to 30°C) – despite the prevalence of natural temperature ecoclines this is the first time such an analysis has been conducted. Initial thermal response‐analysis (growth, mortality, and movement measured between 10 and 30°C) suggested that as temperature increased, the predator might drive the prey to extinction. Thermal preferences (measured at 5 temperatures between 10 and 30°C), indicated that both predator and prey preferred warmer temperatures, with the predator exhibiting the stronger preference, suggesting that cooler regions might act as a prey‐refuge. The landscape level observations, however, did not entirely support the predictions. First, in the unfragmented landscape, increased temperature led to extinctions, but at the highest temperature (where the predator growth can be reduced) the prey survived. Second, at high temperatures the fragmented landscape failed to host metapopulations that would allow predator–prey persistence. Third, the thermal ecocline did not provide heterogeneity that improved stability; rather it forced both species to occupy a smaller realized space, leading toward extinctions. These findings reveal that temperature‐impacted rates and temperature preferences combine to drive predator–prey dynamics and persistence across landscapes.     

A glimpse on the pattern of rodent diversication: a phylogenetic approach

ABSTRACT: BACKGROUND: Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the eld of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversication patterns of organisms, no synthesis has addressed the case of the most diversied mammalian clade: the Rodentia. RESULTS: Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56 % and 81 % of the known specic and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversication rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identied a number of shifts in diversication rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversication factors that might have shaped the rodents radiation. CONCLUSIONS: The present glimpse on the diversication pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversication rates than any other 1rodent group. Different topological signatures suggest distinct diversication processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversication rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversication signal for most of the Paleogene nodes.