Unique functional diversity during early Cenozoic mammal radiation of North America.

Mammals influence nearly all aspects of energy flow and habitat structure in modern terrestrial ecosystems. However, anthropogenic effects have probably altered mammalian community structure, raising the question of how past perturbations have done so. We used functional diversity (FD) to describe how the structure of North American mammal palaeocommunities changed over the past 66 Ma, an interval spanning the radiation following the K/Pg and several subsequent environmental disruptions including the Palaeocene-Eocene Thermal Maximum (PETM), the expansion of grassland, and the onset of Pleistocene glaciation. For 264 fossil communities, we examined three aspects of ecological function: functional evenness, functional richness and functional divergence. We found that shifts in FD were associated with major ecological and environmental transitions. All three measures of FD increased immediately following the extinction of the non-avian dinosaurs, suggesting that high degrees of ecological disturbance can lead to synchronous responses both locally and continentally. Otherwise, the components of FD were decoupled and responded differently to environmental changes over the last ~56 Myr.

Atomic-Scale Rectification and Inelastic Electron Tunneling Spectromicroscopy.

The phenomenon of rectification describes the emergence of a DC current from the application of an oscillating voltage. Although the origin of this effect has been associated with the nonlinearity in the current-voltage I(V) relation, a rigorous understanding of the microscopic mechanisms for this phenomenon remains challenging. Here, we show the close connection between rectification and inelastic electron tunneling spectroscopy and microscopy for single molecules with a scanning tunneling microscope. While both techniques are based on nonlinear features in the I(V) curve, comprehensive line shape analyses reveal notable differences that highlight the two complementary techniques of nonlinear conductivity spectromicroscopy for probing nanoscale systems.

An early burst in brachiopod evolution corresponding with significant climatic shifts during the Great Ordovician Biodiversification Event.

We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of the most abundant and species-rich brachiopod clades to radiate during the Great Ordovician Biodiversification Event (GOBE), to determine if significant environmental changes at this time correlate with the diversification of the clade. Models using origination, extinction and sampling rates to estimate prior probabilities of divergence times strongly support both high rates of anatomical change per million years and rapid divergences shortly before the clade first appears in the fossil record. These divergence times indicate much higher rates of cladogenesis than are typical of brachiopods during this interval. The correspondence of high speciation rates and high anatomical disparity suggests punctuated (speciational) change drove the high frequencies of early anatomical change, which in turn suggests increased ecological opportunities rather than shifting developmental constraints account for high rates of anatomical change. The pulse of rapid evolution began coincident with cooling temperatures, the start of major oscillations in sea level and increased levels of atmospheric oxygen. Our results suggest that these factors permitted major geographical and ecological expansion of strophomenoids with intervals of geographical isolation, resulting in elevated speciation rates and corresponding elevated frequencies of punctuated change.

Detection of Spin-Vibration States in Single Magnetic Molecules.

The spin states of magnetic molecules have advantageous attributes as carriers of quantum information. However, spin-vibration coupling in molecules causes a decay of excited spin states and a loss of spin coherence. Here, we detect excitations of spin-vibration states in single nickelocene molecules on Ag(110) with a scanning tunneling microscope. By transferring a nickelocene to the tip, the joint spin-vibration states with an adsorbed nickelocene were measured. Chemical variations in magnetic molecules offer the opportunity to tune spin-vibration coupling for controlling the spin coherence.

Probing and imaging spin interactions with a magnetic single-molecule sensor.

Magnetic single atoms and molecules are receiving intensifying research focus because of their potential as the smallest possible memory, spintronic, and qubit elements. Scanning probe microscopes used to study these systems have benefited greatly from new techniques that use molecule-functionalized tips to enhance spatial and spectroscopic resolutions and enable new sensing capabilities. We demonstrate a microscopy technique that uses a magnetic molecule, Ni(cyclopentadienyl)2, adsorbed at the apex of a scanning probe tip, to sense exchange interactions with another molecule adsorbed on a Ag(110) surface in a continuously tunable fashion in all three spatial directions. We further used the probe to image contours of exchange interaction strength, revealing angstrom-scale regions where the quantum states of two magnetic molecules strongly mix. Our results pave the way for new nanoscale imaging capabilities based on magnetic single-molecule sensors.

Detection and Characterization of Anharmonic Overtone Vibrations of Single Molecules on a Metal Surface.

Inelastic electron tunneling spectroscopy (IETS) with the scanning tunneling microscope (STM) is a powerful technique used to characterize the vibration and spin states at the single-molecule level. While IETS lacks hard selection rules, historically it has been assumed that vibrational overtones are rarely seen or even absent. Here we provide definitive experimental evidence that the hindered rotation overtone excitation of carbon monoxide molecules adsorbed on Ag(110) can be detected with STM-IETS via isotope substitution. We also demonstrate that the anharmonicity of the overtone excitation can be characterized and compared between adsorption sites and find evidence of anisotropy in the vibrational anharmonicity for CO adsorbed on the [11[over ¯]0] step edge.

Early bursts of disparity and the reorganization of character integration.

'Early bursts' of morphological disparity (i.e. diversity of anatomical types) are common in the fossil record. We typically model such bursts as elevated early rates of independent character change. Developmental theory predicts that modules of linked characters can change together, which would mimic the effects of elevated independent rates on disparity. However, correlated change introducing suboptimal states should encourage breakup (parcellation) of character suites allowing new (or primitive) states to evolve until new suites arise (relinkage). Thus, correlated change-breakup-relinkage presents mechanisms for early bursts followed by constrained evolution. Here, I analyse disparity in 257 published character matrices of fossil taxa. For each clade, I use inverse-modelling to infer most probably rates of independent change given both time-homogeneous and separate 'early versus late' rates. These rates are used to estimate expected disparity given both independent change models. The correlated change-breakup-relinkage model also predicts elevated frequencies of compatible character state-pairs appearing out of order in the fossil record (e.g. 01 appearing after 00 and 11; = low stratigraphic compatibility), as one solution to suboptimal states induced by correlated change is a return to states held before that change. As predicted by the correlated change-breakup-relinkage model, early disparity in the majority of clades both exceeds the expectations of either independent change model and excess early disparity correlates with low stratigraphic compatibility among character-pairs. Although it is possible that other mechanisms for linking characters contribute to these patterns, these results corroborate the idea that reorganization of developmental linkages is often associated with the origin of groups that biologists recognize as new higher taxa and that such reorganization offers a source of new disparity throughout the Phanerozoic.

High ecological complexity in benthic Ediacaran communities.

A long-running debate over the affinities of the Neoproterozoic 'Ediacara biota' has led to contrasting interpretations of Ediacaran ecosystem complexity. A 'simple' model assumes that most, if not all, Ediacaran organisms shared similar basic ecologies. A contrasting 'complex' model suggests that the Ediacara biota more likely represent organisms from a variety of different positions on the eukaryotic tree and thus occupied a wide range of different ecologies. We perform a quantitative test of Ediacaran ecosystem complexity using rank abundance distributions (RADs). We show that the Ediacara biota formed complex-type communities throughout much of their stratigraphic range and thus likely comprised species that competed for different resources and/or created niche for others ('ecosystem engineers'). One possible explanation for this pattern rests in the recent inference of multiple metazoan-style feeding modes among the Ediacara biota; in this scenario, different Ediacaran groups/clades were engaged in different methods of nutrient collection and thus competed for different resources. This result illustrates that the Ediacara biota may not have been as bizarre as it is sometimes suggested, and provides an ecological link with the animal-dominated benthic ecosystems of the Palaeozoic era.

Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions.

BACKGROUND: Phylogenetic comparative methods allow us to test evolutionary hypotheses without the benefit of an extensive fossil record. These methods, however, make simplifying assumptions, among them that clades are always increasing or stable in diversity, an assumption we know to be false. This study simulates hypothetical clades to test whether the Binary State Speciation and Extinction (BiSSE) method can be used to correctly detect relative differences in diversification rate between ancestral and derived character states even as net diversification rates are declining overall. We simulate clades with declining but positive diversification rates, as well those in which speciation rates decline below extinction rates so that they are losing richness for part of their history. We run these analyses both with simulated symmetric and asymmetric speciation rates to test whether BiSSE can be used to detect them correctly. RESULTS: For simulations with a neutral character, the fit for a BiSSE model with a neutral character is better than alternative models so long as net diversification rates remain positive. Once net diversification rates become negative, the BiSSE model with the greatest likelihood often has a non-neutral character, even though there is no such character in the simulation. BiSSE's usefulness in detecting real asymmetry in speciation rates improves with clade age, even well after net diversification rates have become negative. CONCLUSIONS: BiSSE is most useful in analyzing clades of intermediate age, before they have reached peak diversity and gone into decline. After this point, users of BiSSE risk incorrectly inferring differential evolutionary rates when none exist. Fortunately, most studies using BiSSE and similar models focus on rapid, recent diversifications, and are less likely to encounter the biases BiSSE models are subject to for older clades. For extant groups that were once more diverse than now, however, caution should be taken in inferring past diversification patterns without fossil data.

Imaging the halogen bond in self-assembled halogenbenzenes on silver.

Halogens are among the most electronegative elements, and the variations in size and polarizability of halogens require different descriptions of the intermolecular bonds they form. Here we use the inelastic tunneling probe (itProbe) to acquire real-space imaging of intermolecular-bonding structures in the two-dimensional self-assembly of halogenbenzene molecules on a metal surface. Direct visualization is obtained for the intermolecular attraction and the "windmill" pattern of bonding among the fully halogenated molecules. Our results provide a hitherto missing understanding of the nature of the halogen bond.

Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment.

BACKGROUND: Neurodevelopment is a complex process involving both genetic and environmental factors. Prenatal exposure to lead (Pb) has been associated with lower performance on neurodevelopmental tests. Adverse neurodevelopmental outcomes are more frequent and/or more severe when toxic exposures interact with genetic susceptibility. METHODS: To explore possible loci associated with increased susceptibility to prenatal Pb exposure, we performed a genome-wide gene-environment interaction study (GWIS) in young children from Mexico (n = 390) and Bangladesh (n = 497). Prenatal Pb exposure was estimated by cord blood Pb concentration. Neurodevelopment was assessed using the Bayley Scales of Infant Development. RESULTS: We identified a locus on chromosome 8, containing UNC5D, and demonstrated evidence of its genome-wide significance with mental composite scores (rs9642758, p meta = 4.35 × 10-6). Within this locus, the joint effects of two independent single nucleotide polymorphisms (SNPs, rs9642758 and rs10503970) had a p-value of 4.38 × 10-9 for mental composite scores. Correlating GWIS results with in vitro transcriptomic profiles identified one common gene, SLC1A5, which is involved in synaptic function, neuronal development, and excitotoxicity. Further analysis revealed interconnected interactions that formed a large network of 52 genes enriched with oxidative stress genes and neurodevelopmental genes. CONCLUSIONS: Our findings suggest that certain genetic polymorphisms within/near genes relevant to neurodevelopment might modify the toxic effects of Pb exposure via oxidative stress.

In Vitro Effects of Lead on Gene Expression in Neural Stem Cells and Associations between Up-regulated Genes and Cognitive Scores in Children.

BACKGROUND: Lead (Pb) adversely affects neurodevelopment in children. Neural stem cells (NSCs) play an essential role in shaping the developing brain, yet little is known about how Pb perturbs NSC functions and whether such perturbation contributes to impaired neurodevelopment. OBJECTIVES: We aimed to identify Pb-induced transcriptomic changes in NSCs and to link these changes to neurodevelopmental outcomes in children who were exposed to Pb. METHODS: We performed RNA-seq-based transcriptomic profiling in human NSCs treated with 1 µM Pb. We used qRT-PCR, Western blotting, ELISA, and ChIP (chromatin immunoprecipitation) to characterize Pb-induced gene up-regulation. Through interrogation of a genome-wide association study, we examined the association of gene variants with neurodevelopment outcomes in the ELEMENT birth cohort. RESULTS: We identified 19 genes with significantly altered expression, including many known targets of NRF2-the master transcriptional factor for the oxidative stress response. Pb induced the expression of SPP1 (secreted phosphoprotein 1), which has known neuroprotective effects. We demonstrated that SPP1 is a novel direct NRF2 target gene. Single nucleotide polymorphisms (SNPs) (rs12641001) in the regulatory region of SPP1 exhibited a statistically significant association (p = 0.005) with the Cognitive Development Index (CDI). CONCLUSION: Our findings revealed that Pb induces an NRF2-dependent transcriptional response in neural stem cells and identified SPP1 up-regulation as a potential novel mechanism linking Pb exposure with neural stem cell function and neurodevelopment in children.

Exploring the influence of ancient and historic megaherbivore extirpations on the global methane budget.

Globally, large-bodied wild mammals are in peril. Because "megamammals" have a disproportionate influence on vegetation, trophic interactions, and ecosystem function, declining populations are of considerable conservation concern. However, this is not new; trophic downgrading occurred in the past, including the African rinderpest epizootic of the 1890s, the massive Great Plains bison kill-off in the 1860s, and the terminal Pleistocene extinction of megafauna. Examining the consequences of these earlier events yields insights into contemporary ecosystem function. Here, we focus on changes in methane emissions, produced as a byproduct of enteric fermentation by herbivores. Although methane is ∼ 200 times less abundant than carbon dioxide in the atmosphere, the greater efficiency of methane in trapping radiation leads to a significant role in radiative forcing of climate. Using global datasets of late Quaternary mammals, domestic livestock, and human population from the United Nations as well as literature sources, we develop a series of allometric regressions relating mammal body mass to population density and CH4 production, which allows estimation of methane production by wild and domestic herbivores for each historic or ancient time period. We find the extirpation of megaherbivores reduced global enteric emissions between 2.2-69.6 Tg CH4 y(-1) during the various time periods, representing a decrease of 0.8-34.8% of the overall inputs to tropospheric input. Our analyses suggest that large-bodied mammals have a greater influence on methane emissions than previously appreciated and, further, that changes in the source pool from herbivores can influence global biogeochemical cycles and, potentially, climate.

What limits the morphological disparity of clades?

The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even while their species richness or diversity is comparatively low. This pattern of early high-disparity suggests that there are internal constraints (e.g. developmental pleiotropy) or external restrictions (e.g. ecological competition) upon the variety of morphologies that can subsequently evolve. It has also been demonstrated that the rate of evolution of new character states decreases in most clades through time (character saturation), as does the rate of origination of novel bodyplans and higher taxa. Here, we tested whether there was a simple relationship between the level or rate of character state exhaustion and the shape of a clade's disparity profile: specifically, its centre of gravity (CG). In a sample of 93 extinct major clades, most showed some degree of exhaustion, but all continued to evolve new states up until their extinction. Projection of states/steps curves suggested that clades realized an average of 60% of their inferred maximum numbers of states. Despite a weak but significant correlation between overall levels of homoplasy and the CG of clade disparity profiles, there were no significant relationships between any of our indices of exhaustion curve shape and the clade disparity CG. Clades showing early high-disparity were no more likely to have early character saturation than those with maximum disparity late in their evolution.

Response of beta diversity to pulses of Ordovician-Silurian mass extinction.

Ecologists are increasingly using the fossil record of mass extinction to build predictive models for the ongoing biodiversity crisis. During mass extinctions, major depletions in global (i.e., gamma) diversity may reflect decrease in alpha diversity (i.e., local assemblages support fewer taxa), and/or decrease in beta diversity (such that similar pools of taxa are common to a greater number of local areas). Contrasting the effects of extinction on alpha and beta diversity is therefore central to understanding how global richness becomes depleted over these critical events. Here we investigate the spatial effects of mass extinction by examining changes in alpha, beta, and gamma diversity in brachiopod communities over both pulses of Ordovician-Silurian extinction (-445.2 and -438.8 million years ago), which had dramatically different causal mechanisms. We furthermore reconstruct geographic range sizes for brachiopod genera to test competing models for drivers of beta diversity change. We find that: (1) alpha and beta diversity respond differently to extinction; (2) these responses differ between pulses of extinction; (3) changes in beta diversity associated with extinction are accompanied by changes in geographic range size; and (4) changes in global beta diversity were driven by the extinction of taxa with statistically small and large ranges, rather than range expansion/contraction in taxa that survive into the aftermath. A symptom of ongoing biotic crisis may therefore be the extinction of specific narrow- or wide-ranging taxa, rather than the global proliferation of opportunistic and "disaster" forms. In addition, our results illustrate that changes in beta diversity on these longer timescales may largely be dictated by emplacement and removal of barriers to dispersal. Lastly, this study reinforces the utility of the fossil record in addressing questions surrounding the role of global-scale processes (such as mass extinctions) in sculpting and assembling regional biotas.

The Implications of Stratigraphic Compatibility for Character Integration among Fossil Taxa.

Two characters are stratigraphically compatible if some phylogenies indicate that their combinations (state-pairs) evolved without homoplasy and in an order consistent with the fossil record. Simulations assuming independent character change indicate that we expect approximately 95% of compatible character pairs to also be stratigraphically compatible over a wide range of sampling regimes and general evolutionary models. However, two general models of rate heterogeneity elevate expected stratigraphic incompatibility: "early burst" models, where rates of change are higher among early members of a clade than among later members of that clade, and "integration" models, where the evolution of characters is correlated in some manner. Both models have important theoretical and methodological implications. Therefore, we examine 259 metazoan clades for deviations from expected stratigraphic compatibility. We do so first assuming independent change with equal rates of character change through time. We then repeat the analysis assuming independent change with separate "early" and "late" rates (with "early" = the first third of taxa in a clade), with the early and late rates chosen to maximize the probability of the observed compatibility among the early taxa and then the whole clade. We single out Cambrian trilobites as a possible "control" group because morphometric studies suggest that integration patterns are not conserved among closely related species. Even allowing for early bursts, we see excess stratigraphic incompatibility (i.e., negative deviations) in significantly more clades than expected at 0.50, 0.25, and 0.05 [Formula: see text] values. This pattern is particularly strong in chordates, echinoderms, and arthropods. However, stratigraphic compatibility among Cambrian trilobites matches the expectations of integration studies, as they (unlike post-Cambrian trilobites) do not deviate from the expectations of independent change with no early bursts. Thus, these results suggest that processes such as integration strongly affect the data that paleontologists use to study phylogeny, disparity, and rates.

The importance of considering animal body mass in IPCC greenhouse inventories and the underappreciated role of wild herbivores.

Methane is an important greenhouse gas, but characterizing production by source sector has proven difficult. Current estimates suggest herbivores produce ~20% (~76-189 Tg yr(-1) ) of methane globally, with wildlife contributions uncertain. We develop a simple and accurate method to estimate methane emissions and reevaluate production by wildlife. We find a strikingly robust relationship between body mass and methane output exceeding the scaling expected by differences in metabolic rate. Our allometric model gives a significantly better fit to empirical data than IPCC Tier 1 and 2 calculations. Our analysis suggests that (i) the allometric model provides an easier and more robust estimate of methane production than IPCC models currently in use; (ii) output from wildlife is much higher than previously considered; and (iii) because of the allometric scaling of methane output with body mass, national emissions could be reduced if countries favored more, smaller livestock, over fewer, larger ones.