Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene

The accretion of the Indian subcontinent to Eurasia triggered a massive faunal and floral exchange, with Gondwanan taxa entering into Asia and vice versa. The traditional view on the Indian–Asian collision assumes contact of the continental plates during the Early Eocene. Many biogeographic studies rely on this assumption. However, the exact mode and timing of this geological event is still under debate. Here we address, based on an extensive phylogenetic analysis of rhacophorid tree frogs, if there was already a Paleogene biogeographic link between Southeast Asia and India; in which direction faunal exchange occurred between India and Eurasia within the Rhacophoridae; and if the timing of the faunal exchange correlates with one of the recently suggested geological models. Rhacophorid tree frogs showed an early dispersal from India to Asia between 46 and 57 Ma, as reconstructed from the fossil record. During the Middle Eocene, however, faunal exchange ceased, followed by increase of rhacophorid dispersal events between Asia and the Indian subcontinent during the Oligocene that continued until the Middle Miocene. This corroborates recent geological models that argue for a much later final collision between the continental plates. We predict that the Oligocene faunal exchange between the Indian subcontinent and Asia, as shown here for rhacophorid frogs, also applies for other nonvolant organisms with an Indian–Asian distribution, and suggest that previous studies that deal with this faunal interchange should be carefully reinvestigated.     

Fossil slabs attached to unsubducted fragments of the Farallon plate

As the Pacific–Farallon spreading center approached North America, the Farallon plate fragmented into a number of small plates. Some of the microplate fragments ceased subducting before the spreading center reached the trench. Most tectonic models have assumed that the subducting oceanic slab detached from these microplates close to the trench, but recent seismic tomography studies have revealed a high-velocity anomaly beneath Baja California that appears to be a fossil slab still attached to the Guadalupe and Magdalena microplates. Here, using surface wave tomography, we establish the lateral extent of this fossil slab and show that it is correlated with the distribution of high-Mg andesites thought to derive from partial melting of the subducted oceanic crust. We also reinterpret the high seismic velocity anomaly beneath the southern central valley of California as another fossil slab extending to a depth of 200 km or more that is attached to the former Monterey microplate. The existence of these fossil slabs may force a reexamination of models of the tectonic evolution of western North America over the last 30 My.     

Molecular phenotyping of human endometrium distinguishes menstrual cycle phases and underlying biological processes in normo-ovulatory women

Histological evaluation of endometrium has been the gold standard for clinical diagnosis and management of women with endometrial disorders. However, several recent studies have questioned the accuracy and utility of such evaluation, mainly because of significant intra- and interobserver variations in histological interpretation. To examine the possibility that biochemical or molecular signatures of endometrium may prove to be more useful, we have investigated whole-genome molecular phenotyping (54,600 genes and expressed sequence tags) of this tissue sampled across the cycle in 28 normo-ovulatory women, using high-density oligonucleotide microarrays. Unsupervised principal component analysis of all samples revealed that samples self-cluster into four groups consistent with histological phenotypes of proliferative (PE), early-secretory (ESE), mid-secretory (MSE), and late-secretory (LSE) endometrium. Independent hierarchical clustering analysis revealed equivalent results, with two major dendrogram branches corresponding to PE/ESE and MSE/LSE and sub-branching into the four respective phases with heterogeneity among samples within each sub-branch. K-means clustering of genes revealed four major patterns of gene expression (high in PE, high in ESE, high in MSE, and high in LSE), and gene ontology analysis of these clusters demonstrated cycle-phase-specific biological processes and molecular functions. Six samples with ambiguous histology were identically assignable to a cycle phase by both principal component analysis and hierarchical clustering. Additionally, pairwise comparisons of relative gene expression across the cycle revealed genes/families that clearly distinguish the transitions of PE-->ESE, ESE-->MSE, and MSE-->LSE, including receptomes and signaling pathways. Select genes were validated by quantitative RT-PCR. Overall, the results demonstrate that endometrial samples obtained by two different sampling techniques (biopsy and curetting hysterectomy specimens) from subjects who are as normal as possible in a human study and including those with unknown histology, can be classified by their molecular signatures and correspond to known phases of the menstrual cycle with identical results using two independent analytical methods. Also, the results enable global identification of biological processes and molecular mechanisms that occur dynamically in the endometrium in the changing steroid hormone milieu across the menstrual cycle in normo-ovulatory women. The results underscore the potential of gene expression profiling for developing molecular diagnostics of endometrial normalcy and abnormalities and identifying molecular targets for therapeutic purposes in endometrial disorders.     

Preferences for nutrients and sensory food qualities identify biological sources of economic values in monkeys

Value is a foundational concept in reinforcement learning and economic choice theory. In these frameworks, individuals choose by assigning values to objects and learn by updating values with experience. These theories have been instrumental for revealing influences of probability, risk, and delay on choices. However, they do not explain how values are shaped by intrinsic properties of the choice objects themselves. Here, we investigated how economic value derives from the biologically critical components of foods: their nutrients and sensory qualities. When monkeys chose nutrient-defined liquids, they consistently preferred fat and sugar to low-nutrient alternatives. Rather than maximizing energy indiscriminately, they seemed to assign subjective values to specific nutrients, flexibly trading them against offered reward amounts. Nutrient–value functions accurately modeled these preferences, predicted choices across contexts, and accounted for individual differences. The monkeys’ preferences shifted their daily nutrient balance away from dietary reference points, contrary to ecological foraging models but resembling human suboptimal eating in free-choice situations. To identify the sensory basis of nutrient values, we developed engineering tools that measured food textures on biological surfaces, mimicking oral conditions. Subjective valuations of two key texture parameters—viscosity and sliding friction—explained the monkeys’ fat preferences, suggesting a texture-sensing mechanism for nutrient values. Extended reinforcement learning and choice models identified candidate neuronal mechanisms for nutrient-sensitive decision-making. These findings indicate that nutrients and food textures constitute critical reward components that shape economic values. Our nutrient-choice paradigm represents a promising tool for studying food–reward mechanisms in primates to better understand human-like eating behavior and obesity.

The concept of “value” plays a fundamental role in behavioral theories that formalize learning and decision-making. Economic choice theory examines whether individuals behave as if they assigned subjective values to goods, which are inferred from observable choices (1, 2). In reinforcement learning, values integrate past reward experiences to guide future behavior (3, 4). Although these theories have been critical for revealing how choices depend on factors such as probability, risk, and delay (2, 4, 5), they do not explain how values and preferences are shaped by particular properties of the choice objects themselves. Why do we like chocolate, and why do some individuals like chocolate more than others? In classical economics, one famously does not argue about tastes (6). By contrast, biology conceptualizes choice objects as rewards with well-defined components that benefit survival and reproductive success and endow rewards with value (4). Here we followed this approach to investigate how the biologically critical, intrinsic properties of foods—their nutrients and sensory qualities—influence values inferred from behavioral choices and help explain individual differences in preference.The reward value of food is commonly thought to derive from its nutrients and sensory properties: sugar and fat make foods attractive because of their sweet taste and rich mouthfeel. Sensory scientists and food engineers seek to uncover rules that link food composition to palatability (7–10). Similarly, ecological foraging theory links animals’ food choices to nutritional quality (11). By contrast, in behavioral and neuroscience experiments, food components are often only manipulated to elicit choice variation but rarely studied in their own right. Here, we aimed to empirically ground the value concept in the constitutive properties of food rewards. We combined a focus on specific nutrients and food qualities with well-controlled repeated-choice paradigms from behavioral neurophysiology and studied the choices of rhesus monkeys (Macaca mulatta) for nutrient-defined liquid rewards.Like humans, macaques are experts in scrutinizing rewards for sophisticated, value-guided decision-making (4, 12–15). This behavioral complexity, the closeness of the macaque brain’s sensory and reward systems to those of humans (16), and the suitability for single-neuron recordings make macaques an important model for studying food–reward mechanisms with relevance to human eating behavior and obesity (17).Previous studies in macaques uncovered key reward functions and their neuronal implementations, including the assignment of values to choice options (13, 18–25), reinforcement learning (4, 26) and reward-dependence on satiety and thirst (7, 27, 28). Despite these advances, behavioral principles for nutrient rewards in macaques remain largely uncharacterized. The typical diet of these primates includes a broad variety of foods and nutrient compositions (29, 30). Their natural feeding conditions require adaptation to both short-term and seasonal changes in nutrient availability and ecologically diverse habitats (31, 32). Thus, the macaque reward system should be specialized for flexible, nutrient-directed food choices. Accordingly, we manipulated the fat and sugar content of liquid food rewards to study their effects on macaques’ choices. We addressed several aims.First, we tested whether macaques’ choices were sensitive to the nutrient composition of rewards, consistent with the assignment of subjective values. In previous studies, macaques showed subjective trade-offs between flavored liquid rewards (12, 13). We hypothesized that nutrients and nutrient-correlated sensory qualities constitute the intrinsic food properties that shape such preferences. We focused on macronutrients (carbohydrates, fats, and proteins), specifically sugar and fat, because of their relevance for human overeating and obesity, and their role in determining sensory food qualities. As nutrients are critical for survival and well-being, nonsated macaques should prefer foods high in nutrient content. In addition, like humans, they may individually prefer specific nutrients and sensory qualities (e.g., valuing isocaloric sweet taste over fat-like texture). Because nutrients are basic building blocks of foods, establishing an animal’s “nutrient–value function” could enable food choice predictions across contexts.Second, to identify a physical, sensory basis for nutrient preferences, we developed engineering tools to measure nutrient-dependent food textures on biological surfaces that mimicked oral conditions. Although sugar is directly sensed by taste receptors (33), the mechanism for oral fat-sensing remains unclear. While the existence of a “fat taste” in primates is debated (34), substantial evidence points to a somatosensory, oral–texture mechanism (7, 9). Fat-like textures reliably elicit fatty, creamy mouthfeel (8) and activate neural sensory and reward systems in macaques (35) and humans (36, 37). Two distinct texture parameters are implicated in fat-sensing: viscosity and sliding friction, reflecting a food’s thickness and lubricating properties, respectively (38–40). We hypothesized that these parameters mediate the influence of fat content on choices.Third, we compared the monkeys’ choices to ecologically relevant dietary reference points. In optimal foraging theory (41), animals maximize energy as a common currency for choices (“energy maximization”). Alternatively, animals may balance the intake of different nutrients (“nutrient balancing”) (42–44) or choose food based on the reward value of specific sensory and nutrient components (“nutrient reward”) (7, 45). We evaluated these strategies in a repeated-choice paradigm suited for neurophysiological recordings and derived hypotheses about the neuronal mechanisms for nutrient-sensitive decision-making (e.g., “energy-tracking neurons” versus “nutrient–value neurons”—Discussion).Finally, based on our behavioral data, we explored in computational simulations how theories of reinforcement learning and economic choice can be extended by a nutrient–value function. Together with recently proposed homeostatic reinforcement learning (46), nutrient-specific model parameters may optimize predictions when choices depend on nutrient composition and homeostatic set-points.     

A CO2 greenhouse efficiently warmed the early Earth and decreased seawater 18O/16O before the onset of plate tectonics

The low ¹⁸O/¹⁶O stable isotope ratios (δ¹⁸O) of ancient chemical sediments imply ∼70 °C Archean oceans if the oxygen isotopic composition of seawater (sw) was similar to modern values. Models suggesting lower δ¹⁸O_sw of Archean seawater due to intense continental weathering and/or low degrees of hydrothermal alteration are inconsistent with the triple oxygen isotope composition (Δ’¹⁷O) of Precambrian cherts. We show that high CO₂ sequestration fluxes into the oceanic crust, associated with extensive silicification, lowered the δ¹⁸O_sw of seawater on the early Earth without affecting the Δ’¹⁷O. Hence, the controversial long-term trend of increasing δ¹⁸O in chemical sediments over Earth’s history partly reflects increasing δ¹⁸O_sw due to decreasing atmospheric pCO₂. We suggest that δ¹⁸O_sw increased from about −5‰ at 3.2 Ga to a new steady-state value close to −2‰ at 2.6 Ga, coinciding with a profound drop in pCO₂ that has been suggested for this time interval. Using the moderately low δ¹⁸O_sw values, a warm but not hot climate can be inferred from the δ¹⁸O of the most pristine chemical sediments. Our results are most consistent with a model in which the “faint young Sun” was efficiently counterbalanced by a high-pCO₂ greenhouse atmosphere before 3 Ga.

The amount of carbon that degassed from a solidifying magma ocean on the infant Earth 4.5 Ga ago was probably similar to the amount of CO₂ that is now present in the atmosphere of Venus (pCO₂ ∼90 bar) (1). Subsequently, dynamic carbon cycling between the early Earth’s atmosphere (atmospheric reservoir [R_A]), the ocean (R_O), and the oceanic crust (R_OC) reservoirs stabilized a primordial Earth–atmospheric pCO₂ to about 1.5 bar (2). Decreasing pCO₂ over the Earth’s history reflects the net transfer of large masses of carbon out of the atmosphere-ocean-oceanic crust (R_A+O+OC) system into the mantle and the emerging continental crust reservoir (R_CC), the latter providing a long-term sink for carbon in the form of inorganic carbon (carbonate rocks) and organic material (organic matter–rich shales, coal, oil, and gas) (1, 2).Early carbon-cycle models predicted high Archean pCO₂ to account for the faint young Sun paradox (2, 3), whereas direct pCO₂ estimates from the end of the Archean now imply much lower atmospheric pCO₂ [∼0.01 to 0.1 bar (4)]. However, a compilation of evidence from the sedimentary record implies much higher pCO₂ between 3.2 to 3.0 Ga compared to the 2.9 to 2.7 Ga interval (5). These authors state that even several bars pCO₂ are feasible between 3.2 to 3.0 Ga, which is not in conflict with much lower Neoarchean pCO₂ estimates (Fig. 1) or paleo-atmospheric pressure estimates at 2.7 Ga [<2 bar (6) and <0.5 bar (7)]. A fundamental drop in atmospheric CO₂ mixing ratio is also reflected in the observation that >3 Ga, Archean mafic crust (greenstones) is commonly characterized by very intense carbonatization and silicification that is unparalleled in their modern analogs (8–12). Such observations provide evidence for deep-time paleo-pCO₂ fluctuations with a drastic pCO₂ drop starting around 3 Ga ago (5, 13).Open in a separate windowFig. 1.Constraints on the R_A+O+OC size over time with implications for pCO₂. A illustrates the size of the R_A+O+OC carbon reservoir and its distribution between the oceanic crust (R_OC in gray), ocean water (R_O in dark blue), and the atmosphere (R_A in light blue). Transition of this carbon to the long-term R_CC and the mantle (green) decreases the size of the R_A+O+OC reservoir, which was still large at 3.2 Ga (see SI Appendix) and minimal at the onset of the global glaciations at 2.4 Ga. B shows two recent pH curves over Earth’s history to illustrate how the pH-dependent distribution of carbon between R_A and R_O may translate into pCO₂ at a given time. (C) The panel summarizes pCO₂ estimates [adopted from Catling and Zahnle (4)] and proposed pCO₂ evolution curves illustrated as dashed lines: a (2), b (18), and c (proposed here). Qualitative evidence to construct curve c comes from rare evidence for glaciers (44) and lower degrees of carbonatization of oceanic crust at 3.5 Ga compared to 3.2 Ga (13), suggesting a transient interval of somewhat low pCO₂ in the Paleoarchean. Low pCO₂ is indicated prior to the onset of cold climates later in the rock record. The black bar at 4.5 Ga is derived from carbon-flux arguments and the primordial carbon reservoir (1, 2). The black bar at 3.2 Ga applies the same carbon-flux arguments to translate the high carbonate content observed in the oceanic crust in Pilbara into tentative pCO₂ estimates (SI Appendix), which are most consistent with curve a (2).Today, carbonatization, which is the formation of carbonates during alteration of the oceanic crust, mainly occurs in relatively cool, off-axis hydrothermal systems over the first 20 Mya after crust formation at midocean ridges (14–16). Elevated degrees of carbonatization in oceanic crust from the Cretaceous and Jurassic are assigned to higher dissolved inorganic carbon at the time (14). Hence, higher pCO₂ (i.e., a larger R_A+O+OC) directly translates into higher degrees of carbonatization. While carbonate is mainly observed as vein fillings in the upper 300 m of oceanic crust today (14, 15), it extensively replaces glass and igneous minerals in Archean greenstones down to depths of 2 km below the ancient seafloor (8–10, 17). The amount of CO₂ fixed in 3.2-Ga-old oceanic crust from Pilbara, Australia is estimated at 1.2 × 10⁷ mol ⋅ m⁻² (±10%) (17)—a remarkable figure that is about two orders of magnitude more compared to today (SI Appendix). Much lower degrees of carbonatization in oceanic crust are already observed at 2.6 Ga, suggesting a drastic Mesoarchean drop in pCO₂ (13) (Fig. 1A).The qualitative evidence from the sediment record (5) and from the degree of carbonatization and silicification of oceanic crust (13) has not been included in proposed pCO₂ curves (4, 18) because the quantitative conversions into absolute pCO₂ require some assumptions (SI Appendix). Nevertheless, pCO₂ during the early Archean may have been as high as initially predicted by Kasting (2), followed by a pronounced Mesoarchean drop (13) to levels consistent with available paleo-pCO₂ estimates toward the Neoarchean (4) (stippled line “c” in Fig. 1C). Further decreasing pCO₂ toward modern levels partly reflects increasing ocean pH (Fig. 1) rather than a shrinking R_A+O+OC (SI Appendix). Hence, only small effects of carbonatization on the δ¹⁸O_sw value are expected for post-Archean seawater (16). Here, we focus on the very high carbonatization (8–10, 13) and silicification (11, 12) fluxes before the Mesoarchean pCO₂ drop, and we model the respective effects on ancient δ¹⁸O_sw.     

Long‐term evolution of hepatitis B virus genotype F: Strong association between viral diversification and the prehistoric settlement of Central and South America

The genotype F (HBV‐F) is an autochthonous Native American strain of the hepatitis B virus. In this study, we reconstruct the HBV‐F long‐term evolution under a hypothesis of co‐divergence with humans in Central and South America, since their entry into the region 14.5‐16 thousand years ago. The Bayesian phylogeographic reconstruction supported a virus‐host co‐expansion; however, two evolutionary scenarios would have been present. Whereas subgenotype F1 spreads along a Pacific coastal route and would have evolved associated with Central American and Andean cultures from the west of the continent, subgenotypes F2‐F6 spread along the Atlantic coastline and inner pathways associated with communities inhabiting the tropical forest lowlands. Then, we propose a model for HBV‐F evolution in which the selection of differential biological characteristics in these two main groups would be related to their evolution in host populations with different genetic backgrounds and dissimilar demographic conditions.     

微滴度板杂交试验在疟疾种属特异性诊断的应用

本实验应用113份指尖取血制作的滤纸片干血滴样品分离疟原虫DNA进行微滴度板杂交试验。结果表明：1．滤纸片干血滴一微滴度板杂交实验用血量少、经过自然干燥后，样品易于保存和运输，而且提取DNA的方法简便。2．此方法特异性高、敏感性强、其检测极限可达到1．5个原虫／μl血。3．此方法可在进行疟疾诊断的同时进行种属鉴定，并可对多种疟原虫同时感染进行诊断。     

Earth history events shaped the evolution of uneven biodiversity across tropical moist forests

Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.

Tropical and subtropical moist broadleaf forests, including evergreen tropical rain forests and wet seasonal forests (hereafter tropical moist forests), are the most species-rich terrestrial biome on the planet (1–3) and are most broadly distributed throughout the Amazon basin and Atlantic forest in the Neotropics, the Congo basin and Rift Mountains in the Afrotropics, and both mainland and archipelagic South and Southeast Asia in Indomalaya (4). While all three major tropical moist forest regions (hereafter Neotropics, Afrotropics, and Indomalaya) have an exceptionally high species diversity of plants and animals in comparison with other biomes, the total regional diversity (γ-diversity) and number of species that coexist locally (α-diversity) vary dramatically across continents (2). Specifically, moist forests in the Afrotropics typically harbor lower species diversity than the Neotropics and Indomalaya (5–9), leading the Afrotropics to be labeled as the “odd man out” (9). We refer to this phenomenon as pantropical diversity disparity (PDD). This pattern has been highlighted in several keystone taxa, such as palms (family Arecaceae), which—of roughly 2,500 species globally—have ∼1,200 species in Indomalaya and 800 species in the Neotropics but only 66 species in the Afrotropics (excluding Madagascar) (10, 11). Investigating the drivers of variation in species diversity in moist forests across continents could provide an alternative perspective for understanding the processes that have shaped extraordinary tropical diversity.Explanations for the PDD have been expressed in terms of both contemporary differences in carrying capacities between regions based on the distribution of key environmental variables (9, 12, 13) and historical differences in paleoenvironmental dynamics shaping the past distribution of tropical biomes (14–19) and patterns of diversification (20–22). Species diversity in tropical moist forests may be driven by contemporary climate conditions if energy and resource availability from high precipitation, temperature, and solar radiation facilitates a greater number of coexisting species (2, 23). These environmental features have been shown to explain significant variation in species diversity along a terrestrial latitudinal gradient (24), yet they also vary longitudinally between tropical regions (2) with, for example, the Afrotropics lacking analogous sites of aseasonal high precipitation found in the Neotropics and Indomalaya, which are among the most biodiverse in these regions (12). Tropical biomes in different regions also have had dramatically different paleoenvironmental histories, associated with distinct geological and climatic dynamics (2, 9, 14, 25), which may have driven variation in speciation, extinction, and dispersal rates between regions owing to dynamic patterns of fragmentation, connectivity, and habitat heterogeneity (25, 26). For example, previous paleoenvironmental reconstructions indicate that while moist forests in the Neotropics and Indomalaya have remained relatively constant in size since the Eocene, moist forests in the Afrotropics suffered a drastic reduction in area from the Miocene onward (14, 20), which is believed to have driven widespread extinction from range contractions (25, 27). Additionally, Afrotropical moist forests lay at the center of the African tectonic plate and therefore, lack the intersection of active orogeny at plate boundaries with terrestrial mesic equatorial habitat as seen in the Neotropical and Indomalayan regions, leading to the formation of the Andes in the Neotropics and the Himalayan and southwest Chinese mountain chains, as well as the Southeast Asian archipelago in Indomalaya (2, 15). Active orogeny has presented dynamic opportunities for ecological and allopatric speciation (19, 28, 29) and may explain the disparity in biodiversity among tropical regions.Drawing inferences about historical processes that have shaped the PDD has been challenging and restricted by the limited mechanistic understanding of ecological and evolutionary processes from correlative or comparative methods (30). Instead, by combining paleoenvironmental reconstructions with spatially explicit models of ecoevolutionary processes, simulation models offer a unique but largely underused resource (but see, for example, refs. 31–34) to directly explore the evolutionary mechanisms behind the origins of biodiversity patterns in silico (30, 34). In this study, we explored the origins of the PDD in three steps. First, we quantified the ubiquity of the PDD across a wide range of plant and animal taxa. We then tested whether contemporary climate conditions can explain variation in species diversity among continents using a correlative approach. Finally and most innovatively, we assessed the role of paleoenvironmental dynamics in driving pantropical biodiversity patterns using a spatially explicit simulation model of diversification coupled with a paleoenvironmental reconstruction of temperature, aridity, and plate tectonics over the past 110 Ma. Specifically, we explored how major changes in the paleoclimate and plate tectonics have shaped speciation and extinction rates throughout the Mesozoic and Cenozoic and the spatial distribution of phylogenetic diversity. We asked the following questions. 1) Are present-day climatic differences between continents sufficient to explain differences in species diversity? 2) Could deep-time environmental dynamics have driven the emergence of present-day diversity differences between regions? 3) How has spatial and temporal variation in speciation and extinction rates shaped spatial diversity patterns, and how have mountain building, island formation, global cooling, and aridification influenced these rates? 4) What is the deep-time signature of diversification and dispersal in spatial patterns of phylogenetic diversity?     

Reverse engineering dynamic temporal models of biological processes and their relationships

Biological processes such as circadian rhythms, cell division, metabolism, and development occur as ordered sequences of events. The synchronization of these coordinated events is essential for proper cell function, and hence the determination of critical time points in biological processes is an important component of all biological investigations. In particular, such critical time points establish logical ordering constraints on subprocesses, impose prerequisites on temporal regulation and spatial compartmentalization, and situate dynamic reorganization of functional elements in preparation for subsequent stages. Thus, building temporal phenomenological representations of biological processes from genome-wide datasets is relevant in formulating biological hypotheses on: how processes are mechanistically regulated; how the regulations vary on an evolutionary scale, and how their inadvertent disregulation leads to a diseased state or fatality. This paper presents a general framework (GOALIE) to reconstruct temporal models of cellular processes from time-course gene expression data. We mathematically formulate the problem as one of optimally segmenting datasets into a succession of “informative” windows such that time points within a window expose concerted clusters of gene action whereas time points straddling window boundaries constitute points of significant restructuring. We illustrate here how GOALIE successfully brings out the interplay between multiple yeast processes, inferred from combined experimental datasets for the cell cycle and the metabolic cycle.     

Peroxiredoxin Ⅱ基因在Hep3B细胞中的生物学功能和作用机制

目的 探讨peroxiredoxin Ⅱ (Prx Ⅱ)基因在肝癌发生发展中的作用及其机制.方法 化学合成两对针对Prx Ⅱ基因的小干扰RNA,即Prx Ⅱ-1和Prx Ⅱ-2,分别用脂质体LipofectamineTM 2000介导转入人肝癌细胞系Hep3B.通过实时荧光定量PCR和Western blot检测确定Prx Ⅱ在转染细胞中mRNA和蛋白表达水平受到明显抑制后,对Prx Ⅱ基因沉默的Hep3B细胞分别进行细胞生长、细胞凋亡、细胞集落形成等检测,观察Prx Ⅱ对Hep3B细胞生物学功能的影响;通过二氯荧光素双乙酸和硫代巴比妥酸试验,检测细胞内过氧化代谢产物活性氧类和丙二醛的水平,探讨Prx Ⅱ的作用机制.结果 与阴性对照组和空白对照组相比,Prx Ⅱ基因沉默的Hep3B细胞生长受到抑制,生长抑制率在转染96h后达40%以上;细胞凋亡增加;细胞形成集落的能力降低,Prx Ⅱ-1组和PrxⅡ-2组的细胞集落形成数分别为42.0±2.8和40.5±0.7,明显低于阴性对照组和空白对照组的121.5±2.1和130.0±1.4 (P<0.05).Prx Ⅱ基因沉默的Hep3B细胞内活性氧和丙二醛水平明显增加(P<0.05).结论 Prx Ⅱ具有促进Hep3B细胞生长的生物学功能,其机制可能与通过抗氧化作用形成有利于肿瘤细胞生长的微环境有关.     

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

We introduce a conceptual bridge between the previously unlinked fields of phylogenetics and mathematical spatial ecology, which enables the spatial parameters of an emerging epidemic to be directly estimated from sampled pathogen genome sequences. By using phylogenetic history to correct for spatial autocorrelation, we illustrate how a fundamental spatial variable, the diffusion coefficient, can be estimated using robust nonparametric statistics, and how heterogeneity in dispersal can be readily quantified. We apply this framework to the spread of the West Nile virus across North America, an important recent instance of spatial invasion by an emerging infectious disease. We demonstrate that the dispersal of West Nile virus is greater and far more variable than previously measured, such that its dissemination was critically determined by rare, long-range movements that are unlikely to be discerned during field observations. Our results indicate that, by ignoring this heterogeneity, previous models of the epidemic have substantially overestimated its basic reproductive number. More generally, our approach demonstrates that easily obtainable genetic data can be used to measure the spatial dynamics of natural populations that are otherwise difficult or costly to quantify.     

An international reference reagent for the detection of RHD and SRY DNA in plasma

Background and Objectives The determination of foetal RHD genotype using foetal DNA contained in the maternal circulation is increasingly used to manage pregnancies at risk of haemolytic disease of the foetus and newborn (HDFN) caused by maternal anti‐D. The test is becoming increasingly reliable, and routine clinical services have been established in some centres. However, laboratories currently have no reference materials with which to determine the performance of their tests. This report describes the production and evaluation of a freeze‐dried preparation of human plasma, code 07/222, containing RHD and SRY sequences which can be used as a minimum sensitivity reagent. Materials and Methods RhD‐positive male plasma was diluted in an excess of RhD‐negative female plasma, and 1 ml aliquots were freeze‐dried in glass ampoules. To characterise the material, 19 laboratories took part in an international collaborative study. The participants evaluated dilutions of the material using their in‐house routine assays and recorded the highest dilution where the genes could be detected. Results When diluted 1 in 2, most laboratories were able to detect the presence of RHD and SRY sequences in the material and the participants agreed that this was an appropriate level to set as the minimum sensitivity required. Conclusions In October 2010, the WHO Expert Committee on Biological Standardization approved the material 07/222 as an International Reference Reagent for the detection of RHD and SRY DNA in plasma.     

The molecular mechanisms underlying the regulation of the biological activity of corticotropin-releasing hormone receptors: implications for physiology and pathophysiology

The CRH receptor (CRH-R) is a member of the secretin family of G protein-coupled receptors. Wide expression of CRH-Rs in the central nervous system and periphery ensures that their cognate agonists, the family of CRH-like peptides, are capable of exerting a wide spectrum of actions that underpin their critical role in integrating the stress response and coordinating the activity of fundamental physiological functions, such as the regulation of the cardiovascular system, energy balance, and homeostasis. Two types of mammal CRH-R exist, CRH-R1 and CRH-R2, each with unique splicing patterns and remarkably distinct pharmacological properties, but similar signaling properties, probably reflecting their distinct and sometimes contrasting biological functions. The regulation of CRH-R expression and activity is not fully elucidated, and we only now begin to fully understand the impact on mammalian pathophysiology. The focus of this review is the current and evolving understanding of the molecular mechanisms controlling CRH-R biological activity and functional flexibility. This shows notable tissue-specific characteristics, highlighted by their ability to couple to distinct G proteins and activate tissue-specific signaling cascades. The type of activating agonist, receptor, and target cell appears to play a major role in determining the overall signaling and biological responses in health and disease.     

Tectonic-driven climate change and the diversification of angiosperms

In 1879, Charles Darwin characterized the sudden and unexplained rise of angiosperms during the Cretaceous as an “abominable mystery.” The diversification of this clade marked the beginning of a rapid transition among Mesozoic ecosystems and floras formerly dominated by ferns, conifers, and cycads. Although the role of environmental factors has been suggested [Coiffard C, Gómez B (2012) Geol Acta 10(2):181–188], Cretaceous global climate change has barely been considered as a contributor to angiosperm radiation, and focus was put on biotic factors to explain this transition. Here we use a fully coupled climate model driven by Mesozoic paleogeographic maps to quantify and discuss the impact of continental drift on angiosperm expansion and diversification. We show that the decrease of desertic belts between the Triassic and the Cretaceous and the subsequent onset of long-lasting humid conditions during the Late Cretaceous were driven by the breakup of Pangea and were contemporaneous with the first rise of angiosperm diversification. Positioning angiosperm-bearing fossil sites on our paleobioclimatic maps shows a strong match between the location of fossil-rich outcrops and temperate humid zones, indicating that climate change from arid to temperate dominance may have set the stage for the ecological expansion of flowering plants.Angiosperms have gradually dominated terrestrial environments after their appearance during the Early Cretaceous (1, 2). Their radiation was characterized by high and rapid diversification (3, 4), high rates of speciation throughout the Cretaceous (5), and unprecedented ecological dominance. Most hypotheses to explain angiosperm radiation invoke biotic (instrinsic) factors, such as pollinating insects (6), coevolution with herbivorous insects (7), morphological novelties (8), or ecophysiological innovations (9–11) as well as macroevolutionary patterns (1). However, recent studies have shown that extrinsic influences combined with biotic factors may drive species diversity at the multimillion-year time scale (6, 12), reviving the potential role of global climate change (13, 14) on angiosperm radiation. Such a combination is supported by fossil data, as illustrated by the latest studies based on the European megafossil plant record that provided a scenario in which angiosperm radiation was concomitant, in space and time, with the evolution of the physical environment (15).Although the Cretaceous climate is described as warm and equable, onset of such climatic conditions is gradual (16) and results from long-term processes that occurred throughout the Mesozoic. Climate simulations were conducted using a fully coupled ocean–atmosphere general circulation model (FOAM) for five continental configurations, from the Middle Triassic [225 million years ago (Ma)] to the Late Cretaceous (70 Ma). The coupling of the Lund–Potsdam–Jena dynamic global vegetation model (LPJ) within FOAM experiments helped to account for vegetation feedbacks on the climate system and to build the most accurate paleoclimatic maps for each of the five periods. Three atmospheric pCO₂ levels have been tested for each paleogeography (560 ppm, 1,120 ppm, and 2,240 ppm). This range covers the large uncertainties of pCO₂ estimates for these geological periods.To validate our paleoclimatic experiments, the geographical distribution of climate-sensitive sediments such as evaporites (dry or seasonally dry climate indicators) and coals (humid climate indicators) have been compared with our maps of simulated biomes for each time period (Fig. S1). Overall, for every time period, the spatial fit between coals and humid biomes is higher for 1,120-ppm and 2,240-ppm pCO2 scenarios than for 560 ppm (Table S1 and Fig. S1). Still, relative distribution of arid and humid zones does not show major changes between 1,120 and 2,240 ppm (Fig. S1), and coals cannot discriminate between these two scenarios. For the Carnian and Toarcian, we select the 1,120-ppm scenario, which is consistent with most studies that agree on a background pCO₂ of ca. 1,000 ppm for these periods. For the Cretaceous, comparisons of our simulations with oceanic latitudinal thermal gradients reconstructed from paleoceanographic data (17–25) show that pCO₂ of 2,240 ppm is required to produce sea surface temperatures comparable with data for the Aptian and Cenomanian, whereas for the Maastrichian, data-derived sea surface temperature gradient is better reproduced at 1,120 ppm (Fig. S2). Based on these comparisons, the best-fit model–data scenario corresponds to the simulations at 1,120 ppm, except for the Aptian and Cenomanian simulations, for which CO₂ concentrations of 2,240 ppm are used.     

An extinct monkey from Haiti and the origins of the Greater Antillean primates

A new extinct Late Quaternary platyrrhine from Haiti, Insulacebus toussaintiana, is described here from the most complete Caribbean subfossil primate dentition yet recorded, demonstrating the likely coexistence of two primate species on Hispaniola. Like other Caribbean platyrrhines, I. toussaintiana exhibits primitive features resembling early Middle Miocene Patagonian fossils, reflecting an early derivation before the Amazonian community of modern New World anthropoids was configured. This, in combination with the young age of the fossils, provides a unique opportunity to examine a different parallel radiation of platyrrhines that survived into modern times, but is only distantly related to extant mainland forms. Their ecological novelty is indicated by their unique dental proportions, and by their relatively large estimated body weights, possibly an island effect, which places the group in a size class not exploited by mainland South American monkeys. Several features tie the new species to the extinct Jamaican monkey Xenothrix mcgregori, perhaps providing additional evidence for an inter-Antillean clade.     

New Insights on the Zika Virus Arrival in the Americas and Spatiotemporal Reconstruction of the Epidemic Dynamics in Brazil

Zika virus (ZIKV) became a worldwide public health emergency after its introduction in the Americas. Brazil was implicated as central in the ZIKV dispersion, however, a better understanding of the pathways the virus took to arrive in Brazil and the dispersion within the country is needed. An updated genome dataset was assembled with publicly available data. Bayesian phylogeography methods were applied to reconstruct the spatiotemporal history of ZIKV in the Americas and with more detail inside Brazil. Our analyses reconstructed the Brazilian state of Pernambuco as the likely point of introduction of ZIKV in Brazil, possibly during the 2013 Confederations Cup. Pernambuco played an important role in spreading the virus to other Brazilian states. Our results also underscore the long cryptic circulation of ZIKV in all analyzed locations in Brazil. Conclusions: This study brings new insights about the early moments of ZIKV in the Americas, especially regarding the Brazil-Haiti cluster at the base of the American clade and describing for the first time migration patterns within Brazil.     

Global dispersion and local diversification of the methane seep microbiome

Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate–methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.A microbiome is defined as the microbial community and its genomic diversity associated with a particular ecosystem or habitat, such as soil (1) or the human gut (2). A key question in the study of microbiomes concerns the identification of assembly rules that govern microbial community structure and community function (3). Sampling efforts on local to global scales have been used to determine the key drivers of microbial assembly, which include processes such as dispersal, ecological drift, environmental selection, and diversification (3, 4). Major processes shaping the microbial diversity landscape involve environmental selection of organisms according to their traits, niche preferences, biological interactions, and coevolution with hosts (5, 6). In turn, recent findings suggest that fluctuations of key microbial taxa reflect the dynamics of important biogeochemical processes (7).Insights into environmental microbiomes have tremendously improved with the use of next-generation sequencing methods and global databases, which have advanced microbial ecology from the identification of rare members of microbial communities (8) to global microbial distribution patterns (9, 10). Benthic (seafloor-hosted) microbial communities of the ocean are very distinct from pelagic (seawater-hosted) communities (9) and are impacted by water depth (11, 12), sediment depth (13, 14), and by energy availability in the form of deposited organic matter (12, 15, 16). Marine sediments are known to host communities as diverse as those found in soils, with pronounced community turnover on small (decimeter to kilometer), intermediate (hundreds of kilometers), and large (thousands of kilometers) spatial scales (17, 18).Cold seeps are distinct seafloor ecosystems that are defined by the upward advection of methane and other hydrocarbons from the subsurface seabed to the seafloor (19). Gas-emitting methane seeps are found scattered on continental margins worldwide and are separated by large expanses of energy-limited, aerobic deep-sea seafloor where the benthic communities depend on sparse detritus flux. These seeps can be regarded as patches of a certain habitat type, offering niches that differ strongly from the surrounding seafloor (14, 20, 21). Typically, methane seep sediments are highly reduced, and oxygen availability is limited to a few millimeters to centimeters of the sediment surface. Below that thin oxic zone, methane is consumed by microbial consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) mediating the anaerobic oxidation of methane (AOM) coupled to sulfate reduction (22). This microbial conversion of inorganic energy sources fuels communities of microorganisms and marine invertebrates and thus generates hotspots of biomass and diversity in the deep sea (23). Together, micro- and macroorganisms at methane seeps and sulfate methane transition zones (SMTZ) consume 75% of the methane (0.06 Gt of carbon per year) that reaches the surface seafloor from subsurface zones (19). Hence, they provide a globally relevant ecosystem function by controlling the emission of the potential greenhouse gas methane from the ocean.At large scales, however, it is unclear which seep microorganisms are important for the removal of methane and which mechanisms govern their community assembly. Defining the methane seep microbiome is needed to identify the microbial key players responsible for these important biogeochemical functions. In this study, we compared the archaeal and bacterial diversity of 23 globally distributed methane seeps to that of 54 globally distributed sites from other seafloor ecosystems, including deep SMTZ, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We tested (i) whether methane seeps are island-like habitats that are similar to each other but distinct from their surroundings concerning community richness, evenness, similarity, and composition; (ii) if a core set of associated bacteria and archaea dominates seeps globally; and (iii) whether their assembly patterns follow the metacommunity concept of globally dispersed and locally diversified types (24).