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 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.

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.

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.

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.

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.

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.

Trait-based diversification shifts reflect differential extinction among fossil taxa.

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

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.

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 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.

Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates.

Rate distributions are important considerations when testing hypotheses about morphological evolution or phylogeny. They also have implications about general processes underlying character evolution. Molecular systematists often assume that rates are Poisson processes with gamma distributions. However, morphological change is the product of multiple probabilistic processes and should theoretically be affected by hierarchical integration of characters. Both factors predict lognormal rate distributions. Here, a simple inverse modelling approach assesses the best single-rate, gamma and lognormal models given observed character compatibility for 115 invertebrate groups. Tests reject the single-rate model for nearly all cases. Moreover, the lognormal outperforms the gamma for character change rates and (especially) state derivation rates. The latter in particular is consistent with integration affecting morphological character evolution.

Clock-drawing performance predicts inpatient rehabilitation outcomes after traumatic brain injury.

The authors used clock-drawing performance to assess cognition and predict inpatient rehabilitation outcomes among persons with traumatic brain injury. Clock-drawing performance, as assessed with the Clock Drawing Interpretation Scale, predicts rehabilitation length of stay as well as Functional Independence Measure scores at the time of neurobehavioral assessment and rehabilitation discharge.

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.

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.

The effects of taxonomic standardization on sampling-standardized estimates of historical diversity.

Occurrence-based databases such as the Palaeobiology database (PBDB) provide means of accommodating the heterogeneities of the fossil record when evaluating historical diversity patterns. Although palaeontologists have given ample attention to the effects of taxonomic practice on diversity patterns derived from synoptic databases (those using first and last appearances of taxa), workers have not examined the effects of taxonomic error on occurrence-based diversity studies. Here, we contrast diversity patterns and diversity dynamics between raw data and taxonomically vetted data in the PBDB to evaluate the effects of taxonomic errors. We examine three groups: Palaeozoic gastropods, Jurassic bivalves and Cenozoic bivalves. We contrast genus-level diversity patterns based on: (i) all occurrences assigned to a genus (i.e. both species records and records identifying only the genus), (ii) only occurrences for which a species is identified, and (iii) only occurrences for which a species is identified, but after vetting the genus to which the species is assigned. Extensive generic reassignments elevate origination and extinction rates within Palaeozoic gastropods and origination rates within Cenozoic bivalves. However, vetting increases generic richness markedly only for Cenozoic bivalves, and even then the increase is less than 10%. Moreover, the patterns of standing generic richness are highly similar under all three data treatments. Unless our results are unusual, taxonomic standardization can elevate diversity dynamics in some cases, but it will not greatly change inferred richness over time.

Using patterns of fin and limb phylogeny to test developmental-evolutionary scenarios.

Increasing fossil evidence surrounding the evolutionary origin of vertebrate limbs can be used to reconstruct the assembly of a limb ground-plan common to all tetrapods. The sequence of changes at the fin-to-limb transition can be compared to patterns of fin and limb ontogeny, and further comparisons can be made between phylogenetic changes at pectoral and pelvic levels. Such comparisons inform questions about the evolution of developmental autonomy (modularity). Limb evolution mostly concerns terminal additions and losses; from a developmental standpoint, these probably result either from minor adjustments to limb bud proportions or from the relative timing of gene expression or tissue growth. Evolutionary radiations of large clades are widely assumed to be marked by periods of rapid morphological diversification, raising further questions about the impact of restrictions imposed not only by ecology, but also by development and genetics. The early tetrapod data set is now large enough to allow initial tests of evolutionary inference to be conducted. New results are revealing novel patterns of evolutionary rate-change, encompassing the traditional notion of the fish-to-tetrapod transition and the root of the modern (crown-group) tetrapod radiation.